From ddfa6e9cfa3714ecdbf25ac4560cd98e478a07b7 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sun, 19 Feb 2023 13:43:55 +0200 Subject: [PATCH] Update monochrom after ODK 1.4 release --- Makefile | 2 +- chr-base.json | 156615 ++++++------- chr-base.obo | 366 +- chr-base.owl | 736 +- chr-full.json | 172185 +++++++-------- chr-full.obo | 1250 +- chr-full.owl | 2484 +- chr.json | 172185 +++++++-------- chr.obo | 1250 +- chr.owl | 2484 +- components/ce11.owl | 144 +- components/ce11.yaml | 4 + components/galGal6.owl | 1434 +- components/hg38.owl | 18532 +- components/hg38.yaml | 4 + components/mm10.owl | 8086 +- components/mm10.yaml | 46 +- components/rn6.owl | 5440 +- monochrom/chromschema.py | 7 +- src/ontology/components/ucsc.owl | 736 +- src/ontology/imports/geno_import.owl | 476 +- src/ontology/imports/go_import.owl | 3063 +- src/ontology/imports/ncbitaxon_import.owl | 2633 +- src/ontology/imports/ro_import.owl | 5056 +- src/ontology/imports/so_import.owl | 40 +- .../reports/chr-edit.owl-obo-report.tsv | 26 - 26 files changed, 241307 insertions(+), 313977 deletions(-) diff --git a/Makefile b/Makefile index c9ddbfb..a6a02ed 100644 --- a/Makefile +++ b/Makefile @@ -12,7 +12,7 @@ all-components-yaml: $(patsubst %, components/%.yaml, $(BUILDS)) all-components-owl: $(patsubst %, components/%.owl, $(BUILDS)) ontology: - cd src/ontology && make release + cd src/ontology && make prepare_release test: pytest diff --git a/chr-base.json b/chr-base.json index 57d8ce4..7c9db4d 100644 --- a/chr-base.json +++ b/chr-base.json @@ -1,88826 +1,67791 @@ { - "graphs": [ - { - "domainRangeAxioms": [], - "edges": [ - { - "obj": "http://purl.obolibrary.org/obo/CHR_10090-chr1", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CHR_10090-chr1q" - }, - { - "obj": "http://purl.obolibrary.org/obo/CHR_10090-chr10", - "pred": "http://purl.obolibrary.org/obo/BFO_0000050", - "sub": "http://purl.obolibrary.org/obo/CHR_10090-chr10q" 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"http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/CHR_9606-chrYq1" + }, { + "sub" : "http://purl.obolibrary.org/obo/CHR_9606-chrYq12", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + } ] +} \ No newline at end of file diff --git a/chr-base.obo b/chr-base.obo index 3c572b0..3b27c61 100644 --- a/chr-base.obo +++ b/chr-base.obo @@ -1,11 +1,11 @@ format-version: 1.2 -data-version: chr/releases/2022-02-02/chr-base.owl +data-version: chr/releases/2023-02-19/chr-base.owl ontology: chr/chr-base property_value: http://purl.org/dc/elements/1.1/description "Automatic translation of UCSC chromosome bands to OWL classes" xsd:string property_value: http://purl.org/dc/elements/1.1/title "Monochrom Ontology" xsd:string property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ -property_value: owl:versionInfo "2022-02-02" xsd:string +property_value: owl:versionInfo "2023-02-19" xsd:string [Term] id: CHR:10090-chr1 @@ -9677,368 +9677,6 @@ property_value: genome:build "ce11" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "17718942" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer -[Term] -id: CHR:7955-chr1 -name: chromosome 1 (Danio rerio) -synonym: "1" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002885.1 -property_value: exactMatch NC:007112.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "58871917" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr10 -name: chromosome 10 (Danio rerio) -synonym: "10" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002894.1 -property_value: exactMatch NC:007121.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "45574255" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr11 -name: chromosome 11 (Danio rerio) -synonym: "11" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002895.1 -property_value: exactMatch NC:007122.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "45107271" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr12 -name: chromosome 12 (Danio rerio) -synonym: "12" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002896.1 -property_value: exactMatch NC:007123.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "49229541" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr13 -name: chromosome 13 (Danio rerio) -synonym: "13" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002897.1 -property_value: exactMatch NC:007124.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "51780250" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr14 -name: chromosome 14 (Danio rerio) -synonym: "14" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002898.1 -property_value: exactMatch NC:007125.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "51944548" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr15 -name: chromosome 15 (Danio rerio) -synonym: "15" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002899.1 -property_value: exactMatch NC:007126.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "47771147" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr16 -name: chromosome 16 (Danio rerio) -synonym: "16" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002900.1 -property_value: exactMatch NC:007127.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "55381981" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr17 -name: chromosome 17 (Danio rerio) -synonym: "17" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002901.1 -property_value: exactMatch NC:007128.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "53345113" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr18 -name: chromosome 18 (Danio rerio) -synonym: "18" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002902.1 -property_value: exactMatch NC:007129.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "51008593" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr19 -name: chromosome 19 (Danio rerio) -synonym: "19" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002903.1 -property_value: exactMatch NC:007130.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "48790377" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr2 -name: chromosome 2 (Danio rerio) -synonym: "2" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002886.1 -property_value: exactMatch NC:007113.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "59543403" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr20 -name: chromosome 20 (Danio rerio) -synonym: "20" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002904.1 -property_value: exactMatch NC:007131.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "55370968" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr21 -name: chromosome 21 (Danio rerio) -synonym: "21" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002905.1 -property_value: exactMatch NC:007132.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "45895719" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr22 -name: chromosome 22 (Danio rerio) -synonym: "22" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002906.1 -property_value: exactMatch NC:007133.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "39226288" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr23 -name: chromosome 23 (Danio rerio) -synonym: "23" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002907.1 -property_value: exactMatch NC:007134.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "46272358" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr24 -name: chromosome 24 (Danio rerio) -synonym: "24" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002908.1 -property_value: exactMatch NC:007135.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "42251103" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr25 -name: chromosome 25 (Danio rerio) -synonym: "25" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002909.1 -property_value: exactMatch NC:007136.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "36898761" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr3 -name: chromosome 3 (Danio rerio) -synonym: "3" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002887.1 -property_value: exactMatch NC:007114.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "62385949" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr4 -name: chromosome 4 (Danio rerio) -synonym: "4" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002888.1 -property_value: exactMatch NC:007115.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "76625712" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr5 -name: chromosome 5 (Danio rerio) -synonym: "5" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002889.1 -property_value: exactMatch NC:007116.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "71715914" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr6 -name: chromosome 6 (Danio rerio) -synonym: "6" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002890.1 -property_value: exactMatch NC:007117.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "60272633" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr7 -name: chromosome 7 (Danio rerio) -synonym: "7" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002891.1 -property_value: exactMatch NC:007118.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "74082188" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr8 -name: chromosome 8 (Danio rerio) -synonym: "8" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002892.1 -property_value: exactMatch NC:007119.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "54191831" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr9 -name: chromosome 9 (Danio rerio) -synonym: "9" BROAD [] -is_a: GO:0005694 -is_a: GO:0030849 -relationship: BFO:0000050 GO:0005634 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch http://identifiers.org/insdc/CM002893.1 -property_value: exactMatch NC:007120.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "56892771" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chrM -name: chromosome M (Danio rerio) -synonym: "MT" BROAD [] -is_a: GO:0005694 -relationship: BFO:0000050 GO:0005739 -relationship: RO:0002162 NCBITaxon:7955 -property_value: exactMatch NC:002333.2 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "16596" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - [Term] id: CHR:9031-chr1 name: chromosome 1 (Chicken) diff --git a/chr-base.owl b/chr-base.owl index b7a2acf..f003cae 100644 --- a/chr-base.owl +++ b/chr-base.owl @@ -13,12 +13,12 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"http://purl.obolibrary.org/obo/GO_0005737", - "propertyId": "http://purl.obolibrary.org/obo/BFO_0000050" - } - ] - }, - { - "definedClassId": "http://purl.obolibrary.org/obo/GO_0099738", - "genusIds": [ - "http://purl.obolibrary.org/obo/GO_0005938" - ], - "restrictions": [ - { - "fillerId": "http://purl.obolibrary.org/obo/GO_0005938", - "propertyId": "http://purl.obolibrary.org/obo/BFO_0000050" - } - ] - } - ], - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.org/dc/elements/1.1/description", - "val": "Automatic translation of UCSC chromosome bands to OWL classes" - }, - { - "pred": "http://purl.org/dc/elements/1.1/title", - "val": "Monochrom Ontology" - }, - { - "pred": "http://purl.org/dc/terms/license", - "val": "https://creativecommons.org/publicdomain/zero/1.0/" - }, - { - "pred": "http://www.w3.org/2002/07/owl#versionInfo", - "val": "2022-02-02" - } - ], - "subsets": [], - "version": "http://purl.obolibrary.org/obo/chr/releases/2022-02-02/chr-full.json", - "xrefs": [] - }, - "nodes": [ - { - "id": "http://purl.obolibrary.org/obo/BFO_0000002", - "lbl": "continuant", - "meta": { - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000003", - "lbl": "occurrent", - "meta": { - "definition": { - "val": "An entity that has temporal parts and that happens, unfolds or develops through time.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000004", - "lbl": "independent continuant", - "meta": { - "definition": { - "val": "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000015", - "lbl": "process", - "meta": { - "definition": { - "val": "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000040", - "lbl": "material entity", - "meta": { - "definition": { - "val": "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", - "xrefs": [] - } - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl": "part of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "is part of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my brain is part of my body (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this day is part of this year (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "part_of" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000002" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000003" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000004" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000017" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000019" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000020" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0040042", - "val": "http://purl.obolibrary.org/obo/BFO_0000031" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "external" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "part_of" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://www.obofoundry.org/ro/#OBO_REL:part_of" - } - ], - "definition": { - "val": "a core relation that holds between a part and its whole", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_gp2term", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ], - "xrefs": [ - { - "val": "BFO:0000050" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl": "has part", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "has part" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my body has part my brain (continuant parthood, two material entities)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this year has part this day (occurrent parthood)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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'." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has_part" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "external" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val": "has_part" - } - ], - "definition": { - "val": "a core relation that holds between a whole and its part", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ], - "xrefs": [ - { - "val": "BFO:0000051" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl": "preceded by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "is preceded by" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "preceded_by" - }, - { - "pred": "http://purl.org/dc/elements/1.1/source", - "val": "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl": "precedes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "precedes" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl": "occurs in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "occurs in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "occurs_in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "unfolds in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "unfolds_in" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "comments": [ - "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" - ], - "definition": { - "val": "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", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl": "contains process", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "site of" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val": "http://purl.obolibrary.org/obo/bfo.owl" - } - ], - "comments": [ - "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" - ], - "definition": { - "val": "[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", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000000", - "lbl": "anatomical entity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/caro.owl" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/CARO_0000003", - "lbl": "connected anatomical structure", - 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{ - "id": "http://purl.obolibrary.org/obo/GO_0000805", - "lbl": "X chromosome", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/RO_0002161", - "val": "http://purl.obolibrary.org/obo/NCBITaxon_8782" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "definition": { - "val": "The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males.", - "xrefs": [ - "GOC:mah", - "GOC:mr", - "ISBN:0582227089", - "PMID:20622855", - "Wikipedia:XY_sex-determination_system" - ] - }, - "xrefs": [ - { - "val": "Wikipedia:X_chromosome" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0000806", - "lbl": "Y chromosome", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/RO_0002161", - "val": "http://purl.obolibrary.org/obo/NCBITaxon_8782" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "definition": { - "val": "The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males.", - "xrefs": [ - "GOC:mah", - "GOC:mr", - "ISBN:0582227089", - "PMID:20622855", - "Wikipedia:XY_sex-determination_system" - ] - }, - "xrefs": [ - { - "val": "Wikipedia:Y_chromosome" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0003674", - "lbl": "molecular_function", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000589", - "val": "molecular process" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0005575", - "lbl": "cellular_component", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "GO:0008372" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "comments": [ - "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." - ], - "definition": { - "val": "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).", - "xrefs": [ - "GOC:pdt", - "NIF_Subcellular:sao1337158144" - ] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/go#goslim_aspergillus", - "http://purl.obolibrary.org/obo/go#goslim_candida", - "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_generic", - "http://purl.obolibrary.org/obo/go#goslim_metagenomics", - "http://purl.obolibrary.org/obo/go#goslim_pir", - "http://purl.obolibrary.org/obo/go#goslim_plant", - "http://purl.obolibrary.org/obo/go#goslim_yeast" - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "cell or subcellular entity", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "cellular component", - "xrefs": [] - }, - { - "pred": "hasRelatedSynonym", - "val": "subcellular entity", - "xrefs": [ - "NIF_Subcellular:nlx_subcell_100315" - ] - } - ], - "xrefs": [ - { - "val": "NIF_Subcellular:sao1337158144" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0005622", - "lbl": "intracellular anatomical structure", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000233", - "val": "https://github.com/geneontology/go-ontology/issues/17776" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "definition": { - "val": "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.", - "xrefs": [ - "ISBN:0198506732" - ] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", - "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_generic", - "http://purl.obolibrary.org/obo/go#goslim_metagenomics", - "http://purl.obolibrary.org/obo/go#goslim_plant" - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "internal to cell", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "intracellular", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "val": "protoplasm", - "xrefs": [] - }, - { - "pred": "hasRelatedSynonym", - "val": "nucleocytoplasm", - "xrefs": [ - "GOC:mah" - ] - }, - { - "pred": "hasRelatedSynonym", - "val": "protoplast", - "xrefs": [ - "GOC:mah" - ] - } - ], - "xrefs": [ - { - "val": "Wikipedia:Intracellular" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0005634", - "lbl": "nucleus", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000412", - "val": "http://purl.obolibrary.org/obo/go.owl" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "definition": { - "val": "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", - "xrefs": [ - "GOC:go_curators" - ] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/go#goslim_agr", - "http://purl.obolibrary.org/obo/go#goslim_aspergillus", - "http://purl.obolibrary.org/obo/go#goslim_candida", - "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_drosophila", - "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", - "http://purl.obolibrary.org/obo/go#goslim_generic", - "http://purl.obolibrary.org/obo/go#goslim_metagenomics", - "http://purl.obolibrary.org/obo/go#goslim_mouse", - "http://purl.obolibrary.org/obo/go#goslim_pir", - "http://purl.obolibrary.org/obo/go#goslim_plant", - "http://purl.obolibrary.org/obo/go#goslim_yeast" - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "cell nucleus", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "horsetail nucleus", - "xrefs": [ - "GOC:al", - "GOC:mah", - "GOC:vw", - "PMID:15030757" - ] - } - ], - "xrefs": [ - { - "val": "NIF_Subcellular:sao1702920020" - }, - { - "val": "Wikipedia:Cell_nucleus" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0005635", - "lbl": "nuclear envelope", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val": "GO:0005636" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "definition": { - "val": "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).", - "xrefs": [ - "ISBN:0198547684" - ] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_generic", - "http://purl.obolibrary.org/obo/go#goslim_plant" - ], - "xrefs": [ - { - "val": "Wikipedia:Nuclear_envelope" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0005694", - "lbl": "chromosome", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "comments": [ - "Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore." - ], - "definition": { - "val": "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.", - "xrefs": [ - "ISBN:0198547684" - ] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/go#goslim_agr", - "http://purl.obolibrary.org/obo/go#goslim_aspergillus", - "http://purl.obolibrary.org/obo/go#goslim_candida", - "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_drosophila", - "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", - "http://purl.obolibrary.org/obo/go#goslim_generic", - "http://purl.obolibrary.org/obo/go#goslim_metagenomics", - "http://purl.obolibrary.org/obo/go#goslim_pir", - "http://purl.obolibrary.org/obo/go#goslim_yeast" - ], - "synonyms": [ - { - "pred": "hasNarrowSynonym", - "val": "interphase chromosome", - "xrefs": [] - }, - { - "pred": "hasNarrowSynonym", - "val": "prophase chromosome", - "xrefs": [] - }, - { - "pred": "hasRelatedSynonym", - "val": "chromatid", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "Wikipedia:Chromosome" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0005737", - "lbl": "cytoplasm", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "definition": { - "val": "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.", - "xrefs": [ - "ISBN:0198547684" - ] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/go#goslim_candida", - "http://purl.obolibrary.org/obo/go#goslim_chembl", - "http://purl.obolibrary.org/obo/go#goslim_generic", - "http://purl.obolibrary.org/obo/go#goslim_metagenomics", - "http://purl.obolibrary.org/obo/go#goslim_pir", - "http://purl.obolibrary.org/obo/go#goslim_plant", - "http://purl.obolibrary.org/obo/go#goslim_yeast" - ], - "xrefs": [ - { - "val": "Wikipedia:Cytoplasm" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/GO_0005739", - "lbl": "mitochondrion", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "cellular_component" - } - ], - "comments": [ - "Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)" - ], - "definition": { - "val": "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. 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"val": "great apes", - "xrefs": [] - }, - { - "pred": "hasRelatedSynonym", - "synonymType": "http://purl.obolibrary.org/obo/ncbitaxon#synonym", - "val": "Pongidae", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "GC_ID:1" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_9605", - "lbl": "Homo", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val": "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "ncbi_taxonomy" - } - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/ncbitaxon#common_name", - "val": "humans", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "GC_ID:1" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_9606", - "lbl": "Homo sapiens", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val": "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "ncbi_taxonomy" - } - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/ncbitaxon#common_name", - "val": "man", - "xrefs": [] - }, - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", - "val": "human", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "GC_ID:1" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/NCBITaxon_9989", - "lbl": "Rodentia", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val": "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val": "ncbi_taxonomy" - } - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "synonymType": "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", - "val": "rodent", - "xrefs": [] - }, - { - "pred": "hasRelatedSynonym", - "synonymType": "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", - "val": "rodents", - "xrefs": [] - } - ], - "xrefs": [ - { - "val": "GC_ID:1" - } - ] - }, - "type": "CLASS" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0000056", - "lbl": "participates in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "participates in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this blood clot participates in this blood coagulation" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this input material (or this output material) participates in this process" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this investigator participates in this investigation" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "participates_in" - } - ], - "definition": { - "val": "a relation between a continuant and a process, in which the continuant is somehow involved in the process", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0000057", - "lbl": "has participant", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000111", - "val": "has participant" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this blood coagulation has participant this blood clot" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this investigation has participant this investigator" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "this process has participant this input material (or this output material)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has_participant" - }, - { - "pred": "http://purl.org/dc/elements/1.1/source", - "val": "http://www.obofoundry.org/ro/#OBO_REL:has_participant" - } - ], - "definition": { - "val": "a relation between a process and a continuant, in which the continuant is somehow involved in the process", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002013", - "lbl": "has regulatory component activity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-05-24T09:30:46Z" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002014", - "lbl": "has negative regulatory component activity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-05-24T09:31:01Z" - } - ], - "comments": [ - "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'." - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002015", - "lbl": "has positive regulatory component activity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-05-24T09:31:17Z" - } - ], - "comments": [ - "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'." - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002017", - "lbl": "has component activity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-05-24T09:44:33Z" - } - ], - "comments": [ - "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002018", - "lbl": "has component process", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-05-24T09:49:21Z" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002022", - "lbl": "directly regulated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-09-17T13:52:24Z" - } - ], - "comments": [ - "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." - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002023", - "lbl": "directly negatively regulated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-09-17T13:52:38Z" - } - ], - "definition": { - "val": "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.", - "xrefs": [ - "GOC:dos" - ] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002024", - "lbl": "directly positively regulated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-09-17T13:52:47Z" - } - ], - "definition": { - "val": "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.", - "xrefs": [ - "GOC:dos" - ] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002025", - "lbl": "has effector activity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", - "val": "dos" - }, - { - "pred": "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val": "2017-09-22T14:14:36Z" - } - ], - "comments": [ - "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." - ], - "definition": { - "val": "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.", - "xrefs": [ - "GOC:dos" - ] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002086", - "lbl": "ends after", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "David Osumi-Sutherland" - } - ], - "comments": [ - "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" - ], - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002087", - "lbl": "immediately preceded by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "David Osumi-Sutherland" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "starts_at_end_of" - } - ], - "comments": [ - "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002090", - "lbl": "immediately precedes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "David Osumi-Sutherland" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "ends_at_start_of" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "meets" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0002575", - "val": "http://purl.obolibrary.org/obo/BFO_0000063" - } - ], - "comments": [ - "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" - ], - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002131", - "lbl": "overlaps", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000424", - "val": "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - } - ], - "definition": { - "val": "x overlaps y if and only if there exists some z such that x has part z and z part of y", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002162", - "lbl": "in taxon", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Jennifer Deegan" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } - ], - "comments": [ - "Connects a biological entity to its taxon of origin." - ], - "definition": { - "val": "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002180", - "lbl": "has component", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://ontologydesignpatterns.org/wiki/Submissions:Componency" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002202", - "lbl": "develops from", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "David Osumi-Sutherland" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Melissa Haendel" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Terry Meehan" - } - ], - "comments": [ - "This is the transitive form of the develops from relation" - ], - "definition": { - "val": "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002203", - "lbl": "develops into", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "David Osumi-Sutherland" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Terry Meehan" - } - ], - "definition": { - "val": "inverse of develops from", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/RO_0002259" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002211", - "lbl": "regulates", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "David Hill" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Tanya Berardini" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "GO" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000589", - "val": "regulates (processual)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000600", - "val": "false" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002212", - "lbl": "negatively regulates", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000589", - "val": "negatively regulates (process to process)" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0004050", - "val": "http://purl.obolibrary.org/obo/RO_0002211" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002213", - "lbl": "positively regulates", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000589", - "val": "positively regulates (process to process)" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0004049", - "val": "http://purl.obolibrary.org/obo/RO_0002211" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002215", - "lbl": "capable of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has function realized in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "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)\"." - } - ], - "definition": { - "val": "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. ", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002216", - "lbl": "capable of part of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has function in" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002222", - "lbl": "temporally related to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "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." - }, - { - "pred": "http://purl.org/dc/terms/source", - "val": "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } - ], - "comments": [ - "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." - ], - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002233", - "lbl": "has input", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "consumes" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_go_ontology", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002254", - "lbl": "has developmental contribution from", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "x has developmental contribution from y iff x has some part z such that z develops from y", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002255", - "lbl": "developmentally contributes to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "inverse of has developmental contribution from", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/RO_0002259" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002258", - "lbl": "developmentally preceded by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "false" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "In general you should not use this relation to make assertions - use one of the more specific relations below this one" - } - ], - "comments": [ - "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" - ], - "definition": { - "val": "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002263", - "lbl": "acts upstream of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "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." - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://wiki.geneontology.org/index.php/Acts_upstream_of" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_gp2term" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002264", - "lbl": "acts upstream of or within", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_gp2term" - ], - "synonyms": [ - { - "pred": "hasRelatedSynonym", - "val": "affects", - "xrefs": [] - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002286", - "lbl": "developmentally succeeded by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000125" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "Inverse of developmentally preceded by", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002304", - "lbl": "causally upstream of, positive effect", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/RO_0004049", - "val": "http://purl.obolibrary.org/obo/RO_0002411" - }, - { - "pred": "http://purl.org/dc/terms/creator", - "val": "cjm" - } - ], - "comments": [ - "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" - ], - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002305", - "lbl": "causally upstream of, negative effect", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/RO_0004050", - "val": "http://purl.obolibrary.org/obo/RO_0002411" - }, - { - "pred": "http://purl.org/dc/terms/creator", - "val": "cjm" - } - ], - "comments": [ - "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" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002320", - "lbl": "evolutionarily related to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } - ], - "definition": { - "val": "A relationship that holds via some environmental process", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002323", - "lbl": "mereotopologically related to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0001900", - "val": "http://purl.obolibrary.org/obo/RO_0001901" - } - ], - "definition": { - "val": "A mereological relationship or a topological relationship", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002324", - "lbl": "developmentally related to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } - ], - "definition": { - "val": "A relationship that holds between entities participating in some developmental process (GO:0032502)", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002327", - "lbl": "enables", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "a particular instances of akt-2 enables some instance of protein kinase activity" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "catalyzes" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "executes" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "has" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "is catalyzing" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "is executing" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." - } - ], - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_gp2term" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002328", - "lbl": "functionally related to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - } - ], - "definition": { - "val": "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002329", - "lbl": "part of structure that is capable of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "false" - } - ], - "definition": { - "val": "this relation holds between c and p when c is part of some c', and c' is capable of p.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002331", - "lbl": "involved in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "actively involved in" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "enables part of" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://wiki.geneontology.org/index.php/Involved_in" - } - ], - "definition": { - "val": "c involved_in p if and only if c enables some process p', and p' is part of p", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002333", - "lbl": "enabled by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "inverse of enables", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002334", - "lbl": "regulated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000589", - "val": "regulated by (processual)" - } - ], - "definition": { - "val": "inverse of regulates", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/RO_0002259" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002335", - "lbl": "negatively regulated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "inverse of negatively regulates", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/RO_0002259" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002336", - "lbl": "positively regulated by", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "inverse of positively regulates", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/RO_0002259" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002352", - "lbl": "input of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "inverse of has input", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/RO_0002259", - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002384", - "lbl": "has developmental potential involving", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002385", - "lbl": "has potential to developmentally contribute to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002387", - "lbl": "has potential to develop into", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "x has the potential to develop into y iff x develops into y or if x is capable of developing into y", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002388", - "lbl": "has potential to directly develop into", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002404", - "lbl": "causally downstream of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "inverse of upstream of", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002405", - "lbl": "immediately causally downstream of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002410", - "lbl": "causally related to", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } - ], - "definition": { - "val": "This relation groups causal relations between material entities and causal relations between processes", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002411", - "lbl": "causally upstream of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", - "http://purl.obolibrary.org/obo/valid_for_gocam" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002412", - "lbl": "immediately causally upstream of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000114", - "val": "http://purl.obolibrary.org/obo/IAO_0000428" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0002575", - "val": "http://purl.obolibrary.org/obo/RO_0002411" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002418", - "lbl": "causally upstream of or within", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "influences (processual)" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "synonyms": [ - { - "pred": "hasRelatedSynonym", - "val": "affects", - "xrefs": [] - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002427", - "lbl": "causally downstream of or within", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } - ], - "definition": { - "val": "inverse of causally upstream of or within", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/RO_0002259" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002428", - "lbl": "involved in regulation of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "c involved in regulation of p if c is involved in some p' and p' regulates some p", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002429", - "lbl": "involved in positive regulation of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0004049", - "val": "http://purl.obolibrary.org/obo/RO_0002428" - } - ], - "definition": { - "val": "c involved in regulation of p if c is involved in some p' and p' positively regulates some p", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002430", - "lbl": "involved in negative regulation of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/RO_0004050", - "val": "http://purl.obolibrary.org/obo/RO_0002428" - } - ], - "definition": { - "val": "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002431", - "lbl": "involved in or involved in regulation of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "OWL does not allow defining object properties via a Union" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "involved in or reguates" - } - ], - "definition": { - "val": "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", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002432", - "lbl": "is active in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000112", - "val": "A protein that enables activity in a cytosol." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "executes activity in" - } - ], - "comments": [ - "" - ], - "definition": { - "val": "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.", - "xrefs": [ - "GOC:cjm", - "GOC:dos" - ] - }, - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "enables activity in", - "xrefs": [] - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002434", - "lbl": "interacts with", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Considering relabeling as 'pairwise interacts with'" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "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." - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "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." - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://purl.obolibrary.org/obo/MI_0914" - }, - { - "pred": "http://xmlns.com/foaf/0.1/page", - "val": "https://github.com/oborel/obo-relations/wiki/InteractionRelations" - } - ], - "definition": { - "val": "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ], - "synonyms": [ - { - "pred": "hasExactSynonym", - "val": "in pairwise interaction with", - "xrefs": [] - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002436", - "lbl": "molecularly interacts with", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "binds" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "molecularly binds with" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://purl.obolibrary.org/obo/ECO_0000353" - }, - { - "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val": "http://purl.obolibrary.org/obo/MI_0915" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002447", - "lbl": "phosphorylates", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000116", - "val": "Axiomatization to GO to be added later" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000118", - "val": "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002448", - "lbl": "directly regulates activity of", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Vasundra Touré" - } - ], - "definition": { - "val": "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. 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These properties exist as helper properties that are used to support OWL reasoning." - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002479", - "lbl": "has part that occurs in", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ], - "definition": { - "val": "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.", - "xrefs": [] - }, - "subsets": [ - "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002481", - "lbl": "is kinase activity", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - } - ] - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002500", - "lbl": "causal agent in process", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } - ], - "definition": { - "val": "A relationship between a material entity and a process where the material entity has some causal role that influences the process", - "xrefs": [] - } - }, - "type": "PROPERTY" - }, - { - "id": "http://purl.obolibrary.org/obo/RO_0002501", - "lbl": "causal relation between processes", - "meta": { - "basicPropertyValues": [ - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000117", - "val": "Chris Mungall" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000119", - "val": "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, - { - "pred": "http://purl.obolibrary.org/obo/IAO_0000232", - "val": "Do not use this relation directly. 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}, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/RO_0002327", - "http://purl.obolibrary.org/obo/RO_0004046" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0004033" - }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/RO_0002327", - "http://purl.obolibrary.org/obo/RO_0004047" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0004032" - }, - { - "chainPredicateIds": [ - "http://purl.obolibrary.org/obo/RO_0002578", - "http://purl.obolibrary.org/obo/RO_0002578" - ], - "predicateId": "http://purl.obolibrary.org/obo/RO_0002211" + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "lbl" : "occurrent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "lbl" : "independent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "lbl" : "process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl" : "disposition", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl" : "realizable entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl" : "quality", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl" : "specifically dependent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "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." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl" : "role", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl" : "function", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl" : "material entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000000", + "lbl" : "anatomical entity", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", + "val" : "http://purl.obolibrary.org/obo/caro.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "lbl" : "organism or virus or viroid", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0030000", + "lbl" : "biological entity", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CHR_10090-chr1", + "lbl" : "chromosome 1 (Mouse)", + "type" : "CLASS", + "meta" : { + 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This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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'." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "comments" : [ "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'." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "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." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "lbl" : "overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Jennifer Deegan" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Terry Meehan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Terry Meehan" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Hill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Tanya Berardini" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "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)\"." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "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." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "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." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "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" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "cjm" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "cjm" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "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." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has input" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "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." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "lbl" : "phosphorylates", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "lbl" : "directly regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "lbl" : "directly positively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly activates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "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" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "lbl" : "causally influenced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "lbl" : "interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "lbl" : "molecular interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Vasundra Touré" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." } - ] - } - ] -} + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "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." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'causal agent in process'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + 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"http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002596", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002211" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002597", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002212" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002598", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002213" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0017001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002233" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002314", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002331", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002211" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002448", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002333" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002212" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002213" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004034", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002304" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004035", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002305" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002263", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002233" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002333" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002264", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002418" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002450", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002333" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002449", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002333" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004033", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004046" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004032", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0004047" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002331", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002430", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002212" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002429", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002213" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + } ] + } ] +} \ No newline at end of file diff --git a/chr-full.obo b/chr-full.obo index 66183eb..22366de 100644 --- a/chr-full.obo +++ b/chr-full.obo @@ -1,9 +1,8 @@ format-version: 1.2 -data-version: chr/releases/2022-02-02/chr-full.owl +data-version: chr/releases/2023-02-19/chr-full.owl subsetdef: gocheck_do_not_annotate "" subsetdef: gocheck_do_not_manually_annotate "" subsetdef: goslim_agr "" -subsetdef: goslim_aspergillus "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" subsetdef: goslim_drosophila "" @@ -18,13 +17,21 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: prokaryote_subset "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" +synonymtypedef: blast_name "" +synonymtypedef: common_name "" +synonymtypedef: equivalent_name "" +synonymtypedef: genbank_common_name "" +synonymtypedef: in_part "" +synonymtypedef: scientific_name "" +synonymtypedef: synonym "" ontology: chr/chr-full property_value: http://purl.org/dc/elements/1.1/description "Automatic translation of UCSC chromosome bands to OWL classes" xsd:string property_value: http://purl.org/dc/elements/1.1/title "Monochrom Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ -property_value: owl:versionInfo "2022-02-02" xsd:string +property_value: owl:versionInfo "2023-02-19" xsd:string [Term] id: BFO:0000002 @@ -44,6 +51,7 @@ 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 relationship: part_of BFO:0000004 ! independent continuant [Term] @@ -52,6 +60,44 @@ 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 +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +relationship: part_of BFO:0000017 ! realizable entity + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +relationship: part_of BFO:0000019 ! quality + +[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 +relationship: part_of BFO:0000020 ! specifically dependent continuant + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: BFO:0000017 ! realizable entity + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + [Term] id: BFO:0000040 name: material entity @@ -64,19 +110,6 @@ name: anatomical entity is_a: CARO:0030000 ! biological entity property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl -[Term] -id: CARO:0000003 -name: connected anatomical structure -is_a: CARO:0000006 ! material anatomical entity -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl - -[Term] -id: CARO:0000006 -name: material anatomical entity -is_a: BFO:0000040 ! material entity -is_a: CARO:0000000 ! anatomical entity -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl - [Term] id: CARO:0001010 name: organism or virus or viroid @@ -9701,349 +9734,13 @@ property_value: genome:build "ce11" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "17718942" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer -[Term] -id: CHR:7955-chr1 -name: chromosome 1 (Danio rerio) -synonym: "1" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002885.1 -property_value: exactMatch NC:007112.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "58871917" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr10 -name: chromosome 10 (Danio rerio) -synonym: "10" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002894.1 -property_value: exactMatch NC:007121.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "45574255" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr11 -name: chromosome 11 (Danio rerio) -synonym: "11" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002895.1 -property_value: exactMatch NC:007122.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "45107271" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr12 -name: chromosome 12 (Danio rerio) -synonym: "12" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002896.1 -property_value: exactMatch NC:007123.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "49229541" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr13 -name: chromosome 13 (Danio rerio) -synonym: "13" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002897.1 -property_value: exactMatch NC:007124.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "51780250" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr14 -name: chromosome 14 (Danio rerio) -synonym: "14" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002898.1 -property_value: exactMatch NC:007125.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "51944548" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr15 -name: chromosome 15 (Danio rerio) -synonym: "15" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002899.1 -property_value: exactMatch NC:007126.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "47771147" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr16 -name: chromosome 16 (Danio rerio) -synonym: "16" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002900.1 -property_value: exactMatch NC:007127.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "55381981" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr17 -name: chromosome 17 (Danio rerio) -synonym: "17" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002901.1 -property_value: exactMatch NC:007128.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "53345113" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr18 -name: chromosome 18 (Danio rerio) -synonym: "18" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002902.1 -property_value: exactMatch NC:007129.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "51008593" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr19 -name: chromosome 19 (Danio rerio) -synonym: "19" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002903.1 -property_value: exactMatch NC:007130.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "48790377" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr2 -name: chromosome 2 (Danio rerio) -synonym: "2" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002886.1 -property_value: exactMatch NC:007113.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "59543403" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr20 -name: chromosome 20 (Danio rerio) -synonym: "20" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002904.1 -property_value: exactMatch NC:007131.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "55370968" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr21 -name: chromosome 21 (Danio rerio) -synonym: "21" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002905.1 -property_value: exactMatch NC:007132.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "45895719" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr22 -name: chromosome 22 (Danio rerio) -synonym: "22" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002906.1 -property_value: exactMatch NC:007133.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "39226288" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr23 -name: chromosome 23 (Danio rerio) -synonym: "23" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002907.1 -property_value: exactMatch NC:007134.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "46272358" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr24 -name: chromosome 24 (Danio rerio) -synonym: "24" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002908.1 -property_value: exactMatch NC:007135.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "42251103" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr25 -name: chromosome 25 (Danio rerio) -synonym: "25" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002909.1 -property_value: exactMatch NC:007136.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "36898761" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr3 -name: chromosome 3 (Danio rerio) -synonym: "3" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002887.1 -property_value: exactMatch NC:007114.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "62385949" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr4 -name: chromosome 4 (Danio rerio) -synonym: "4" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002888.1 -property_value: exactMatch NC:007115.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "76625712" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr5 -name: chromosome 5 (Danio rerio) -synonym: "5" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002889.1 -property_value: exactMatch NC:007116.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "71715914" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr6 -name: chromosome 6 (Danio rerio) -synonym: "6" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002890.1 -property_value: exactMatch NC:007117.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "60272633" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr7 -name: chromosome 7 (Danio rerio) -synonym: "7" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002891.1 -property_value: exactMatch NC:007118.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "74082188" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr8 -name: chromosome 8 (Danio rerio) -synonym: "8" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002892.1 -property_value: exactMatch NC:007119.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "54191831" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chr9 -name: chromosome 9 (Danio rerio) -synonym: "9" BROAD [] -is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch http://identifiers.org/insdc/CM002893.1 -property_value: exactMatch NC:007120.6 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "56892771" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - -[Term] -id: CHR:7955-chrM -name: chromosome M (Danio rerio) -synonym: "MT" BROAD [] -is_a: GO:0000262 ! mitochondrial chromosome -relationship: RO:0002162 NCBITaxon:7955 ! in taxon Danio rerio -property_value: exactMatch NC:002333.2 -property_value: genome:build "danRer10" xsd:string -property_value: https://w3id.org/biodatamodels/gff/end "16596" xsd:integer -property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer - [Term] id: CHR:9031-chr1 name: chromosome 1 (Chicken) synonym: "1" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000093.5 property_value: exactMatch NC:006088.5 property_value: genome:build "galGal6" xsd:string @@ -10056,7 +9753,7 @@ name: chromosome 10 (Chicken) synonym: "10" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000102.5 property_value: exactMatch NC:006097.5 property_value: genome:build "galGal6" xsd:string @@ -10068,7 +9765,7 @@ id: CHR:9031-chr10cen name: 10cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr10 ! chromosome 10 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "500000" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "250000" xsd:integer @@ -10078,7 +9775,7 @@ id: CHR:9031-chr10q name: 10q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr10 ! chromosome 10 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "21119840" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "500000" xsd:integer @@ -10089,7 +9786,7 @@ name: chromosome 11 (Chicken) synonym: "11" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000103.5 property_value: exactMatch NC:006098.5 property_value: genome:build "galGal6" xsd:string @@ -10101,7 +9798,7 @@ id: CHR:9031-chr11cen name: 11cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr11 ! chromosome 11 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "3230744" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "2980744" xsd:integer @@ -10111,7 +9808,7 @@ id: CHR:9031-chr11p name: 11p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr11 ! chromosome 11 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "2730744" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10121,7 +9818,7 @@ id: CHR:9031-chr11q name: 11q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr11 ! chromosome 11 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "20200042" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "3230744" xsd:integer @@ -10132,7 +9829,7 @@ name: chromosome 12 (Chicken) synonym: "12" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000104.5 property_value: exactMatch NC:006099.5 property_value: genome:build "galGal6" xsd:string @@ -10145,7 +9842,7 @@ name: chromosome 13 (Chicken) synonym: "13" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000105.5 property_value: exactMatch NC:006100.5 property_value: genome:build "galGal6" xsd:string @@ -10157,7 +9854,7 @@ id: CHR:9031-chr13cen name: 13cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr13 ! chromosome 13 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "500000" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "250000" xsd:integer @@ -10167,7 +9864,7 @@ id: CHR:9031-chr13q name: 13q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr13 ! chromosome 13 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "19166714" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "500000" xsd:integer @@ -10178,7 +9875,7 @@ name: chromosome 14 (Chicken) synonym: "14" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000106.5 property_value: exactMatch NC:006101.5 property_value: genome:build "galGal6" xsd:string @@ -10190,7 +9887,7 @@ id: CHR:9031-chr14cen name: 14cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr14 ! chromosome 14 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "15978998" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "15728998" xsd:integer @@ -10200,7 +9897,7 @@ id: CHR:9031-chr14p name: 14p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr14 ! chromosome 14 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "15478998" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10210,7 +9907,7 @@ id: CHR:9031-chr14q name: 14q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr14 ! chromosome 14 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "16219308" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "15978998" xsd:integer @@ -10221,7 +9918,7 @@ name: chromosome 15 (Chicken) synonym: "15" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000107.5 property_value: exactMatch NC:006102.5 property_value: genome:build "galGal6" xsd:string @@ -10234,7 +9931,7 @@ name: chromosome 16 (Chicken) synonym: "16" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000108.5 property_value: exactMatch NC:006103.5 property_value: genome:build "galGal6" xsd:string @@ -10246,7 +9943,7 @@ id: CHR:9031-chr16cen name: 16cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr16 ! chromosome 16 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "500000" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "250000" xsd:integer @@ -10256,7 +9953,7 @@ id: CHR:9031-chr16q name: 16q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr16 ! chromosome 16 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "2844601" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "500000" xsd:integer @@ -10267,7 +9964,7 @@ name: chromosome 17 (Chicken) synonym: "17" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000109.5 property_value: exactMatch NC:006104.5 property_value: genome:build "galGal6" xsd:string @@ -10279,7 +9976,7 @@ id: CHR:9031-chr17cen name: 17cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr17 ! chromosome 17 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "500000" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "250000" xsd:integer @@ -10289,7 +9986,7 @@ id: CHR:9031-chr17q name: 17q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr17 ! chromosome 17 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "10762512" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "500000" xsd:integer @@ -10300,7 +9997,7 @@ name: chromosome 18 (Chicken) synonym: "18" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000110.5 property_value: exactMatch NC:006105.5 property_value: genome:build "galGal6" xsd:string @@ -10313,7 +10010,7 @@ name: chromosome 19 (Chicken) synonym: "19" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000111.5 property_value: exactMatch NC:006106.5 property_value: genome:build "galGal6" xsd:string @@ -10325,7 +10022,7 @@ id: CHR:9031-chr1cen name: 1cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr1 ! chromosome 1 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "77108038" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "76858038" xsd:integer @@ -10335,7 +10032,7 @@ id: CHR:9031-chr1p name: 1p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr1 ! chromosome 1 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "76608038" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10345,7 +10042,7 @@ id: CHR:9031-chr1q name: 1q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr1 ! chromosome 1 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "197608386" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "77108038" xsd:integer @@ -10356,7 +10053,7 @@ name: chromosome 2 (Chicken) synonym: "2" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000094.5 property_value: exactMatch NC:006089.5 property_value: genome:build "galGal6" xsd:string @@ -10369,7 +10066,7 @@ name: chromosome 20 (Chicken) synonym: "20" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000112.5 property_value: exactMatch NC:006107.5 property_value: genome:build "galGal6" xsd:string @@ -10382,7 +10079,7 @@ name: chromosome 21 (Chicken) synonym: "21" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000113.5 property_value: exactMatch NC:006108.5 property_value: genome:build "galGal6" xsd:string @@ -10395,7 +10092,7 @@ name: chromosome 22 (Chicken) synonym: "22" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000114.5 property_value: exactMatch NC:006109.5 property_value: genome:build "galGal6" xsd:string @@ -10407,7 +10104,7 @@ id: CHR:9031-chr22cen name: 22cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr22 ! chromosome 22 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "3570996" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "3320996" xsd:integer @@ -10417,7 +10114,7 @@ id: CHR:9031-chr22p name: 22p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr22 ! chromosome 22 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "3070996" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10427,7 +10124,7 @@ id: CHR:9031-chr22q name: 22q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr22 ! chromosome 22 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "5459462" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "3570996" xsd:integer @@ -10438,7 +10135,7 @@ name: chromosome 23 (Chicken) synonym: "23" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000115.5 property_value: exactMatch NC:006110.5 property_value: genome:build "galGal6" xsd:string @@ -10451,7 +10148,7 @@ name: chromosome 24 (Chicken) synonym: "24" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000116.5 property_value: exactMatch NC:006111.5 property_value: genome:build "galGal6" xsd:string @@ -10464,7 +10161,7 @@ name: chromosome 25 (Chicken) synonym: "25" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000124.5 property_value: exactMatch NC:006112.4 property_value: genome:build "galGal6" xsd:string @@ -10476,7 +10173,7 @@ id: CHR:9031-chr25cen name: 25cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr25 ! chromosome 25 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "1240762" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "990762" xsd:integer @@ -10486,7 +10183,7 @@ id: CHR:9031-chr25p name: 25p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr25 ! chromosome 25 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "740762" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10496,7 +10193,7 @@ id: CHR:9031-chr25q name: 25q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr25 ! chromosome 25 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "3980610" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "1240762" xsd:integer @@ -10507,7 +10204,7 @@ name: chromosome 26 (Chicken) synonym: "26" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000117.5 property_value: exactMatch NC:006113.5 property_value: genome:build "galGal6" xsd:string @@ -10519,7 +10216,7 @@ id: CHR:9031-chr26cen name: 26cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr26 ! chromosome 26 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "6055710" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "5805710" xsd:integer @@ -10529,7 +10226,7 @@ id: CHR:9031-chr26p name: 26p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr26 ! chromosome 26 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "5555710" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10540,7 +10237,7 @@ name: chromosome 27 (Chicken) synonym: "27" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000118.5 property_value: exactMatch NC:006114.5 property_value: genome:build "galGal6" xsd:string @@ -10553,7 +10250,7 @@ name: chromosome 28 (Chicken) synonym: "28" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000119.5 property_value: exactMatch NC:006115.5 property_value: genome:build "galGal6" xsd:string @@ -10565,7 +10262,7 @@ id: CHR:9031-chr2cen name: 2cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr2 ! chromosome 2 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "52651238" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "52401238" xsd:integer @@ -10575,7 +10272,7 @@ id: CHR:9031-chr2p name: 2p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr2 ! chromosome 2 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "52151238" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10585,7 +10282,7 @@ id: CHR:9031-chr2q name: 2q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr2 ! chromosome 2 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "149682049" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "52651238" xsd:integer @@ -10596,7 +10293,7 @@ name: chromosome 3 (Chicken) synonym: "3" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000095.5 property_value: exactMatch NC:006090.5 property_value: genome:build "galGal6" xsd:string @@ -10609,7 +10306,7 @@ name: chromosome 30 (Chicken) synonym: "30" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM003637.2 property_value: exactMatch NC:028739.2 property_value: genome:build "galGal6" xsd:string @@ -10622,7 +10319,7 @@ name: chromosome 31 (Chicken) synonym: "31" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM003638.2 property_value: exactMatch NC:028740.2 property_value: genome:build "galGal6" xsd:string @@ -10635,7 +10332,7 @@ name: chromosome 32 (Chicken) synonym: "32" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000120.4 property_value: exactMatch NC:006119.4 property_value: genome:build "galGal6" xsd:string @@ -10648,7 +10345,7 @@ name: chromosome 33 (Chicken) synonym: "33" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000123.5 property_value: exactMatch NC:008465.4 property_value: genome:build "galGal6" xsd:string @@ -10660,7 +10357,7 @@ id: CHR:9031-chr3cen name: 3cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr3 ! chromosome 3 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "6301976" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "6051976" xsd:integer @@ -10670,7 +10367,7 @@ id: CHR:9031-chr3p name: 3p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr3 ! chromosome 3 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "5801976" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10680,7 +10377,7 @@ id: CHR:9031-chr3q name: 3q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr3 ! chromosome 3 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "110838418" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "6301976" xsd:integer @@ -10691,7 +10388,7 @@ name: chromosome 4 (Chicken) synonym: "4" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000096.5 property_value: exactMatch NC:006091.5 property_value: genome:build "galGal6" xsd:string @@ -10703,7 +10400,7 @@ id: CHR:9031-chr4cen name: 4cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr4 ! chromosome 4 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "19261804" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "19011804" xsd:integer @@ -10713,7 +10410,7 @@ id: CHR:9031-chr4p name: 4p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr4 ! chromosome 4 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "18761804" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10723,7 +10420,7 @@ id: CHR:9031-chr4q name: 4q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr4 ! chromosome 4 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "91315245" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "19261804" xsd:integer @@ -10734,7 +10431,7 @@ name: chromosome 5 (Chicken) synonym: "5" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000097.5 property_value: exactMatch NC:006092.5 property_value: genome:build "galGal6" xsd:string @@ -10746,7 +10443,7 @@ id: CHR:9031-chr5cen name: 5cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr5 ! chromosome 5 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "6509601" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "6259601" xsd:integer @@ -10756,7 +10453,7 @@ id: CHR:9031-chr5p name: 5p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr5 ! chromosome 5 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "6009601" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10766,7 +10463,7 @@ id: CHR:9031-chr5q name: 5q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr5 ! chromosome 5 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "59809098" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "6509601" xsd:integer @@ -10777,7 +10474,7 @@ name: chromosome 6 (Chicken) synonym: "6" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000098.5 property_value: exactMatch NC:006093.5 property_value: genome:build "galGal6" xsd:string @@ -10789,7 +10486,7 @@ id: CHR:9031-chr6cen name: 6cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr6 ! chromosome 6 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "500000" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "250000" xsd:integer @@ -10799,7 +10496,7 @@ id: CHR:9031-chr6q name: 6q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr6 ! chromosome 6 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "36374701" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "500000" xsd:integer @@ -10810,7 +10507,7 @@ name: chromosome 7 (Chicken) synonym: "7" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000099.5 property_value: exactMatch NC:006094.5 property_value: genome:build "galGal6" xsd:string @@ -10822,7 +10519,7 @@ id: CHR:9031-chr7cen name: 7cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr7 ! chromosome 7 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "7831533" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "7581533" xsd:integer @@ -10832,7 +10529,7 @@ id: CHR:9031-chr7p name: 7p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr7 ! chromosome 7 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "7331533" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10842,7 +10539,7 @@ id: CHR:9031-chr7q name: 7q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr7 ! chromosome 7 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "36742308" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "7831533" xsd:integer @@ -10853,7 +10550,7 @@ name: chromosome 8 (Chicken) synonym: "8" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000100.5 property_value: exactMatch NC:006095.5 property_value: genome:build "galGal6" xsd:string @@ -10865,7 +10562,7 @@ id: CHR:9031-chr8cen name: 8cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr8 ! chromosome 8 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "9826743" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "9576743" xsd:integer @@ -10875,7 +10572,7 @@ id: CHR:9031-chr8p name: 8p (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr8 ! chromosome 8 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "9326743" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "0" xsd:integer @@ -10885,7 +10582,7 @@ id: CHR:9031-chr8q name: 8q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr8 ! chromosome 8 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "30219446" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "9826743" xsd:integer @@ -10896,7 +10593,7 @@ name: chromosome 9 (Chicken) synonym: "9" BROAD [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0030849 ! autosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000101.5 property_value: exactMatch NC:006096.5 property_value: genome:build "galGal6" xsd:string @@ -10908,7 +10605,7 @@ id: CHR:9031-chr9cen name: 9cen (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr9 ! chromosome 9 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "500000" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "250000" xsd:integer @@ -10918,7 +10615,7 @@ id: CHR:9031-chr9q name: 9q (Chicken) is_a: GO:0098687 ! chromosomal region relationship: part_of CHR:9031-chr9 ! chromosome 9 (Chicken) -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: genome:build "galGal6" xsd:string property_value: https://w3id.org/biodatamodels/gff/end "24153086" xsd:integer property_value: https://w3id.org/biodatamodels/gff/start "500000" xsd:integer @@ -10928,7 +10625,7 @@ id: CHR:9031-chrM name: chromosome M (Chicken) synonym: "MT" BROAD [] is_a: GO:0000262 ! mitochondrial chromosome -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/X52392.1 property_value: exactMatch NC:001323.1 property_value: genome:build "galGal6" xsd:string @@ -10940,9 +10637,8 @@ id: CHR:9031-chrW name: chromosome W (Chicken) synonym: "W" BROAD [] is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0000803 ! sex chromosome -is_a: GO:0000804 -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +is_a: GO:0000804 ! W chromosome +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000121.5 property_value: exactMatch NC:006126.5 property_value: genome:build "galGal6" xsd:string @@ -10954,9 +10650,8 @@ id: CHR:9031-chrZ name: chromosome Z (Chicken) synonym: "Z" BROAD [] is_a: GO:0000228 ! nuclear chromosome -is_a: GO:0000803 ! sex chromosome -is_a: GO:0000807 -relationship: RO:0002162 NCBITaxon:9031 ! in taxon +is_a: GO:0000807 ! Z chromosome +relationship: RO:0002162 NCBITaxon:9031 ! in taxon Gallus gallus property_value: exactMatch http://identifiers.org/insdc/CM000122.5 property_value: exactMatch NC:006127.5 property_value: genome:build "galGal6" xsd:string @@ -24412,19 +24107,6 @@ intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0031981 ! nuclear lumen -[Term] -id: GO:0000229 -name: cytoplasmic chromosome -namespace: cellular_component -def: "A chromosome found in the cytoplasm." [GOC:mah] -subset: goslim_chembl -subset: goslim_generic -synonym: "cytoplasmic interphase chromosome" NARROW [] -is_a: GO:0005694 ! chromosome -intersection_of: GO:0005694 ! chromosome -intersection_of: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0005737 ! cytoplasm - [Term] id: GO:0000262 name: mitochondrial chromosome @@ -24434,7 +24116,7 @@ synonym: "mitochondrial DNA" NARROW [] synonym: "mitochondrial genome" RELATED [] synonym: "mtDNA" NARROW [] xref: NIF_Subcellular:sao1186327184 -is_a: GO:0000229 ! cytoplasmic chromosome +is_a: GO:0005694 ! chromosome intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0042645 ! mitochondrial nucleoid @@ -24446,6 +24128,15 @@ namespace: cellular_component def: "A chromosome involved in sex determination." [GOC:elh] is_a: GO:0005694 ! chromosome +[Term] +id: GO:0000804 +name: W chromosome +namespace: cellular_component +def: "The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females." [GOC:mah, GOC:mr, ISBN:0321000382, PMID:20622855] +xref: Wikipedia:ZW_sex-determination_system +is_a: GO:0000803 ! sex chromosome +property_value: RO:0002161 NCBITaxon:40674 + [Term] id: GO:0000805 name: X chromosome @@ -24464,6 +24155,15 @@ xref: Wikipedia:Y_chromosome is_a: GO:0000803 ! sex chromosome property_value: RO:0002161 NCBITaxon:8782 +[Term] +id: GO:0000807 +name: Z chromosome +namespace: cellular_component +def: "The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females." [GOC:mah, GOC:mr, ISBN:0321000382, PMID:20622855] +xref: Wikipedia:ZW_sex-determination_system +is_a: GO:0000803 ! sex chromosome +property_value: RO:0002161 NCBITaxon:40674 + [Term] id: GO:0003674 name: molecular_function @@ -24482,10 +24182,8 @@ namespace: cellular_component alt_id: GO:0008372 def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [GOC:pdt, NIF_Subcellular:sao1337158144] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component 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 @@ -24502,7 +24200,6 @@ namespace: cellular_component def: "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] subset: gocheck_do_not_annotate subset: goslim_chembl -subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant synonym: "internal to cell" EXACT [] @@ -24520,7 +24217,6 @@ name: nucleus namespace: cellular_component def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] subset: goslim_agr -subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -24536,7 +24232,6 @@ synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle -is_a: GO:0044464 ! cell part property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] @@ -24558,9 +24253,8 @@ id: GO:0005694 name: chromosome namespace: cellular_component def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [ISBN:0198547684] -comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. +comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. subset: goslim_agr -subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -24569,6 +24263,7 @@ subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_yeast +subset: prokaryote_subset synonym: "chromatid" RELATED [] synonym: "interphase chromosome" NARROW [] synonym: "prophase chromosome" NARROW [] @@ -24579,17 +24274,18 @@ is_a: GO:0043232 ! intracellular non-membrane-bounded organelle id: GO:0005737 name: cytoplasm namespace: cellular_component -def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] +def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684] subset: goslim_candida subset: goslim_chembl -subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast +subset: prokaryote_subset xref: Wikipedia:Cytoplasm is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/23023 xsd:anyURI [Term] id: GO:0005739 @@ -24598,7 +24294,6 @@ namespace: cellular_component def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GOC:giardia, ISBN:0198506732] comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) subset: goslim_agr -subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -24643,7 +24338,6 @@ name: vacuole namespace: cellular_component def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] subset: goslim_agr -subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -24674,7 +24368,6 @@ name: cytosol namespace: cellular_component def: "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." [GOC:hjd, GOC:jl] subset: goslim_agr -subset: goslim_aspergillus subset: goslim_chembl subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -24690,10 +24383,10 @@ relationship: part_of GO:0005737 ! cytoplasm id: GO:0005886 name: plasma membrane namespace: cellular_component +alt_id: GO:0005887 alt_id: GO:0005904 def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [ISBN:0716731363] subset: goslim_agr -subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -24702,11 +24395,14 @@ subset: goslim_metagenomics subset: goslim_mouse subset: goslim_plant subset: goslim_yeast +subset: prokaryote_subset synonym: "bacterial inner membrane" NARROW [] synonym: "cell membrane" EXACT [] synonym: "cellular membrane" EXACT [NIF_Subcellular:sao6433132645] synonym: "cytoplasmic membrane" EXACT [] synonym: "inner endospore membrane" NARROW [] +synonym: "integral component of plasma membrane" NARROW [] +synonym: "integral to plasma membrane" NARROW [] synonym: "juxtamembrane" BROAD [] synonym: "plasma membrane lipid bilayer" NARROW [GOC:mah] synonym: "plasmalemma" EXACT [] @@ -24720,7 +24416,6 @@ id: GO:0005938 name: cell cortex namespace: cellular_component def: "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins." [GOC:mah, ISBN:0815316194] -subset: goslim_aspergillus subset: goslim_candida subset: goslim_yeast synonym: "cell periphery" RELATED [] @@ -24762,7 +24457,7 @@ id: GO:0009508 name: plastid chromosome namespace: cellular_component def: "A circular DNA molecule containing plastid encoded genes." [ISBN:0943088399] -is_a: GO:0000229 ! cytoplasmic chromosome +is_a: GO:0005694 ! chromosome intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0009536 ! plastid relationship: part_of GO:0042646 ! plastid nucleoid @@ -24815,7 +24510,6 @@ id: GO:0012505 name: endomembrane system namespace: cellular_component def: "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." [GOC:lh] -subset: goslim_aspergillus subset: goslim_candida subset: goslim_flybase_ribbon subset: goslim_yeast @@ -24828,10 +24522,10 @@ relationship: has_part GO:0005886 ! plasma membrane id: GO:0016020 name: membrane namespace: cellular_component +alt_id: GO:0016021 alt_id: GO:0098589 alt_id: GO:0098805 -def: "A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] -subset: goslim_aspergillus +def: "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." [GOC:dos, GOC:mah, ISBN:0815316194] subset: goslim_candida subset: goslim_chembl subset: goslim_flybase_ribbon @@ -24839,10 +24533,14 @@ subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast +synonym: "integral component of membrane" NARROW [] +synonym: "integral to membrane" NARROW [] synonym: "membrane region" NARROW [] synonym: "region of membrane" NARROW [] +synonym: "transmembrane" RELATED [GOC:mah] synonym: "whole membrane" NARROW [] xref: Wikipedia:Biological_membrane +xref: Wikipedia:Transmembrane_protein is_a: GO:0110165 ! cellular anatomical entity creation_date: 2014-03-06T11:37:54Z @@ -24996,6 +24694,7 @@ def: "Organized structure of distinctive morphology and function. Includes the n subset: goslim_chembl subset: goslim_generic subset: goslim_pir +subset: prokaryote_subset xref: NIF_Subcellular:sao1539965131 xref: Wikipedia:Organelle is_a: GO:0110165 ! cellular anatomical entity @@ -25017,9 +24716,12 @@ id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: goslim_mouse +synonym: "biological condensate" NARROW [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/21881 xsd:anyURI [Term] id: GO:0043229 @@ -25049,7 +24751,6 @@ id: GO:0043232 name: intracellular non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] -subset: goslim_mouse subset: goslim_pir synonym: "intracellular non-membrane-enclosed organelle" EXACT [] is_a: GO:0043228 ! non-membrane-bounded organelle @@ -25062,23 +24763,17 @@ id: GO:0043233 name: organelle lumen namespace: cellular_component def: "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen." [GOC:jl, GOC:mah] +subset: goslim_mouse is_a: GO:0031974 ! membrane-enclosed lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: part_of GO:0043226 ! organelle relationship: part_of GO:0043226 ! organelle -[Term] -id: GO:0044464 -name: cell part -is_a: CARO:0000003 ! connected anatomical structure -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - [Term] id: GO:0070013 name: intracellular organelle lumen namespace: cellular_component def: "An organelle lumen that is part of an intracellular organelle." [GOC:mah] -subset: goslim_mouse is_a: GO:0043233 ! organelle lumen intersection_of: GO:0031974 ! membrane-enclosed lumen intersection_of: part_of GO:0043229 ! intracellular organelle @@ -25114,16 +24809,18 @@ id: GO:0098687 name: chromosomal region namespace: cellular_component def: "Any subdivision of a chromosome along its length." [GOC:dos] -comment: Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. +comment: Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome region" EXACT [] is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome [Term] id: GO:0099522 -name: region of cytosol +name: cytosolic region namespace: cellular_component def: "Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol." [GOC:dos] +subset: gocheck_do_not_annotate +synonym: "region of cytosol" EXACT [] is_a: GO:0005829 ! cytosol intersection_of: GO:0005829 ! cytosol intersection_of: part_of GO:0005829 ! cytosol @@ -25134,6 +24831,7 @@ id: GO:0099568 name: cytoplasmic region namespace: cellular_component def: "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm." [GOC:dos] +subset: gocheck_do_not_annotate is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of GO:0005737 ! cytoplasm @@ -25144,6 +24842,7 @@ id: GO:0099738 name: cell cortex region namespace: cellular_component def: "The complete extent of cell cortex that underlies some some region of the plasma membrane." [GOC:dos] +subset: gocheck_do_not_annotate synonym: "perimembrane region" EXACT [] is_a: GO:0005938 ! cell cortex is_a: GO:0099568 ! cytoplasmic region @@ -25265,6 +24964,18 @@ synonym: "biota" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:1 ! root +[Term] +id: NCBITaxon:1329799 +name: Archelosauria +namespace: ncbi_taxonomy +synonym: "Archosauria-Testudines" RELATED synonym [] +synonym: "Testudines + Archosauria group" RELATED synonym [] +xref: GC_ID:1 +xref: PMID:22839753 +xref: PMID:25450099 +is_a: NCBITaxon:32561 ! Sauria +property_value: has_rank NCBITaxon:clade + [Term] id: NCBITaxon:1338369 name: Dipnotetrapodomorpha @@ -25285,56 +24996,15 @@ is_a: NCBITaxon:9347 ! Eutheria property_value: has_rank NCBITaxon:clade [Term] -id: NCBITaxon:1489341 -name: Osteoglossocephalai -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:32443 ! Teleostei -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:186623 -name: Actinopteri -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:7898 ! Actinopterygii -property_value: has_rank NCBITaxon:class - -[Term] -id: NCBITaxon:186625 -name: Clupeocephala -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:1489341 ! Osteoglossocephalai - -[Term] -id: NCBITaxon:186626 -name: Otophysi -namespace: ncbi_taxonomy -synonym: "Otophysa" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:32519 ! Ostariophysi -property_value: has_rank NCBITaxon:clade - -[Term] -id: NCBITaxon:186627 -name: Cypriniphysae +id: NCBITaxon:1549675 +name: Galloanserae namespace: ncbi_taxonomy -synonym: "Cypriniphysi" RELATED synonym [] +synonym: "ducks, geese, chickens, fowl, quail, currasows and allies" RELATED synonym [] +synonym: "Galloanseri" RELATED synonym [] xref: GC_ID:1 -is_a: NCBITaxon:186626 ! Otophysi +is_a: NCBITaxon:8825 ! Neognathae property_value: has_rank NCBITaxon:superorder -[Term] -id: NCBITaxon:186634 -name: Otomorpha -namespace: ncbi_taxonomy -synonym: "Ostarioclupeomorpha" RELATED synonym [] -synonym: "Otocephala" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:186625 ! Clupeocephala -property_value: has_rank NCBITaxon:cohort - [Term] id: NCBITaxon:1963758 name: Myomorpha @@ -25370,22 +25040,6 @@ xref: GC_ID:1 is_a: NCBITaxon:2301116 ! Rhabditina property_value: has_rank NCBITaxon:infraorder -[Term] -id: NCBITaxon:2743709 -name: Danionidae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:30727 ! Cyprinoidei -property_value: has_rank NCBITaxon:family - -[Term] -id: NCBITaxon:2743711 -name: Danioninae -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:2743709 ! Danionidae -property_value: has_rank NCBITaxon:subfamily - [Term] id: NCBITaxon:2759 name: Eukaryota @@ -25403,15 +25057,6 @@ xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms property_value: has_rank NCBITaxon:superkingdom -[Term] -id: NCBITaxon:30727 -name: Cyprinoidei -namespace: ncbi_taxonomy -synonym: "Cyprinoidea" RELATED synonym [] -xref: GC_ID:1 -is_a: NCBITaxon:7952 ! Cypriniformes -property_value: has_rank NCBITaxon:suborder - [Term] id: NCBITaxon:314146 name: Euarchontoglires @@ -25455,23 +25100,6 @@ xref: GC_ID:1 is_a: NCBITaxon:9526 ! Catarrhini property_value: has_rank NCBITaxon:superfamily -[Term] -id: NCBITaxon:32443 -name: Teleostei -namespace: ncbi_taxonomy -synonym: "teleost fishes" EXACT genbank_common_name [] -xref: GC_ID:1 -is_a: NCBITaxon:41665 ! Neopterygii -property_value: has_rank NCBITaxon:infraclass - -[Term] -id: NCBITaxon:32519 -name: Ostariophysi -namespace: ncbi_taxonomy -xref: GC_ID:1 -is_a: NCBITaxon:186634 ! Otomorpha -property_value: has_rank NCBITaxon:subcohort - [Term] id: NCBITaxon:32523 name: Tetrapoda @@ -25499,6 +25127,16 @@ xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia property_value: has_rank NCBITaxon:clade +[Term] +id: NCBITaxon:32561 +name: Sauria +namespace: ncbi_taxonomy +synonym: "Diapsida" RELATED synonym [] +synonym: "diapsids" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:8457 ! Sauropsida +property_value: has_rank NCBITaxon:clade + [Term] id: NCBITaxon:33154 name: Opisthokonta @@ -25584,13 +25222,38 @@ is_a: NCBITaxon:32524 ! Amniota property_value: has_rank NCBITaxon:class [Term] -id: NCBITaxon:41665 -name: Neopterygii +id: NCBITaxon:436486 +name: Dinosauria +namespace: ncbi_taxonomy +synonym: "dinosaur" EXACT common_name [] +synonym: "dinosaurs" EXACT common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:8492 ! Archosauria +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:436489 +name: Saurischia +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:436486 ! Dinosauria +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:436491 +name: Theropoda namespace: ncbi_taxonomy -synonym: "Neopterygi" RELATED synonym [] xref: GC_ID:1 -is_a: NCBITaxon:186623 ! Actinopteri -property_value: has_rank NCBITaxon:subclass +is_a: NCBITaxon:436489 ! Saurischia +property_value: has_rank NCBITaxon:clade + +[Term] +id: NCBITaxon:436492 +name: Coelurosauria +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:436491 ! Theropoda +property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:55879 @@ -25652,7 +25315,6 @@ id: NCBITaxon:6239 name: Caenorhabditis elegans namespace: ncbi_taxonomy synonym: "Rhabditis elegans" RELATED synonym [] -synonym: "roundworm" EXACT common_name [] xref: GC_ID:1 is_a: NCBITaxon:6237 ! Caenorhabditis property_value: has_rank NCBITaxon:species @@ -25698,75 +25360,57 @@ is_a: NCBITaxon:7742 ! Vertebrata property_value: has_rank NCBITaxon:clade [Term] -id: NCBITaxon:7898 -name: Actinopterygii +id: NCBITaxon:8287 +name: Sarcopterygii namespace: ncbi_taxonomy -synonym: "Actinopterygi" RELATED synonym [] -synonym: "bony fishes" RELATED blast_name [] -synonym: "fish" EXACT common_name [] -synonym: "fishes" EXACT common_name [] -synonym: "Osteichthyes" RELATED in_part [] -synonym: "ray-finned fishes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi property_value: has_rank NCBITaxon:superclass [Term] -id: NCBITaxon:7952 -name: Cypriniformes +id: NCBITaxon:8457 +name: Sauropsida namespace: ncbi_taxonomy -synonym: "carps and others" EXACT genbank_common_name [] +synonym: "sauropsids" EXACT genbank_common_name [] xref: GC_ID:1 -is_a: NCBITaxon:186627 ! Cypriniphysae -property_value: has_rank NCBITaxon:order +is_a: NCBITaxon:32524 ! Amniota +property_value: has_rank NCBITaxon:clade [Term] -id: NCBITaxon:7954 -name: Danio +id: NCBITaxon:8492 +name: Archosauria namespace: ncbi_taxonomy -alt_id: NCBITaxon:46777 -alt_id: NCBITaxon:487617 -synonym: "Brachydanio" RELATED synonym [] -synonym: "Celestichthys" RELATED synonym [] xref: GC_ID:1 -is_a: NCBITaxon:2743711 ! Danioninae -property_value: has_rank NCBITaxon:genus +is_a: NCBITaxon:1329799 ! Archelosauria +property_value: has_rank NCBITaxon:clade [Term] -id: NCBITaxon:7955 -name: Danio rerio +id: NCBITaxon:862507 +name: Mus namespace: ncbi_taxonomy -alt_id: NCBITaxon:27702 -alt_id: NCBITaxon:37966 -synonym: "Brachydanio rerio" RELATED synonym [] -synonym: "Brachydanio rerio frankei" RELATED synonym [] -synonym: "Cyprinus rerio" RELATED synonym [] -synonym: "Danio frankei" RELATED synonym [] -synonym: "Danio rerio frankei" RELATED synonym [] -synonym: "leopard danio" EXACT common_name [] -synonym: "zebra danio" EXACT common_name [] -synonym: "zebra fish" EXACT common_name [] -synonym: "zebrafish" EXACT genbank_common_name [] +synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 -is_a: NCBITaxon:7954 ! Danio -property_value: has_rank NCBITaxon:species +is_a: NCBITaxon:10088 ! Mus +property_value: has_rank NCBITaxon:subgenus [Term] -id: NCBITaxon:8287 -name: Sarcopterygii +id: NCBITaxon:8782 +name: Aves namespace: ncbi_taxonomy +synonym: "avian" RELATED synonym [] +synonym: "birds" EXACT genbank_common_name [] +synonym: "birds" RELATED blast_name [] xref: GC_ID:1 -is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass +is_a: NCBITaxon:436492 ! Coelurosauria +property_value: has_rank NCBITaxon:class [Term] -id: NCBITaxon:862507 -name: Mus +id: NCBITaxon:8825 +name: Neognathae namespace: ncbi_taxonomy -synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 -is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus +is_a: NCBITaxon:8782 ! Aves +property_value: has_rank NCBITaxon:infraclass [Term] id: NCBITaxon:89593 @@ -25777,6 +25421,55 @@ xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata property_value: has_rank NCBITaxon:subphylum +[Term] +id: NCBITaxon:8976 +name: Galliformes +namespace: ncbi_taxonomy +synonym: "landfowls" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:1549675 ! Galloanserae +property_value: has_rank NCBITaxon:order + +[Term] +id: NCBITaxon:9005 +name: Phasianidae +namespace: ncbi_taxonomy +alt_id: NCBITaxon:9099 +synonym: "turkeys" EXACT genbank_common_name [] +xref: GC_ID:1 +is_a: NCBITaxon:8976 ! Galliformes +property_value: has_rank NCBITaxon:family + +[Term] +id: NCBITaxon:9030 +name: Gallus +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:9072 ! Phasianinae +property_value: has_rank NCBITaxon:genus + +[Term] +id: NCBITaxon:9031 +name: Gallus gallus +namespace: ncbi_taxonomy +synonym: "bantam" EXACT common_name [] +synonym: "chicken" EXACT genbank_common_name [] +synonym: "chickens" EXACT common_name [] +synonym: "Gallus domesticus" EXACT equivalent_name [] +synonym: "Gallus gallus domesticus" RELATED synonym [] +synonym: "Phasianus gallus" RELATED synonym [] +xref: GC_ID:1 +is_a: NCBITaxon:9030 ! Gallus +property_value: has_rank NCBITaxon:species + +[Term] +id: NCBITaxon:9072 +name: Phasianinae +namespace: ncbi_taxonomy +xref: GC_ID:1 +is_a: NCBITaxon:9005 ! Phasianidae +property_value: has_rank NCBITaxon:subfamily + [Term] id: NCBITaxon:9347 name: Eutheria @@ -25833,7 +25526,6 @@ id: NCBITaxon:9606 name: Homo sapiens namespace: ncbi_taxonomy synonym: "human" EXACT genbank_common_name [] -synonym: "man" EXACT common_name [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species @@ -25848,6 +25540,12 @@ xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires property_value: has_rank NCBITaxon:order +[Term] +id: PATO:0000001 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string + [Typedef] id: BFO:0000062 name: preceded by @@ -25878,31 +25576,32 @@ 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 -holds_over_chain: part_of BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: part_of ! part of +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: RO:0002314 ! characteristic of part of +inverse_of: RO:0000053 ! has characteristic [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 +id: RO:0000053 +name: has characteristic +def: "Inverse of characteristic_of" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant +is_inverse_functional: true [Typedef] id: RO:0000056 @@ -25932,6 +25631,92 @@ domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: has_part RO:0000057 +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! has characteristic +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +is_a: RO:0000052 ! characteristic of + [Typedef] id: RO:0002013 name: has regulatory component activity @@ -26057,6 +25842,7 @@ 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_symmetric: true 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)" [] @@ -26126,12 +25912,10 @@ is_a: RO:0002388 ! has potential to directly develop into [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." [] +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] 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 @@ -26151,7 +25935,7 @@ transitive_over: RO:0002025 ! has effector activity [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." [] +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] 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 @@ -26166,7 +25950,7 @@ 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." [] +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] 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 @@ -26202,7 +25986,7 @@ 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: seeAlso "defining-property-chains-involving-reflexivity" +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/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 @@ -26305,6 +26089,7 @@ is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002304 name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] 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 @@ -26316,12 +26101,28 @@ 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 +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +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: 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:0002314 +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: RO:0000052 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002502 ! depends on +transitive_over: part_of ! part of + [Typedef] id: RO:0002320 name: evolutionarily related to @@ -26347,6 +26148,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a [Typedef] id: RO:0002327 name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] 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 @@ -26356,7 +26158,6 @@ 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 is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part @@ -26491,22 +26292,49 @@ 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:0002407 +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 +is_transitive: true +is_a: RO:0002213 ! positively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates + +[Typedef] +id: RO:0002409 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "indirectly inhibits" xsd:string +property_value: RO:0002579 RO:0002212 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 +is_transitive: true +is_a: RO:0002212 ! negatively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates + [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 +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] +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 [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" [] +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] 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 is_transitive: true is_a: BFO:0000063 ! precedes @@ -26515,8 +26343,7 @@ 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 +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: RO:0002575 RO:0002411 is_a: RO:0002090 ! immediately precedes @@ -26525,7 +26352,7 @@ 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." [] +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of 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 @@ -26585,30 +26412,18 @@ 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 -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: closeMatch http://purl.obolibrary.org/obo/MI_0914 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: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true @@ -26617,11 +26432,11 @@ is_symmetric: true 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: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI 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: seeAlso ECO:0000353 -property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI is_symmetric: true is_a: RO:0002434 ! interacts with @@ -26675,16 +26490,6 @@ 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 -[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 -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 name: is kinase activity @@ -26702,7 +26507,7 @@ 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." [] +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 where the execution of p influences the execution of q. 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 @@ -26710,6 +26515,12 @@ domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002502 +name: depends on +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso BFO:0000169 + [Typedef] id: RO:0002506 name: causal relation between entities @@ -26733,9 +26544,9 @@ 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: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] @@ -26759,7 +26570,7 @@ 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." [] +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] 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 @@ -26827,7 +26638,7 @@ 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." [] +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] 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 @@ -26840,7 +26651,7 @@ 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." [] +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] 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 @@ -26931,6 +26742,63 @@ domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + +[Typedef] +id: RO:0017001 +name: device utilizes material +def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] +synonym: "utilizes" BROAD [] +property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string +property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string +property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string +holds_over_chain: RO:0002215 RO:0002233 +creation_date: 2021-11-08T12:00:00Z + +[Typedef] +id: RO:0019000 +name: regulates characteristic +def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +domain: BFO:0000015 ! process +range: PATO:0000001 ! quality +holds_over_chain: RO:0002211 RO:0019000 +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0019001 +name: positively regulates characteristic +def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: RO:0002213 RO:0019001 +is_a: RO:0019000 ! regulates characteristic + +[Typedef] +id: RO:0019002 +name: negatively regulates characteristic +def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: RO:0002212 RO:0019001 +holds_over_chain: RO:0002213 RO:0019002 +is_a: RO:0019000 ! regulates characteristic + [Typedef] id: has_part name: has part @@ -26945,7 +26813,7 @@ property_value: IAO:0000112 "my body has part my brain (continuant parthood, two 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:0000116 "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: IAO:0000116 "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: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "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:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 @@ -26967,7 +26835,7 @@ property_value: IAO:0000112 "my brain is part of my body (continuant parthood, t 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:0000116 "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: IAO:0000116 "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: IAO:0000116 "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000116 "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:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 diff --git a/chr-full.owl b/chr-full.owl index 1a0e513..36b1284 100644 --- a/chr-full.owl +++ b/chr-full.owl @@ -9,7 +9,6 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" @@ -21,11 +20,11 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + Automatic translation of UCSC chromosome bands to OWL classes Monochrom Ontology - 2022-02-02 + 2023-02-19 @@ -151,6 +150,12 @@ + + + + + + @@ -243,14 +248,6 @@ - - - - - - - - @@ -331,12 +328,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -363,6 +424,12 @@ + + + + + + @@ -393,6 +460,12 @@ + + + + + + @@ -485,15 +558,15 @@ - + - + - + - + @@ -538,7 +611,7 @@ 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -579,7 +652,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An this year has part this day (occurrent parthood) 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -641,43 +714,38 @@ 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 + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of - + - - site of - [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 - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + has characteristic @@ -721,6 +789,124 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + @@ -910,6 +1096,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -1056,9 +1243,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - 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. - 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 + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1081,7 +1266,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1105,7 +1290,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -1151,7 +1336,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall has function in capable of part of - + @@ -1309,6 +1494,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -1324,14 +1510,49 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm - 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 + + causally upstream of, negative effect + + + + + + + + + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + Chris Mungall + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + @@ -1380,6 +1601,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -1387,7 +1609,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. is catalyzing 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 @@ -1597,18 +1818,75 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. 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. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The 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. @@ -1621,6 +1899,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -1630,8 +1914,7 @@ 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 + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -1645,8 +1928,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - 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. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -1660,7 +1942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -1759,42 +2041,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - 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. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - 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 - - - - @@ -1809,8 +2055,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different in pairwise interaction with interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 @@ -1826,7 +2072,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 + http://purl.obolibrary.org/obo/MI_0915 @@ -1920,32 +2166,6 @@ 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 - - - - @@ -1974,7 +2194,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + 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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -1983,6 +2203,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + Chris Mungall + depends on + + + + + @@ -2018,7 +2248,7 @@ For example, A and B may be gene products and binding of B by A positively regul Chris Mungall interaction relation helper property - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -2064,7 +2294,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -2172,7 +2402,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -2189,7 +2419,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -2329,6 +2559,102 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + A diagnostic testing device utilizes a specimen. + X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. + https://orcid.org/0000-0001-9625-1899 + https://orcid.org/0000-0003-2620-0345 + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08T12:00:00Z + utilizes + device utilizes material + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity + + + + disposition - + - - - - anatomical entity + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity - + - - - - connected anatomical structure + + + + + + + + + quality - + - - - + + + + + + + + + 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 + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + function + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + - material anatomical entity + anatomical entity @@ -25085,576 +25468,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - 1 - chromosome 1 (Danio rerio) - - - 58871917 - 0 - danRer10 - - - - - - - - - - - - - - - - 10 - chromosome 10 (Danio rerio) - - - 45574255 - 0 - danRer10 - - - - - - - - - - - - - - - - 11 - chromosome 11 (Danio rerio) - - - 45107271 - 0 - danRer10 - - - - - - - - - - - - - - - - 12 - chromosome 12 (Danio rerio) - - - 49229541 - 0 - danRer10 - - - - - - - - - - - - - - - - 13 - chromosome 13 (Danio rerio) - - - 51780250 - 0 - danRer10 - - - - - - - - - - - - - - - - 14 - chromosome 14 (Danio rerio) - - - 51944548 - 0 - danRer10 - - - - - - - - - - - - - - - - 15 - chromosome 15 (Danio rerio) - - - 47771147 - 0 - danRer10 - - - - - - - - - - - - - - - - 16 - chromosome 16 (Danio rerio) - - - 55381981 - 0 - danRer10 - - - - - - - - - - - - - - - - 17 - chromosome 17 (Danio rerio) - - - 53345113 - 0 - danRer10 - - - - - - - - - - - - - - - - 18 - chromosome 18 (Danio rerio) - - - 51008593 - 0 - danRer10 - - - - - - - - - - - - - - - - 19 - chromosome 19 (Danio rerio) - - - 48790377 - 0 - danRer10 - - - - - - - - - - - - - - - - 2 - chromosome 2 (Danio rerio) - - - 59543403 - 0 - danRer10 - - - - - - - - - - - - - - - - 20 - chromosome 20 (Danio rerio) - - - 55370968 - 0 - danRer10 - - - - - - - - - - - - - - - - 21 - chromosome 21 (Danio rerio) - - - 45895719 - 0 - danRer10 - - - - - - - - - - - - - - - - 22 - chromosome 22 (Danio rerio) - - - 39226288 - 0 - danRer10 - - - - - - - - - - - - - - - - 23 - chromosome 23 (Danio rerio) - - - 46272358 - 0 - danRer10 - - - - - - - - - - - - - - - - 24 - chromosome 24 (Danio rerio) - - - 42251103 - 0 - danRer10 - - - - - - - - - - - - - - - - 25 - chromosome 25 (Danio rerio) - - - 36898761 - 0 - danRer10 - - - - - - - - - - - - - - - - 3 - chromosome 3 (Danio rerio) - - - 62385949 - 0 - danRer10 - - - - - - - - - - - - - - - - 4 - chromosome 4 (Danio rerio) - - - 76625712 - 0 - danRer10 - - - - - - - - - - - - - - - - 5 - chromosome 5 (Danio rerio) - - - 71715914 - 0 - danRer10 - - - - - - - - - - - - - - - - 6 - chromosome 6 (Danio rerio) - - - 60272633 - 0 - danRer10 - - - - - - - - - - - - - - - - 7 - chromosome 7 (Danio rerio) - - - 74082188 - 0 - danRer10 - - - - - - - - - - - - - - - - 8 - chromosome 8 (Danio rerio) - - - 54191831 - 0 - danRer10 - - - - - - - - - - - - - - - - 9 - chromosome 9 (Danio rerio) - - - 56892771 - 0 - danRer10 - - - - - - - - - - - - - - - MT - chromosome M (Danio rerio) - - 16596 - 0 - danRer10 - - - - @@ -27512,7 +27325,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -27535,7 +27347,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -59706,44 +59517,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - A chromosome found in the cytoplasm. - cytoplasmic interphase chromosome - cellular_component - GO:0000229 - - - cytoplasmic chromosome - - - - - A chromosome found in the cytoplasm. - GOC:mah - - - - @@ -59758,7 +59531,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -59803,7 +59576,24 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females. + + Wikipedia:ZW_sex-determination_system + cellular_component + GO:0000804 + W chromosome + + + + + The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females. + GOC:mah + GOC:mr + ISBN:0321000382 + PMID:20622855 + @@ -59857,7 +59647,24 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females. + + Wikipedia:ZW_sex-determination_system + cellular_component + GO:0000807 + Z chromosome + + + + + The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females. + GOC:mah + GOC:mr + ISBN:0321000382 + PMID:20622855 + @@ -59891,10 +59698,8 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component subcellular entity GO:0005575 - - @@ -59906,7 +59711,7 @@ For example, A and B may be gene products and binding of B by A positively regul A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - GOC:pdt + GOC:pdt NIF_Subcellular:sao1337158144 @@ -59934,7 +59739,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0005622 - intracellular anatomical structure @@ -59964,7 +59768,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 @@ -59974,7 +59777,6 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component GO:0005634 - @@ -60053,7 +59855,6 @@ For example, A and B may be gene products and binding of B by A positively regul chromatid GO:0005694 - @@ -60062,7 +59863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. + + Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome @@ -60084,23 +59886,24 @@ For example, A and B may be gene products and binding of B by A positively regul - All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + https://github.com/geneontology/go-ontology/issues/23023 Wikipedia:Cytoplasm cellular_component GO:0005737 - + cytoplasm - All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 @@ -60123,7 +59926,6 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component GO:0005739 - @@ -60219,7 +60021,6 @@ For example, A and B may be gene products and binding of B by A positively regul vacuolar carboxypeptidase Y GO:0005773 - @@ -60292,7 +60093,6 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component GO:0005829 - @@ -60322,6 +60122,7 @@ For example, A and B may be gene products and binding of B by A positively regul The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. + GO:0005887 GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 @@ -60332,11 +60133,12 @@ For example, A and B may be gene products and binding of B by A positively regul plasmalemma bacterial inner membrane inner endospore membrane + integral component of plasma membrane + integral to plasma membrane plasma membrane lipid bilayer cellular_component GO:0005886 - @@ -60345,6 +60147,7 @@ For example, A and B may be gene products and binding of B by A positively regul + plasma membrane @@ -60395,7 +60198,6 @@ For example, A and B may be gene products and binding of B by A positively regul cell periphery peripheral cytoplasm GO:0005938 - cell cortex @@ -60459,7 +60261,7 @@ For example, A and B may be gene products and binding of B by A positively regul A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma. - ISBN:0471245208 + ISBN:0471245208 @@ -60478,7 +60280,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -60627,7 +60429,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Endomembrane_system cellular_component GO:0012505 - @@ -60646,17 +60447,21 @@ For example, A and B may be gene products and binding of B by A positively regul - A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z + GO:0016021 GO:0098589 GO:0098805 Wikipedia:Biological_membrane + Wikipedia:Transmembrane_protein + integral component of membrane + integral to membrane membrane region region of membrane whole membrane cellular_component + transmembrane GO:0016020 - @@ -60669,11 +60474,17 @@ For example, A and B may be gene products and binding of B by A positively regul - A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GOC:dos GOC:mah ISBN:0815316194 + + + + transmembrane + GOC:mah + @@ -61132,6 +60943,7 @@ For example, A and B may be gene products and binding of B by A positively regul + organelle @@ -61185,10 +60997,13 @@ For example, A and B may be gene products and binding of B by A positively regul Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/21881 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle + biological condensate cellular_component GO:0043228 + non-membrane-bounded organelle @@ -61288,7 +61103,6 @@ For example, A and B may be gene products and binding of B by A positively regul intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle @@ -61325,6 +61139,7 @@ For example, A and B may be gene products and binding of B by A positively regul The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. cellular_component GO:0043233 + organelle lumen @@ -61337,16 +61152,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - cell part - - - - @@ -61371,7 +61176,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organelle lumen that is part of an intracellular organelle. cellular_component GO:0070013 - intracellular organelle lumen @@ -61458,7 +61262,7 @@ For example, A and B may be gene products and binding of B by A positively regul chromosome region cellular_component GO:0098687 - Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. + Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. chromosomal region @@ -61492,9 +61296,11 @@ For example, A and B may be gene products and binding of B by A positively regul Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol. + region of cytosol cellular_component GO:0099522 - region of cytosol + + cytosolic region @@ -61529,6 +61335,7 @@ For example, A and B may be gene products and binding of B by A positively regul Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. cellular_component GO:0099568 + cytoplasmic region @@ -61566,6 +61373,7 @@ For example, A and B may be gene products and binding of B by A positively regul perimembrane region cellular_component GO:0099738 + cell cortex region @@ -61847,6 +61655,35 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + PMID:22839753 + PMID:25450099 + ncbi_taxonomy + Archosauria-Testudines + Testudines + Archosauria group + NCBITaxon:1329799 + Archelosauria + + + + + Archosauria-Testudines + + + + + + Testudines + Archosauria group + + + + + @@ -61882,106 +61719,28 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1489341 - Osteoglossocephalai - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:186623 - Actinopteri - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:186625 - Clupeocephala - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Otophysa - NCBITaxon:186626 - Otophysi - - - - - Otophysa - - - - - - - - - + + GC_ID:1 ncbi_taxonomy - Cypriniphysi - NCBITaxon:186627 - Cypriniphysae - - - - - Cypriniphysi - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ostarioclupeomorpha - Otocephala - NCBITaxon:186634 - Otomorpha + Galloanseri + ducks, geese, chickens, fowl, quail, currasows and allies + NCBITaxon:1549675 + Galloanserae - + - Ostarioclupeomorpha + Galloanseri - + - Otocephala + ducks, geese, chickens, fowl, quail, currasows and allies @@ -62060,32 +61819,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2743709 - Danionidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2743711 - Danioninae - - - - @@ -62150,26 +61883,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - GC_ID:1 - ncbi_taxonomy - Cyprinoidea - NCBITaxon:30727 - Cyprinoidei - - - - - Cyprinoidea - - - - - @@ -62257,39 +61970,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - GC_ID:1 - teleost fishes - ncbi_taxonomy - NCBITaxon:32443 - Teleostei - - - - - teleost fishes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32519 - Ostariophysi - - - - @@ -62350,6 +62030,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + diapsids + ncbi_taxonomy + Diapsida + NCBITaxon:32561 + Sauria + + + + + diapsids + + + + + + Diapsida + + + + + @@ -62533,23 +62240,69 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - + + + GC_ID:1 + dinosaur + dinosaurs ncbi_taxonomy - Neopterygi - NCBITaxon:41665 - Neopterygii + NCBITaxon:436486 + Dinosauria - - - Neopterygi - + + + dinosaur + + + + + dinosaurs + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436489 + Saurischia + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436491 + Theropoda + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436492 + Coelurosauria + @@ -62680,18 +62433,11 @@ For example, A and B may be gene products and binding of B by A positively regul GC_ID:1 - roundworm ncbi_taxonomy Rhabditis elegans NCBITaxon:6239 Caenorhabditis elegans - - - - roundworm - - @@ -62803,244 +62549,258 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + GC_ID:1 - fish - fishes - ray-finned fishes ncbi_taxonomy - Actinopterygi - Osteichthyes - bony fishes - NCBITaxon:7898 - Actinopterygii + NCBITaxon:8287 + Sarcopterygii + + + + + + + + + + GC_ID:1 + sauropsids + ncbi_taxonomy + NCBITaxon:8457 + Sauropsida - + - fish - + sauropsids + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:8492 + Archosauria + + + + + + + + + + GC_ID:1 + Mus + ncbi_taxonomy + NCBITaxon:862507 + Mus <subgenus> + - + - fishes - + Mus + + + + + + + + + + GC_ID:1 + birds + ncbi_taxonomy + avian + birds + NCBITaxon:8782 + Aves + - + - ray-finned fishes + birds - + - Actinopterygi + avian - + - Osteichthyes - + birds + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:8825 + Neognathae + + + + + + + + + + GC_ID:1 + Craniata + ncbi_taxonomy + NCBITaxon:89593 + Craniata <chordates> + - - - bony fishes - + + + Craniata + - + - - + + GC_ID:1 - carps and others + landfowls ncbi_taxonomy - NCBITaxon:7952 - Cypriniformes + NCBITaxon:8976 + Galliformes - + - carps and others + landfowls - + - - - - NCBITaxon:46777 - NCBITaxon:487617 + + + + NCBITaxon:9099 GC_ID:1 + turkeys ncbi_taxonomy - Brachydanio - Celestichthys - NCBITaxon:7954 - Danio + NCBITaxon:9005 + Phasianidae - - - Brachydanio - - - - - - Celestichthys - + + + turkeys + - + - - + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:9030 + Gallus + + + + + + + + - NCBITaxon:27702 - NCBITaxon:37966 GC_ID:1 - leopard danio - zebra danio - zebra fish - zebrafish + Gallus domesticus + bantam + chicken + chickens ncbi_taxonomy - Brachydanio rerio - Brachydanio rerio frankei - Cyprinus rerio - Danio frankei - Danio rerio frankei - NCBITaxon:7955 - Danio rerio + Gallus gallus domesticus + Phasianus gallus + NCBITaxon:9031 + Gallus gallus - + - leopard danio - - - - - - zebra danio - + Gallus domesticus + - + - zebra fish + bantam - + - zebrafish + chicken - - - Brachydanio rerio - - - - - - Brachydanio rerio frankei - - - - - - Cyprinus rerio - + + + chickens + - + - Danio frankei + Gallus gallus domesticus - + - Danio rerio frankei + Phasianus gallus - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:8287 - Sarcopterygii - - - - - - - - - - GC_ID:1 - Mus - ncbi_taxonomy - NCBITaxon:862507 - Mus <subgenus> - - - - - Mus - - - - - - + - - - + + + GC_ID:1 - Craniata ncbi_taxonomy - NCBITaxon:89593 - Craniata <chordates> + NCBITaxon:9072 + Phasianinae - - - - Craniata - - - - - - - - @@ -63193,7 +62953,6 @@ For example, A and B may be gene products and binding of B by A positively regul GC_ID:1 human - man ncbi_taxonomy NCBITaxon:9606 Homo sapiens @@ -63204,12 +62963,6 @@ For example, A and B may be gene products and binding of B by A positively regul human - - - - man - - @@ -63240,6 +62993,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + quality (PATO) + quality + + + + + + + + + @@ -243,14 +248,6 @@ - - - - - - - - @@ -331,12 +328,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -363,6 +424,12 @@ + + + + + + @@ -393,6 +460,12 @@ + + + + + + @@ -485,15 +558,15 @@ - + - + - + - + @@ -538,7 +611,7 @@ 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -579,7 +652,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An this year has part this day (occurrent parthood) 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 + 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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'. @@ -641,43 +714,38 @@ 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 + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of - + - - site of - [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 - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + has characteristic @@ -721,6 +789,124 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + @@ -910,6 +1096,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + @@ -1056,9 +1243,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - 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. - 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 + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. Chris Mungall David Hill Tanya Berardini @@ -1081,7 +1266,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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. + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. Chris Mungall negatively regulates (process to process) @@ -1105,7 +1290,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - 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. + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. Chris Mungall positively regulates (process to process) @@ -1151,7 +1336,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Chris Mungall has function in capable of part of - + @@ -1309,6 +1494,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. cjm @@ -1324,14 +1510,49 @@ A continuant cannot have an occurrent as part: use 'participates in'. + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. cjm - 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 + + causally upstream of, negative effect + + + + + + + + + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + Chris Mungall + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + @@ -1380,6 +1601,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. Chris Mungall catalyzes executes @@ -1387,7 +1609,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. is catalyzing 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 @@ -1597,18 +1818,75 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + Chris Mungall + indirectly activates + + indirectly positively regulates + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + Chris Mungall + indirectly inhibits + + indirectly negatively regulates + + + + - - This relation groups causal relations between material entities and causal relations between processes + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. 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. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? - * Is the influence positive or negative + * Is the influence positive or negative? The 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. @@ -1621,6 +1899,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + @@ -1630,8 +1914,7 @@ 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 + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. Chris Mungall @@ -1645,8 +1928,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - 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. + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. Chris Mungall immediately causally upstream of @@ -1660,7 +1942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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. + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) @@ -1759,42 +2041,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - A protein that enables activity in a cytosol. - 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. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - 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 - - - - @@ -1809,8 +2055,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different in pairwise interaction with interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 @@ -1826,7 +2072,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 + http://purl.obolibrary.org/obo/MI_0915 @@ -1920,32 +2166,6 @@ 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 - - - - @@ -1974,7 +2194,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + 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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. @@ -1983,6 +2203,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + Chris Mungall + depends on + + + + + @@ -2018,7 +2248,7 @@ For example, A and B may be gene products and binding of B by A positively regul Chris Mungall interaction relation helper property - https://github.com/oborel/obo-relations/wiki/InteractionRelations + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -2064,7 +2294,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + p directly regulates q iff p is immediately causally upstream of q and p regulates q. Chris Mungall directly regulates (processual) @@ -2172,7 +2402,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) @@ -2189,7 +2419,7 @@ For example, A and B may be gene products and binding of B by A positively regul - 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. + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) @@ -2329,6 +2559,102 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + A diagnostic testing device utilizes a specimen. + X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. + https://orcid.org/0000-0001-9625-1899 + https://orcid.org/0000-0003-2620-0345 + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08T12:00:00Z + utilizes + device utilizes material + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity + + + + disposition - + - - - - anatomical entity + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity - + - - - - connected anatomical structure + + + + + + + + + quality - + - - - + + + + + + + + + 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 + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + function + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + - material anatomical entity + anatomical entity @@ -25085,576 +25468,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - 1 - chromosome 1 (Danio rerio) - - - 58871917 - 0 - danRer10 - - - - - - - - - - - - - - - - 10 - chromosome 10 (Danio rerio) - - - 45574255 - 0 - danRer10 - - - - - - - - - - - - - - - - 11 - chromosome 11 (Danio rerio) - - - 45107271 - 0 - danRer10 - - - - - - - - - - - - - - - - 12 - chromosome 12 (Danio rerio) - - - 49229541 - 0 - danRer10 - - - - - - - - - - - - - - - - 13 - chromosome 13 (Danio rerio) - - - 51780250 - 0 - danRer10 - - - - - - - - - - - - - - - - 14 - chromosome 14 (Danio rerio) - - - 51944548 - 0 - danRer10 - - - - - - - - - - - - - - - - 15 - chromosome 15 (Danio rerio) - - - 47771147 - 0 - danRer10 - - - - - - - - - - - - - - - - 16 - chromosome 16 (Danio rerio) - - - 55381981 - 0 - danRer10 - - - - - - - - - - - - - - - - 17 - chromosome 17 (Danio rerio) - - - 53345113 - 0 - danRer10 - - - - - - - - - - - - - - - - 18 - chromosome 18 (Danio rerio) - - - 51008593 - 0 - danRer10 - - - - - - - - - - - - - - - - 19 - chromosome 19 (Danio rerio) - - - 48790377 - 0 - danRer10 - - - - - - - - - - - - - - - - 2 - chromosome 2 (Danio rerio) - - - 59543403 - 0 - danRer10 - - - - - - - - - - - - - - - - 20 - chromosome 20 (Danio rerio) - - - 55370968 - 0 - danRer10 - - - - - - - - - - - - - - - - 21 - chromosome 21 (Danio rerio) - - - 45895719 - 0 - danRer10 - - - - - - - - - - - - - - - - 22 - chromosome 22 (Danio rerio) - - - 39226288 - 0 - danRer10 - - - - - - - - - - - - - - - - 23 - chromosome 23 (Danio rerio) - - - 46272358 - 0 - danRer10 - - - - - - - - - - - - - - - - 24 - chromosome 24 (Danio rerio) - - - 42251103 - 0 - danRer10 - - - - - - - - - - - - - - - - 25 - chromosome 25 (Danio rerio) - - - 36898761 - 0 - danRer10 - - - - - - - - - - - - - - - - 3 - chromosome 3 (Danio rerio) - - - 62385949 - 0 - danRer10 - - - - - - - - - - - - - - - - 4 - chromosome 4 (Danio rerio) - - - 76625712 - 0 - danRer10 - - - - - - - - - - - - - - - - 5 - chromosome 5 (Danio rerio) - - - 71715914 - 0 - danRer10 - - - - - - - - - - - - - - - - 6 - chromosome 6 (Danio rerio) - - - 60272633 - 0 - danRer10 - - - - - - - - - - - - - - - - 7 - chromosome 7 (Danio rerio) - - - 74082188 - 0 - danRer10 - - - - - - - - - - - - - - - - 8 - chromosome 8 (Danio rerio) - - - 54191831 - 0 - danRer10 - - - - - - - - - - - - - - - - 9 - chromosome 9 (Danio rerio) - - - 56892771 - 0 - danRer10 - - - - - - - - - - - - - - - MT - chromosome M (Danio rerio) - - 16596 - 0 - danRer10 - - - - @@ -27512,7 +27325,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -27535,7 +27347,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -59706,44 +59517,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - - - - - A chromosome found in the cytoplasm. - cytoplasmic interphase chromosome - cellular_component - GO:0000229 - - - cytoplasmic chromosome - - - - - A chromosome found in the cytoplasm. - GOC:mah - - - - @@ -59758,7 +59531,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -59803,7 +59576,24 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females. + + Wikipedia:ZW_sex-determination_system + cellular_component + GO:0000804 + W chromosome + + + + + The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females. + GOC:mah + GOC:mr + ISBN:0321000382 + PMID:20622855 + @@ -59857,7 +59647,24 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females. + + Wikipedia:ZW_sex-determination_system + cellular_component + GO:0000807 + Z chromosome + + + + + The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females. + GOC:mah + GOC:mr + ISBN:0321000382 + PMID:20622855 + @@ -59891,10 +59698,8 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component subcellular entity GO:0005575 - - @@ -59906,7 +59711,7 @@ For example, A and B may be gene products and binding of B by A positively regul A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - GOC:pdt + GOC:pdt NIF_Subcellular:sao1337158144 @@ -59934,7 +59739,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0005622 - intracellular anatomical structure @@ -59964,7 +59768,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 @@ -59974,7 +59777,6 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component GO:0005634 - @@ -60053,7 +59855,6 @@ For example, A and B may be gene products and binding of B by A positively regul chromatid GO:0005694 - @@ -60062,7 +59863,8 @@ For example, A and B may be gene products and binding of B by A positively regul - Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. + + Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. chromosome @@ -60084,23 +59886,24 @@ For example, A and B may be gene products and binding of B by A positively regul - All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + https://github.com/geneontology/go-ontology/issues/23023 Wikipedia:Cytoplasm cellular_component GO:0005737 - + cytoplasm - All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. + The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 @@ -60123,7 +59926,6 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component GO:0005739 - @@ -60219,7 +60021,6 @@ For example, A and B may be gene products and binding of B by A positively regul vacuolar carboxypeptidase Y GO:0005773 - @@ -60292,7 +60093,6 @@ For example, A and B may be gene products and binding of B by A positively regul cellular_component GO:0005829 - @@ -60322,6 +60122,7 @@ For example, A and B may be gene products and binding of B by A positively regul The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. + GO:0005887 GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 @@ -60332,11 +60133,12 @@ For example, A and B may be gene products and binding of B by A positively regul plasmalemma bacterial inner membrane inner endospore membrane + integral component of plasma membrane + integral to plasma membrane plasma membrane lipid bilayer cellular_component GO:0005886 - @@ -60345,6 +60147,7 @@ For example, A and B may be gene products and binding of B by A positively regul + plasma membrane @@ -60395,7 +60198,6 @@ For example, A and B may be gene products and binding of B by A positively regul cell periphery peripheral cytoplasm GO:0005938 - cell cortex @@ -60459,7 +60261,7 @@ For example, A and B may be gene products and binding of B by A positively regul A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma. - ISBN:0471245208 + ISBN:0471245208 @@ -60478,7 +60280,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -60627,7 +60429,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Endomembrane_system cellular_component GO:0012505 - @@ -60646,17 +60447,21 @@ For example, A and B may be gene products and binding of B by A positively regul - A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 2014-03-06T11:37:54Z + GO:0016021 GO:0098589 GO:0098805 Wikipedia:Biological_membrane + Wikipedia:Transmembrane_protein + integral component of membrane + integral to membrane membrane region region of membrane whole membrane cellular_component + transmembrane GO:0016020 - @@ -60669,11 +60474,17 @@ For example, A and B may be gene products and binding of B by A positively regul - A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. + A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GOC:dos GOC:mah ISBN:0815316194 + + + + transmembrane + GOC:mah + @@ -61132,6 +60943,7 @@ For example, A and B may be gene products and binding of B by A positively regul + organelle @@ -61185,10 +60997,13 @@ For example, A and B may be gene products and binding of B by A positively regul Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. + https://github.com/geneontology/go-ontology/issues/21881 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle + biological condensate cellular_component GO:0043228 + non-membrane-bounded organelle @@ -61288,7 +61103,6 @@ For example, A and B may be gene products and binding of B by A positively regul intracellular non-membrane-enclosed organelle cellular_component GO:0043232 - intracellular non-membrane-bounded organelle @@ -61325,6 +61139,7 @@ For example, A and B may be gene products and binding of B by A positively regul The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. cellular_component GO:0043233 + organelle lumen @@ -61337,16 +61152,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - cell part - - - - @@ -61371,7 +61176,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organelle lumen that is part of an intracellular organelle. cellular_component GO:0070013 - intracellular organelle lumen @@ -61458,7 +61262,7 @@ For example, A and B may be gene products and binding of B by A positively regul chromosome region cellular_component GO:0098687 - Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. + Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. chromosomal region @@ -61492,9 +61296,11 @@ For example, A and B may be gene products and binding of B by A positively regul Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol. + region of cytosol cellular_component GO:0099522 - region of cytosol + + cytosolic region @@ -61529,6 +61335,7 @@ For example, A and B may be gene products and binding of B by A positively regul Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. cellular_component GO:0099568 + cytoplasmic region @@ -61566,6 +61373,7 @@ For example, A and B may be gene products and binding of B by A positively regul perimembrane region cellular_component GO:0099738 + cell cortex region @@ -61847,6 +61655,35 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + PMID:22839753 + PMID:25450099 + ncbi_taxonomy + Archosauria-Testudines + Testudines + Archosauria group + NCBITaxon:1329799 + Archelosauria + + + + + Archosauria-Testudines + + + + + + Testudines + Archosauria group + + + + + @@ -61882,106 +61719,28 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1489341 - Osteoglossocephalai - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:186623 - Actinopteri - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:186625 - Clupeocephala - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Otophysa - NCBITaxon:186626 - Otophysi - - - - - Otophysa - - - - - - - - - + + GC_ID:1 ncbi_taxonomy - Cypriniphysi - NCBITaxon:186627 - Cypriniphysae - - - - - Cypriniphysi - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ostarioclupeomorpha - Otocephala - NCBITaxon:186634 - Otomorpha + Galloanseri + ducks, geese, chickens, fowl, quail, currasows and allies + NCBITaxon:1549675 + Galloanserae - + - Ostarioclupeomorpha + Galloanseri - + - Otocephala + ducks, geese, chickens, fowl, quail, currasows and allies @@ -62060,32 +61819,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2743709 - Danionidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2743711 - Danioninae - - - - @@ -62150,26 +61883,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - GC_ID:1 - ncbi_taxonomy - Cyprinoidea - NCBITaxon:30727 - Cyprinoidei - - - - - Cyprinoidea - - - - - @@ -62257,39 +61970,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - GC_ID:1 - teleost fishes - ncbi_taxonomy - NCBITaxon:32443 - Teleostei - - - - - teleost fishes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32519 - Ostariophysi - - - - @@ -62350,6 +62030,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + GC_ID:1 + diapsids + ncbi_taxonomy + Diapsida + NCBITaxon:32561 + Sauria + + + + + diapsids + + + + + + Diapsida + + + + + @@ -62533,23 +62240,69 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - + + + GC_ID:1 + dinosaur + dinosaurs ncbi_taxonomy - Neopterygi - NCBITaxon:41665 - Neopterygii + NCBITaxon:436486 + Dinosauria - - - Neopterygi - + + + dinosaur + + + + + dinosaurs + + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436489 + Saurischia + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436491 + Theropoda + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436492 + Coelurosauria + @@ -62680,18 +62433,11 @@ For example, A and B may be gene products and binding of B by A positively regul GC_ID:1 - roundworm ncbi_taxonomy Rhabditis elegans NCBITaxon:6239 Caenorhabditis elegans - - - - roundworm - - @@ -62803,244 +62549,258 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + GC_ID:1 - fish - fishes - ray-finned fishes ncbi_taxonomy - Actinopterygi - Osteichthyes - bony fishes - NCBITaxon:7898 - Actinopterygii + NCBITaxon:8287 + Sarcopterygii + + + + + + + + + + GC_ID:1 + sauropsids + ncbi_taxonomy + NCBITaxon:8457 + Sauropsida - + - fish - + sauropsids + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:8492 + Archosauria + + + + + + + + + + GC_ID:1 + Mus + ncbi_taxonomy + NCBITaxon:862507 + Mus <subgenus> + - + - fishes - + Mus + + + + + + + + + + GC_ID:1 + birds + ncbi_taxonomy + avian + birds + NCBITaxon:8782 + Aves + - + - ray-finned fishes + birds - + - Actinopterygi + avian - + - Osteichthyes - + birds + + + + + + + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:8825 + Neognathae + + + + + + + + + + GC_ID:1 + Craniata + ncbi_taxonomy + NCBITaxon:89593 + Craniata <chordates> + - - - bony fishes - + + + Craniata + - + - - + + GC_ID:1 - carps and others + landfowls ncbi_taxonomy - NCBITaxon:7952 - Cypriniformes + NCBITaxon:8976 + Galliformes - + - carps and others + landfowls - + - - - - NCBITaxon:46777 - NCBITaxon:487617 + + + + NCBITaxon:9099 GC_ID:1 + turkeys ncbi_taxonomy - Brachydanio - Celestichthys - NCBITaxon:7954 - Danio + NCBITaxon:9005 + Phasianidae - - - Brachydanio - - - - - - Celestichthys - + + + turkeys + - + - - + + + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:9030 + Gallus + + + + + + + + - NCBITaxon:27702 - NCBITaxon:37966 GC_ID:1 - leopard danio - zebra danio - zebra fish - zebrafish + Gallus domesticus + bantam + chicken + chickens ncbi_taxonomy - Brachydanio rerio - Brachydanio rerio frankei - Cyprinus rerio - Danio frankei - Danio rerio frankei - NCBITaxon:7955 - Danio rerio + Gallus gallus domesticus + Phasianus gallus + NCBITaxon:9031 + Gallus gallus - + - leopard danio - - - - - - zebra danio - + Gallus domesticus + - + - zebra fish + bantam - + - zebrafish + chicken - - - Brachydanio rerio - - - - - - Brachydanio rerio frankei - - - - - - Cyprinus rerio - + + + chickens + - + - Danio frankei + Gallus gallus domesticus - + - Danio rerio frankei + Phasianus gallus - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:8287 - Sarcopterygii - - - - - - - - - - GC_ID:1 - Mus - ncbi_taxonomy - NCBITaxon:862507 - Mus <subgenus> - - - - - Mus - - - - - - + - - - + + + GC_ID:1 - Craniata ncbi_taxonomy - NCBITaxon:89593 - Craniata <chordates> + NCBITaxon:9072 + Phasianinae - - - - Craniata - - - - - - - - @@ -63193,7 +62953,6 @@ For example, A and B may be gene products and binding of B by A positively regul GC_ID:1 human - man ncbi_taxonomy NCBITaxon:9606 Homo sapiens @@ -63204,12 +62963,6 @@ For example, A and B may be gene products and binding of B by A positively regul human - - - - man - - @@ -63240,6 +62993,16 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + quality (PATO) + quality + + + + - - - - - - - - - - - - - - - - - 1 - chromosome 1 (Danio rerio) - - - 58871917 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 10 - chromosome 10 (Danio rerio) - - - 45574255 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 11 - chromosome 11 (Danio rerio) - - - 45107271 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 12 - chromosome 12 (Danio rerio) - - - 49229541 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 13 - chromosome 13 (Danio rerio) - - - 51780250 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 14 - chromosome 14 (Danio rerio) - - - 51944548 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 15 - chromosome 15 (Danio rerio) - - - 47771147 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 16 - chromosome 16 (Danio rerio) - - - 55381981 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 17 - chromosome 17 (Danio rerio) - - - 53345113 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 18 - chromosome 18 (Danio rerio) - - - 51008593 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 19 - chromosome 19 (Danio rerio) - - - 48790377 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 2 - chromosome 2 (Danio rerio) - - - 59543403 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 20 - chromosome 20 (Danio rerio) - - - 55370968 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 21 - chromosome 21 (Danio rerio) - - - 45895719 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 22 - chromosome 22 (Danio rerio) - - - 39226288 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 23 - chromosome 23 (Danio rerio) - - - 46272358 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 24 - chromosome 24 (Danio rerio) - - - 42251103 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 25 - chromosome 25 (Danio rerio) - - - 36898761 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 3 - chromosome 3 (Danio rerio) - - - 62385949 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 4 - chromosome 4 (Danio rerio) - - - 76625712 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 5 - chromosome 5 (Danio rerio) - - - 71715914 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 6 - chromosome 6 (Danio rerio) - - - 60272633 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 7 - chromosome 7 (Danio rerio) - - - 74082188 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 8 - chromosome 8 (Danio rerio) - - - 54191831 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - - 9 - chromosome 9 (Danio rerio) - - - 56892771 - 0 - danRer10 - - - - - - - - - - - - - - - - - - - - - MT - chromosome M (Danio rerio) - - 16596 - 0 - danRer10 - - - - @@ -57451,12 +56725,6 @@ - - - - - - diff --git a/src/ontology/imports/geno_import.owl b/src/ontology/imports/geno_import.owl index 242df37..b51065c 100644 --- a/src/ontology/imports/geno_import.owl +++ b/src/ontology/imports/geno_import.owl @@ -1,14 +1,462 @@ - - - - - - +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2023-02-19") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (has broad synonym) + +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") + + +############################ +# Object Properties +############################ + +# Object Property: (is part of) + +AnnotationAssertion(rdfs:label "is part of") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion(rdfs:label "has part") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (derives from) + +AnnotationAssertion(rdfs:label "derives from") + +# Object Property: (overlaps) + +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion(rdfs:label "overlaps"@en) +SymmetricObjectProperty() + +# Object Property: (in taxon) + +AnnotationAssertion( "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.") +AnnotationAssertion(rdfs:label "in taxon"@en) + +# Object Property: (is member of) + +AnnotationAssertion(rdfs:label "is member of") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has member) + +AnnotationAssertion( "Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes + +Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component") +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion(rdfs:label "has member") +SubObjectPropertyOf( ) + + + +############################ +# Classes +############################ + +# Class: (entity) + +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "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"@en) +AnnotationAssertion( "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"@en) +AnnotationAssertion( "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "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"@en) +AnnotationAssertion( "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion( "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "continuant") +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) + +# Class: (independent continuant) + +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "independent continuant") +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion( "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "generically dependent continuant") +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion( "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "material entity") +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) + +# Class: (organismal entity) + +AnnotationAssertion( "true"^^xsd:boolean) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is an organism, derived from an organism, or composed of organisms (e.g. a cell line, biosample, tissue culture, population, etc).") +AnnotationAssertion( "useful organizational term to collect entities that have genomes/genotypes.") +AnnotationAssertion(rdfs:label "organismal entity"@en) +EquivalentClasses( ObjectUnionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion( ) +AnnotationAssertion( "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity"@en) +AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000142"@en) +AnnotationAssertion(rdfs:label "information content entity") +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "ontology metadata") +AnnotationAssertion(rdfs:label "data about an ontology part") +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (Mus musculus) + +AnnotationAssertion(rdfs:label "Mus musculus") +SubClassOf( ) + +# Class: (Homo sapiens) + +AnnotationAssertion(rdfs:label "Homo sapiens") +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.") +AnnotationAssertion(rdfs:label "organism") +SubClassOf( ) + + +############################ +# Named Individuals +############################ + +# Individual: (exploratory term) + +AnnotationAssertion(rdfs:label "exploratory term"@en) +ClassAssertion( ) + +# Individual: (exemplar term) + +AnnotationAssertion(rdfs:label "exemplar term"@en) +ClassAssertion( ) + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) +ClassAssertion( ) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) +ClassAssertion( ) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) +ClassAssertion( ) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) +ClassAssertion( ) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) +ClassAssertion( ) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) +ClassAssertion( ) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) +ClassAssertion( ) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) +ClassAssertion( ) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) +ClassAssertion( ) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) +ClassAssertion( ) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) +ClassAssertion( ) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) +ClassAssertion( ) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) +ClassAssertion( ) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +ClassAssertion( ) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + +# Individual: (out of scope) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") +AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(rdfs:label "out of scope") +ClassAssertion( ) + + +DifferentIndividuals( ) +DifferentIndividuals( ) +) \ No newline at end of file diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index 1868ab9..56b2d92 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -1,2137 +1,968 @@ - - - - - - 2021-06-16 - - +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2023-02-19"^^xsd:string) + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () +SubAnnotationPropertyOf( ) - +# Annotation Property: () - +SubAnnotationPropertyOf( ) +# Annotation Property: () - +SubAnnotationPropertyOf( ) - - +# Annotation Property: (has_broad_synonym) +AnnotationAssertion(rdfs:label "has_broad_synonym") - - - +############################ +# Object Properties +############################ +# Object Property: (part of) - +AnnotationAssertion( "BFO:0000050") +AnnotationAssertion( "external") +AnnotationAssertion( "part_of") +AnnotationAssertion( "part_of") +AnnotationAssertion(rdfs:label "part of") +InverseObjectProperties( ) +TransitiveObjectProperty() - - +# Object Property: (has part) +AnnotationAssertion( "BFO:0000051") +AnnotationAssertion( "external") +AnnotationAssertion( "has_part") +AnnotationAssertion( "has_part") +AnnotationAssertion(rdfs:label "has part") +TransitiveObjectProperty() - - - - - +############################ +# Classes +############################ - +# Class: (nuclear chromosome) - - - - +AnnotationAssertion(Annotation( "GOC:dph"^^xsd:string) Annotation( "GOC:mah"^^xsd:string) "A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.") +AnnotationAssertion( "nuclear interphase chromosome") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0000228") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nuclear chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +# Class: (mitochondrial chromosome) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - has_broad_synonym - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BFO:0000050 - external - part_of - part_of - part of - - - - - - - - - BFO:0000051 - external - has_part - has_part - has part - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. - nuclear interphase chromosome - cellular_component - GO:0000228 - - - nuclear chromosome - - - - - A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact. - GOC:dph - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - A chromosome found in the cytoplasm. - cytoplasmic interphase chromosome - cellular_component - GO:0000229 - - - cytoplasmic chromosome - - - - - A chromosome found in the cytoplasm. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - A chromosome found in the mitochondrion of a eukaryotic cell. - NIF_Subcellular:sao1186327184 - mitochondrial DNA - mtDNA - cellular_component - mitochondrial genome - GO:0000262 - mitochondrial chromosome - - - - - A chromosome found in the mitochondrion of a eukaryotic cell. - GOC:mah - - - - - - - - - A chromosome involved in sex determination. - cellular_component - GO:0000803 - sex chromosome - - - - - A chromosome involved in sex determination. - GOC:elh - - - - - - - - - The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males. - - Wikipedia:X_chromosome - cellular_component - GO:0000805 - X chromosome - - - - - The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males. - GOC:mah - GOC:mr - ISBN:0582227089 - PMID:20622855 - Wikipedia:XY_sex-determination_system - - - - - - - - - The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males. - - Wikipedia:Y_chromosome - cellular_component - GO:0000806 - Y chromosome - - - - - The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males. - GOC:mah - GOC:mr - ISBN:0582227089 - PMID:20622855 - Wikipedia:XY_sex-determination_system - - - - - - - - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - GO:0008372 - NIF_Subcellular:sao1337158144 - cell or subcellular entity - cellular component - cellular_component - subcellular entity - GO:0005575 - - - - - - - - - Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. - cellular_component - - - - - A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). - GOC:pdt - NIF_Subcellular:sao1337158144 - - - - - subcellular entity - NIF_Subcellular:nlx_subcell_100315 - - - - - - - - - A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. - https://github.com/geneontology/go-ontology/issues/17776 - Wikipedia:Intracellular - internal to cell - intracellular - protoplasm - cellular_component - nucleocytoplasm - protoplast - GO:0005622 - - - - - - intracellular anatomical structure - - - - - A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. - ISBN:0198506732 - - - - - nucleocytoplasm - GOC:mah - - - - - protoplast - GOC:mah - - - - - - - - - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. - NIF_Subcellular:sao1702920020 - Wikipedia:Cell_nucleus - cell nucleus - horsetail nucleus - cellular_component - GO:0005634 - - - - - - - - - - - - - nucleus - - - - - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. - GOC:go_curators - - - - - horsetail nucleus - GOC:al - GOC:mah - GOC:vw - PMID:15030757 - - - - - - - - - - - - - - - - - - - - - The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). - GO:0005636 - Wikipedia:Nuclear_envelope - cellular_component - GO:0005635 - - - - nuclear envelope - - - - - The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). - ISBN:0198547684 - - - - - - - - - A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. - Wikipedia:Chromosome - interphase chromosome - prophase chromosome - cellular_component - chromatid - GO:0005694 - - - - - - - - - - - Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. - chromosome - - - - - A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. - ISBN:0198547684 - - - - - - - - - - - - - - - All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. - Wikipedia:Cytoplasm - cellular_component - GO:0005737 - - - - - - - - cytoplasm - - - - - All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. - ISBN:0198547684 - - - - - - - - - - - - - - - A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. - NIF_Subcellular:sao1860313010 - Wikipedia:Mitochondrion - mitochondria - cellular_component - GO:0005739 - - - - - - - - - - - - Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) - mitochondrion - - - - - A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. - GOC:giardia - ISBN:0198506732 - - - - - - - - - - - - - - - The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space. - cellular_component - GO:0005740 - - - mitochondrial envelope - - - - - The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space. - GOC:ai - GOC:pz - - - - - - - - - - - - - - - The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. - GO:0031980 - NIF_Subcellular:sao1804523077 - Wikipedia:Mitochondrial_matrix - mitochondrial lumen - mitochondrial stroma - cellular_component - GO:0005759 - mitochondrial matrix - - - - - The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation. - GOC:as - ISBN:0198506732 - - - - - - - - - - - - - - - A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. - Wikipedia:Vacuole - cellular_component - vacuolar carboxypeptidase Y - GO:0005773 - - - - - - - - - - - - vacuole - - - - - A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. - GOC:mtg_sensu - ISBN:0198506732 - - - - - - - - - - - - - - - - - - - - - - - - - - The volume enclosed within the vacuolar membrane. - cellular_component - GO:0005775 - vacuolar lumen - - - - - The volume enclosed within the vacuolar membrane. - ISBN:0198506732 - - - - - - - - - - - - - - - The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. - NIF_Subcellular:sao101633890 - Wikipedia:Cytosol - cellular_component - GO:0005829 - - - - - - - - - cytosol - - - - - The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. - GOC:hjd - GOC:jl - - - - - - - - - - - - - - - The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - GO:0005904 - juxtamembrane - NIF_Subcellular:sao1663586795 - Wikipedia:Cell_membrane - cell membrane - cellular membrane - cytoplasmic membrane - plasmalemma - bacterial inner membrane - inner endospore membrane - plasma membrane lipid bilayer - cellular_component - GO:0005886 - - - - - - - - - - - plasma membrane - - - - - The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. - ISBN:0716731363 - - - - - cellular membrane - NIF_Subcellular:sao6433132645 - - - - - plasma membrane lipid bilayer - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. - Wikipedia:Cell_cortex - cellular_component - cell periphery - peripheral cytoplasm - GO:0005938 - - - - cell cortex - - - - - The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. - GOC:mah - ISBN:0815316194 - - - - - - - - - The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined. - Wikipedia:Nucleoid - cellular_component - GO:0009295 - nucleoid - - - - - The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined. - GOC:bm - GOC:ma - ISBN:3540076689 - - - - - - - - - A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma. - - - - - Wikipedia:Chloroplast - cellular_component - GO:0009507 - - chloroplast - - - - - A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma. - ISBN:0471245208 - - - - - - - - - - - - - - - - - - - - - - - - - - A circular DNA molecule containing plastid encoded genes. - cellular_component - GO:0009508 - plastid chromosome - - - - - A circular DNA molecule containing plastid encoded genes. - ISBN:0943088399 - - - - - - - - - - - - - - - The double lipid bilayer enclosing a plastid and separating its contents from the rest of the cytoplasm; includes the intermembrane space. - cellular_component - GO:0009526 - plastid envelope - - - - - The double lipid bilayer enclosing a plastid and separating its contents from the rest of the cytoplasm; includes the intermembrane space. - GOC:jy - - - - - - - - - - - - - - - The proteinaceous ground substance of plastids. - cellular_component - GO:0009532 - plastid stroma - - - - - The proteinaceous ground substance of plastids. - ISBN:0943088399 - - - - - - - - - - - - - - - Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid. - - - - - - - Wikipedia:Plastid - cellular_component - GO:0009536 - - - - - plastid - - - - - Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid. - GOC:jl - ISBN:0198547684 - - - - - - - - - - - - - - - The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis. - cellular_component - GO:0009570 - chloroplast stroma - - - - - The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis. - ISBN:0198547684 - - - - - - - - - - - - - - - - - - - - - A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. - Wikipedia:Endomembrane_system - cellular_component - GO:0012505 - - - - - endomembrane system - - - - - A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. - GOC:lh - - - - - - - - - A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. - 2014-03-06T11:37:54Z - GO:0098589 - GO:0098805 - Wikipedia:Biological_membrane - membrane region - region of membrane - whole membrane - cellular_component - GO:0016020 - - - - - - - - - membrane - - - - - A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. - GOC:dos - GOC:mah - ISBN:0815316194 - - - - - - - - - Any chromosome other than a sex chromosome. - Wikipedia:Autosome - cellular_component - GO:0030849 - Note that this term is mainly relevant in organisms that have both sex chromosomes and non-sex-determining chromosomes in an individual organism. - autosome - - - - - Any chromosome other than a sex chromosome. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. - NIF_Subcellular:sao830981606 - cellular_component - intracellular membrane - GO:0031090 - organelle membrane - - - - - A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. - GOC:dos - GOC:mah - - - - - intracellular membrane - NIF_Subcellular:sao830981606 - - - - - - - - - - - - - - - - - - - - - - - - - - Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. - NIF_Subcellular:sao1687101204 - cellular_component - GO:0031965 - nuclear membrane - - - - - Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. - GOC:mah - GOC:pz - - - - - - - - - - - - - - - - - - - - - - - - - - Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. - NIF_Subcellular:sao1045389829 - cellular_component - GO:0031966 - mitochondrial membrane - - - - - Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope. - GOC:mah - NIF_Subcellular:sao1045389829 - - - - - - - - - - - - - - - - - - - - - A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. - cellular_component - GO:0031967 - - organelle envelope - - - - - A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. - GOC:mah - GOC:pz - - - - - - - - - The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. - cellular_component - GO:0031974 - membrane-enclosed lumen - - - - - The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen. - GOC:add - GOC:mah - - - - - - - - - A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. - cellular_component - GO:0031975 - envelope - - - - - A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. - GOC:mah - GOC:pz - - - - - - - - - - - - - - - The volume enclosed by the nuclear inner membrane. - cellular_component - GO:0031981 - nuclear lumen - - - - - The volume enclosed by the nuclear inner membrane. - GOC:mah - GOC:pz - - - - - - - - - - - - - - - - - - - - - - - - - - Either of the lipid bilayers that surround a plastid and form the plastid envelope. - cellular_component - GO:0042170 - plastid membrane - - - - - Either of the lipid bilayers that surround a plastid and form the plastid envelope. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - The region of a chloroplast to which the DNA is confined. - cellular_component - GO:0042644 - chloroplast nucleoid - - - - - The region of a chloroplast to which the DNA is confined. - GOC:jl - - - - - - - - - - - - - - - - - - - - - - - - - - - The region of a mitochondrion to which the DNA is confined. - cellular_component - GO:0042645 - mitochondrial nucleoid - - - - - The region of a mitochondrion to which the DNA is confined. - GOC:jl - - - - - - - - - - - - - - - - - - - - - - - - - - - The region of a plastid to which the DNA is confined. - cellular_component - GO:0042646 - plastid nucleoid - - - - - The region of a plastid to which the DNA is confined. - GOC:jl - - - - - - - - - - - - - - - - - - - - - - - - - - A circular DNA molecule containing chloroplast encoded genes. - cellular_component - GO:0042648 - chloroplast chromosome - - - - - A circular DNA molecule containing chloroplast encoded genes. - GOC:jl - - - - - - - - - Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. - NIF_Subcellular:sao1539965131 - Wikipedia:Organelle - cellular_component - GO:0043226 - - - - organelle - - - - - Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. - NIF_Subcellular:sao414196390 - membrane-enclosed organelle - cellular_component - GO:0043227 - membrane-bounded organelle - - - - - Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. - GOC:go_curators - - - - - - - - - Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. - NIF_Subcellular:sao1456184038 - non-membrane-enclosed organelle - cellular_component - GO:0043228 - non-membrane-bounded organelle - - - - - Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - cellular_component - GO:0043229 - - intracellular organelle - - - - - Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. - intracellular membrane-enclosed organelle - cellular_component - GO:0043231 - - intracellular membrane-bounded organelle - - - - - Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. - intracellular non-membrane-enclosed organelle - cellular_component - GO:0043232 - - - intracellular non-membrane-bounded organelle - - - - - Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. - GOC:go_curators - - - - - - - - - - - - - - - - - - - - - - - - - - The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. - cellular_component - GO:0043233 - organelle lumen - - - - - The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen. - GOC:jl - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - An organelle lumen that is part of an intracellular organelle. - cellular_component - GO:0070013 - - intracellular organelle lumen - - - - - An organelle lumen that is part of an intracellular organelle. - GOC:mah - - - - - - - - - The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. - mah - 2010-10-04T01:51:47Z - cellular_component - GO:0071944 - - cell periphery - - - - - The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - A membrane that is a (regional) part of the plasma membrane. - dos - 2014-03-06T11:55:32Z - region of plasma membrane - cellular_component - GO:0098590 - - Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. - plasma membrane region - - - - - A membrane that is a (regional) part of the plasma membrane. - GOC:dos - - - - - - - - - - - - - - - Any subdivision of a chromosome along its length. - chromosome region - cellular_component - GO:0098687 - Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore. - chromosomal region - - - - - Any subdivision of a chromosome along its length. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol. - cellular_component - GO:0099522 - region of cytosol - - - - - Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. - cellular_component - GO:0099568 - cytoplasmic region - - - - - Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - - The complete extent of cell cortex that underlies some some region of the plasma membrane. - perimembrane region - cellular_component - GO:0099738 - cell cortex region - - - - - The complete extent of cell cortex that underlies some some region of the plasma membrane. - GOC:dos - - - - - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - kmv - 2019-08-12T18:01:37Z - cellular_component - GO:0110165 - cellular anatomical entity - - - - - A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. - GOC:kmv - - - - - - +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "A chromosome found in the mitochondrion of a eukaryotic cell.") +AnnotationAssertion( "NIF_Subcellular:sao1186327184") +AnnotationAssertion( "mitochondrial DNA") +AnnotationAssertion( "mtDNA") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "mitochondrial genome") +AnnotationAssertion( "GO:0000262") +AnnotationAssertion(rdfs:label "mitochondrial chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +# Class: (sex chromosome) + +AnnotationAssertion(Annotation( "GOC:elh"^^xsd:string) "A chromosome involved in sex determination.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0000803") +AnnotationAssertion(rdfs:label "sex chromosome") +SubClassOf( ) + +# Class: (W chromosome) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:mr"^^xsd:string) Annotation( "ISBN:0321000382"^^xsd:string) Annotation( "PMID:20622855") "The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females.") +AnnotationAssertion( ) +AnnotationAssertion( "Wikipedia:ZW_sex-determination_system") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0000804") +AnnotationAssertion(rdfs:label "W chromosome") +SubClassOf( ) + +# Class: (X chromosome) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:mr"^^xsd:string) Annotation( "ISBN:0582227089"^^xsd:string) Annotation( "PMID:20622855") Annotation( "Wikipedia:XY_sex-determination_system") "The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males.") +AnnotationAssertion( ) +AnnotationAssertion( "Wikipedia:X_chromosome") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0000805") +AnnotationAssertion(rdfs:label "X chromosome") +SubClassOf( ) + +# Class: (Y chromosome) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:mr"^^xsd:string) Annotation( "ISBN:0582227089"^^xsd:string) Annotation( "PMID:20622855") Annotation( "Wikipedia:XY_sex-determination_system") "The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males.") +AnnotationAssertion( ) +AnnotationAssertion( "Wikipedia:Y_chromosome") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0000806") +AnnotationAssertion(rdfs:label "Y chromosome") +SubClassOf( ) + +# Class: (Z chromosome) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:mr"^^xsd:string) Annotation( "ISBN:0321000382"^^xsd:string) Annotation( "PMID:20622855") "The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females.") +AnnotationAssertion( ) +AnnotationAssertion( "Wikipedia:ZW_sex-determination_system") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0000807") +AnnotationAssertion(rdfs:label "Z chromosome") +SubClassOf( ) + +# Class: (cellular_component) + +AnnotationAssertion(Annotation( "GOC:pdt") Annotation( "NIF_Subcellular:sao1337158144") "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).") +AnnotationAssertion( "GO:0008372") +AnnotationAssertion( "NIF_Subcellular:sao1337158144") +AnnotationAssertion( "cell or subcellular entity") +AnnotationAssertion( "cellular component") +AnnotationAssertion( "cellular_component") +AnnotationAssertion(Annotation( "NIF_Subcellular:nlx_subcell_100315") "subcellular entity") +AnnotationAssertion( "GO:0005575") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "cellular_component") + +# Class: (intracellular anatomical structure) + +AnnotationAssertion(Annotation( "ISBN:0198506732"^^xsd:string) "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/17776"^^xsd:anyURI) +AnnotationAssertion( "Wikipedia:Intracellular") +AnnotationAssertion( "internal to cell") +AnnotationAssertion( "intracellular") +AnnotationAssertion( "protoplasm") +AnnotationAssertion( "cellular_component") +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "nucleocytoplasm") +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "protoplast") +AnnotationAssertion( "GO:0005622") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "intracellular anatomical structure") +SubClassOf( ) + +# Class: (nucleus) + +AnnotationAssertion(Annotation( "GOC:go_curators"^^xsd:string) "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.") +AnnotationAssertion( "NIF_Subcellular:sao1702920020") +AnnotationAssertion( "Wikipedia:Cell_nucleus") +AnnotationAssertion( "cell nucleus") +AnnotationAssertion(Annotation( "GOC:al"^^xsd:string) Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:vw"^^xsd:string) Annotation( "PMID:15030757") "horsetail nucleus") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005634") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nucleus") +SubClassOf( ) + +# Class: (nuclear envelope) + +AnnotationAssertion(Annotation( "ISBN:0198547684"^^xsd:string) "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).") +AnnotationAssertion( "GO:0005636") +AnnotationAssertion( "Wikipedia:Nuclear_envelope") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005635") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nuclear envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chromosome) + +AnnotationAssertion(Annotation( "ISBN:0198547684"^^xsd:string) "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.") +AnnotationAssertion( "Wikipedia:Chromosome") +AnnotationAssertion( "interphase chromosome") +AnnotationAssertion( "prophase chromosome") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "chromatid") +AnnotationAssertion( "GO:0005694") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.") +AnnotationAssertion(rdfs:label "chromosome") +SubClassOf( ) + +# Class: (cytoplasm) + +AnnotationAssertion(Annotation( "ISBN:0198547684"^^xsd:string) "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23023"^^xsd:anyURI) +AnnotationAssertion( "Wikipedia:Cytoplasm") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005737") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cytoplasm") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrion) + +AnnotationAssertion(Annotation( "GOC:giardia"^^xsd:string) Annotation( "ISBN:0198506732"^^xsd:string) "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.") +AnnotationAssertion( "NIF_Subcellular:sao1860313010") +AnnotationAssertion( "Wikipedia:Mitochondrion") +AnnotationAssertion( "mitochondria") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005739") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)") +AnnotationAssertion(rdfs:label "mitochondrion") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial envelope) + +AnnotationAssertion(Annotation( "GOC:ai"^^xsd:string) Annotation( "GOC:pz"^^xsd:string) "The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005740") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mitochondrial envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial matrix) + +AnnotationAssertion(Annotation( "GOC:as") Annotation( "ISBN:0198506732"^^xsd:string) "The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.") +AnnotationAssertion( "GO:0031980") +AnnotationAssertion( "NIF_Subcellular:sao1804523077") +AnnotationAssertion( "Wikipedia:Mitochondrial_matrix") +AnnotationAssertion( "mitochondrial lumen") +AnnotationAssertion( "mitochondrial stroma") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005759") +AnnotationAssertion(rdfs:label "mitochondrial matrix") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vacuole) + +AnnotationAssertion(Annotation( "GOC:mtg_sensu"^^xsd:string) Annotation( "ISBN:0198506732"^^xsd:string) "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.") +AnnotationAssertion( "Wikipedia:Vacuole") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "vacuolar carboxypeptidase Y") +AnnotationAssertion( "GO:0005773") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "vacuole") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (vacuolar lumen) + +AnnotationAssertion(Annotation( "ISBN:0198506732"^^xsd:string) "The volume enclosed within the vacuolar membrane.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005775") +AnnotationAssertion(rdfs:label "vacuolar lumen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cytosol) + +AnnotationAssertion(Annotation( "GOC:hjd"^^xsd:string) Annotation( "GOC:jl"^^xsd:string) "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.") +AnnotationAssertion( "NIF_Subcellular:sao101633890") +AnnotationAssertion( "Wikipedia:Cytosol") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005829") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cytosol") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plasma membrane) + +AnnotationAssertion(Annotation( "ISBN:0716731363"^^xsd:string) "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.") +AnnotationAssertion( "GO:0005887") +AnnotationAssertion( "GO:0005904") +AnnotationAssertion( "juxtamembrane") +AnnotationAssertion( "NIF_Subcellular:sao1663586795") +AnnotationAssertion( "Wikipedia:Cell_membrane") +AnnotationAssertion( "cell membrane") +AnnotationAssertion(Annotation( "NIF_Subcellular:sao6433132645") "cellular membrane") +AnnotationAssertion( "cytoplasmic membrane") +AnnotationAssertion( "plasmalemma") +AnnotationAssertion( "bacterial inner membrane") +AnnotationAssertion( "inner endospore membrane") +AnnotationAssertion( "integral component of plasma membrane") +AnnotationAssertion( "integral to plasma membrane") +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "plasma membrane lipid bilayer") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005886") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "plasma membrane") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell cortex) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "ISBN:0815316194"^^xsd:string) "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.") +AnnotationAssertion( "Wikipedia:Cell_cortex") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "cell periphery") +AnnotationAssertion( "peripheral cytoplasm") +AnnotationAssertion( "GO:0005938") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cell cortex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleoid) + +AnnotationAssertion(Annotation( "GOC:bm"^^xsd:string) Annotation( "GOC:ma"^^xsd:string) Annotation( "ISBN:3540076689") "The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.") +AnnotationAssertion( "Wikipedia:Nucleoid") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0009295") +AnnotationAssertion(rdfs:label "nucleoid") +SubClassOf( ) + +# Class: (chloroplast) + +AnnotationAssertion(Annotation( "ISBN:0471245208"^^xsd:string) "A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Wikipedia:Chloroplast") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0009507") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "chloroplast") +SubClassOf( ) + +# Class: (plastid chromosome) + +AnnotationAssertion(Annotation( "ISBN:0943088399") "A circular DNA molecule containing plastid encoded genes.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0009508") +AnnotationAssertion(rdfs:label "plastid chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid envelope) + +AnnotationAssertion(Annotation( "GOC:jy") "The double lipid bilayer enclosing a plastid and separating its contents from the rest of the cytoplasm; includes the intermembrane space.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0009526") +AnnotationAssertion(rdfs:label "plastid envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid stroma) + +AnnotationAssertion(Annotation( "ISBN:0943088399") "The proteinaceous ground substance of plastids.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0009532") +AnnotationAssertion(rdfs:label "plastid stroma") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid) + +AnnotationAssertion(Annotation( "GOC:jl"^^xsd:string) Annotation( "ISBN:0198547684"^^xsd:string) "Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Wikipedia:Plastid") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0009536") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "plastid") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast stroma) + +AnnotationAssertion(Annotation( "ISBN:0198547684"^^xsd:string) "The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0009570") +AnnotationAssertion(rdfs:label "chloroplast stroma") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (endomembrane system) + +AnnotationAssertion(Annotation( "GOC:lh") "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.") +AnnotationAssertion( "Wikipedia:Endomembrane_system") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0012505") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "endomembrane system") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membrane) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) Annotation( "GOC:mah"^^xsd:string) Annotation( "ISBN:0815316194"^^xsd:string) "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.") +AnnotationAssertion( "2014-03-06T11:37:54Z") +AnnotationAssertion( "GO:0016021") +AnnotationAssertion( "GO:0098589") +AnnotationAssertion( "GO:0098805") +AnnotationAssertion( "Wikipedia:Biological_membrane") +AnnotationAssertion( "Wikipedia:Transmembrane_protein") +AnnotationAssertion( "integral component of membrane") +AnnotationAssertion( "integral to membrane") +AnnotationAssertion( "membrane region") +AnnotationAssertion( "region of membrane") +AnnotationAssertion( "whole membrane") +AnnotationAssertion( "cellular_component") +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "transmembrane") +AnnotationAssertion( "GO:0016020") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "membrane") +SubClassOf( ) + +# Class: (autosome) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "Any chromosome other than a sex chromosome.") +AnnotationAssertion( "Wikipedia:Autosome") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0030849") +AnnotationAssertion(rdfs:comment "Note that this term is mainly relevant in organisms that have both sex chromosomes and non-sex-determining chromosomes in an individual organism.") +AnnotationAssertion(rdfs:label "autosome") +SubClassOf( ) + +# Class: (organelle membrane) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) Annotation( "GOC:mah"^^xsd:string) "A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.") +AnnotationAssertion( "NIF_Subcellular:sao830981606") +AnnotationAssertion( "cellular_component") +AnnotationAssertion(Annotation( "NIF_Subcellular:sao830981606") "intracellular membrane") +AnnotationAssertion( "GO:0031090") +AnnotationAssertion(rdfs:label "organelle membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nuclear membrane) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:pz"^^xsd:string) "Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.") +AnnotationAssertion( "NIF_Subcellular:sao1687101204") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031965") +AnnotationAssertion(rdfs:label "nuclear membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial membrane) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "NIF_Subcellular:sao1045389829") "Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.") +AnnotationAssertion( "NIF_Subcellular:sao1045389829") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031966") +AnnotationAssertion(rdfs:label "mitochondrial membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organelle envelope) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:pz"^^xsd:string) "A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031967") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organelle envelope") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (membrane-enclosed lumen) + +AnnotationAssertion(Annotation( "GOC:add"^^xsd:string) Annotation( "GOC:mah"^^xsd:string) "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031974") +AnnotationAssertion(rdfs:label "membrane-enclosed lumen") +SubClassOf( ) + +# Class: (envelope) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:pz"^^xsd:string) "A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031975") +AnnotationAssertion(rdfs:label "envelope") +SubClassOf( ) + +# Class: (nuclear lumen) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) Annotation( "GOC:pz"^^xsd:string) "The volume enclosed by the nuclear inner membrane.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0031981") +AnnotationAssertion(rdfs:label "nuclear lumen") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid membrane) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "Either of the lipid bilayers that surround a plastid and form the plastid envelope.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0042170") +AnnotationAssertion(rdfs:label "plastid membrane") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast nucleoid) + +AnnotationAssertion(Annotation( "GOC:jl"^^xsd:string) "The region of a chloroplast to which the DNA is confined.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0042644") +AnnotationAssertion(rdfs:label "chloroplast nucleoid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (mitochondrial nucleoid) + +AnnotationAssertion(Annotation( "GOC:jl"^^xsd:string) "The region of a mitochondrion to which the DNA is confined.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0042645") +AnnotationAssertion(rdfs:label "mitochondrial nucleoid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (plastid nucleoid) + +AnnotationAssertion(Annotation( "GOC:jl"^^xsd:string) "The region of a plastid to which the DNA is confined.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0042646") +AnnotationAssertion(rdfs:label "plastid nucleoid") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chloroplast chromosome) + +AnnotationAssertion(Annotation( "GOC:jl"^^xsd:string) "A circular DNA molecule containing chloroplast encoded genes.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0042648") +AnnotationAssertion(rdfs:label "chloroplast chromosome") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organelle) + +AnnotationAssertion(Annotation( "GOC:go_curators"^^xsd:string) "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.") +AnnotationAssertion( "NIF_Subcellular:sao1539965131") +AnnotationAssertion( "Wikipedia:Organelle") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0043226") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organelle") +SubClassOf( ) + +# Class: (membrane-bounded organelle) + +AnnotationAssertion(Annotation( "GOC:go_curators"^^xsd:string) "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.") +AnnotationAssertion( "NIF_Subcellular:sao414196390") +AnnotationAssertion( "membrane-enclosed organelle") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0043227") +AnnotationAssertion(rdfs:label "membrane-bounded organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (non-membrane-bounded organelle) + +AnnotationAssertion(Annotation( "GOC:go_curators"^^xsd:string) "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/21881"^^xsd:anyURI) +AnnotationAssertion( "NIF_Subcellular:sao1456184038") +AnnotationAssertion( "non-membrane-enclosed organelle") +AnnotationAssertion( "biological condensate") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0043228") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "non-membrane-bounded organelle") +SubClassOf( ) + +# Class: (intracellular organelle) + +AnnotationAssertion(Annotation( "GOC:go_curators"^^xsd:string) "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0043229") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "intracellular organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (intracellular membrane-bounded organelle) + +AnnotationAssertion(Annotation( "GOC:go_curators"^^xsd:string) "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.") +AnnotationAssertion( "intracellular membrane-enclosed organelle") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0043231") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "intracellular membrane-bounded organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (intracellular non-membrane-bounded organelle) + +AnnotationAssertion(Annotation( "GOC:go_curators"^^xsd:string) "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.") +AnnotationAssertion( "intracellular non-membrane-enclosed organelle") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0043232") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "intracellular non-membrane-bounded organelle") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (organelle lumen) + +AnnotationAssertion(Annotation( "GOC:jl"^^xsd:string) Annotation( "GOC:mah"^^xsd:string) "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0043233") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "organelle lumen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (intracellular organelle lumen) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "An organelle lumen that is part of an intracellular organelle.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0070013") +AnnotationAssertion(rdfs:label "intracellular organelle lumen") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell periphery) + +AnnotationAssertion(Annotation( "GOC:mah"^^xsd:string) "The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.") +AnnotationAssertion( "mah") +AnnotationAssertion( "2010-10-04T01:51:47Z") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0071944") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cell periphery") +SubClassOf( ) + +# Class: (plasma membrane region) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "A membrane that is a (regional) part of the plasma membrane.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2014-03-06T11:55:32Z") +AnnotationAssertion( "region of plasma membrane") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0098590") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.") +AnnotationAssertion(rdfs:label "plasma membrane region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (chromosomal region) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "Any subdivision of a chromosome along its length.") +AnnotationAssertion( "chromosome region") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0098687") +AnnotationAssertion(rdfs:comment "Chromosomal regions include parts that are not part of the chromatin. Examples include the kinetochore.") +AnnotationAssertion(rdfs:label "chromosomal region") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cytosolic region) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol.") +AnnotationAssertion( "region of cytosol") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0099522") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cytosolic region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cytoplasmic region) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0099568") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cytoplasmic region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cell cortex region) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "The complete extent of cell cortex that underlies some some region of the plasma membrane.") +AnnotationAssertion( "perimembrane region") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0099738") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "cell cortex region") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular anatomical entity) + +AnnotationAssertion(Annotation( "GOC:kmv"^^xsd:string) "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "kmv") +AnnotationAssertion( "2019-08-12T18:01:37Z") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0110165") +AnnotationAssertion(rdfs:label "cellular anatomical entity") +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/ncbitaxon_import.owl b/src/ontology/imports/ncbitaxon_import.owl index 4957233..637d0cb 100644 --- a/src/ontology/imports/ncbitaxon_import.owl +++ b/src/ontology/imports/ncbitaxon_import.owl @@ -1,1735 +1,898 @@ - - - - - 2021-06-16 - - - - - - - - - - - - - - - - - - - - - - - - - has_broad_synonym - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - all - NCBITaxon:1 - root - - - - - all - - - - - - - - - - - GC_ID:1 - PMID:15371245 - ncbi_taxonomy - NCBITaxon:10066 - Muridae - - - - - - - - - - GC_ID:1 - Mus - mice - mouse - ncbi_taxonomy - NCBITaxon:10088 - Mus <genus> - - - - - Mus - - - - - - mice - - - - - - mouse - - - - - - - - - - - NCBITaxon:85055 - GC_ID:1 - house mouse - mouse - ncbi_taxonomy - NCBITaxon:10090 - Mus musculus - - - - - house mouse - - - - - - mouse - - - - - - - - - - - GC_ID:1 - rat - rats - ncbi_taxonomy - NCBITaxon:10114 - Rattus - - - - - rat - - - - - - rats - - - - - - - - - - - NCBITaxon:36465 - GC_ID:1 - Norway rat - brown rat - rat - rats - ncbi_taxonomy - NCBITaxon:10116 - Rattus norvegicus - - - - - brown rat - - - - - - rat - - - - - - rats - - - - - - Norway rat - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:117570 - Teleostomi - - - - - - - - - - NCBITaxon:40673 - GC_ID:1 - bony vertebrates - ncbi_taxonomy - NCBITaxon:117571 - Euteleostomi - - - - - bony vertebrates - - - - - - - - - - - NCBITaxon:27837 - GC_ID:1 - ncbi_taxonomy - Adenophorea - NCBITaxon:119089 - Chromadorea - - - - - Adenophorea - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1206794 - Ecdysozoa - - - - - - - - - GC_ID:1 - ncbi_taxonomy - biota - NCBITaxon:131567 - cellular organisms - - - - - biota - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1338369 - Dipnotetrapodomorpha - - - - - - - - - - GC_ID:1 - PMID:11743200 - PMID:11791233 - ncbi_taxonomy - Boreotheria - NCBITaxon:1437010 - Boreoeutheria - - - - - Boreotheria - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:1489341 - Osteoglossocephalai - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:186623 - Actinopteri - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:186625 - Clupeocephala - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Otophysa - NCBITaxon:186626 - Otophysi - - - - - Otophysa - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cypriniphysi - NCBITaxon:186627 - Cypriniphysae - - - - - Cypriniphysi - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Ostarioclupeomorpha - Otocephala - NCBITaxon:186634 - Otomorpha - - - - - Ostarioclupeomorpha - - - - - - Otocephala - - - - - - - - - - - GC_ID:1 - mice and others - ncbi_taxonomy - Sciurognathi - NCBITaxon:1963758 - Myomorpha - - - - - mice and others - - - - - - Sciurognathi - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Homo/Pan/Gorilla group - NCBITaxon:207598 - Homininae - - - - - Homo/Pan/Gorilla group - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2301116 - Rhabditina - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2301119 - Rhabditomorpha - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2743709 - Danionidae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:2743711 - Danioninae - - - - - - - - - - GC_ID:1 - PMID:23020233 - PMID:30257078 - eucaryotes - eukaryotes - ncbi_taxonomy - Eucarya - Eucaryotae - Eukarya - Eukaryotae - eukaryotes - NCBITaxon:2759 - Eukaryota - - - - - eucaryotes - - - - - - eukaryotes - - - - - - Eucarya - - - - - - Eucaryotae - - - - - - Eukarya - - - - - - Eukaryotae - - - - - - eukaryotes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Cyprinoidea - NCBITaxon:30727 - Cyprinoidei - - - - - Cyprinoidea - - - - - - - - - - - GC_ID:1 - PMID:11214319 - PMID:12082125 - PMID:12878460 - PMID:15522813 - ncbi_taxonomy - NCBITaxon:314146 - Euarchontoglires - - - - - - - - - - GC_ID:1 - PMID:11214319 - PMID:12082125 - PMID:15522813 - Rodents and rabbits - ncbi_taxonomy - NCBITaxon:314147 - Glires - - - - - Rodents and rabbits - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Anthropoidea - NCBITaxon:314293 - Simiiformes - - - - - Anthropoidea - - - - - - - - - - - GC_ID:1 - ape - apes - ncbi_taxonomy - NCBITaxon:314295 - Hominoidea - - - - - ape - - - - - - apes - - - - - - - - - - - GC_ID:1 - teleost fishes - ncbi_taxonomy - NCBITaxon:32443 - Teleostei - - - - - teleost fishes - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:32519 - Ostariophysi - - - - - - - - - - GC_ID:1 - tetrapods - ncbi_taxonomy - NCBITaxon:32523 - Tetrapoda - - - - - tetrapods - - - - - - - - - - - GC_ID:1 - amniotes - ncbi_taxonomy - NCBITaxon:32524 - Amniota - - - - - amniotes - - - - - - - - - - - GC_ID:1 - Theria - ncbi_taxonomy - NCBITaxon:32525 - Theria <mammals> - - - - - Theria - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Fungi/Metazoa group - opisthokonts - NCBITaxon:33154 - Opisthokonta - - - - - Fungi/Metazoa group - - - - - - opisthokonts - - - - - - - - - - - GC_ID:1 - metazoans - multicellular animals - ncbi_taxonomy - Animalia - animals - NCBITaxon:33208 - Metazoa - - - - - metazoans - - - - - - multicellular animals - - - - - - Animalia - - - - - - animals - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33213 - Bilateria - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:33317 - Protostomia - - - - - - - - - - GC_ID:1 - deuterostomes - ncbi_taxonomy - NCBITaxon:33511 - Deuterostomia - - - - - deuterostomes - - - - - - - - - - - GC_ID:1 - PMID:15019624 - PMID:15371245 - ncbi_taxonomy - NCBITaxon:337687 - Muroidea - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:376913 - Haplorrhini - - - - - - - - - - NCBITaxon:109679 - GC_ID:1 - ncbi_taxonomy - NCBITaxon:39107 - Murinae - - - - - - - - - - GC_ID:1 - mammals - ncbi_taxonomy - mammals - NCBITaxon:40674 - Mammalia - - - - - mammals - - - - - - mammals - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - Neopterygi - NCBITaxon:41665 - Neopterygii - - - - - Neopterygi - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:55879 - Rhabditoidea - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:55885 - Peloderinae - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:6072 - Eumetazoa - - - - - - - - - - GC_ID:1 - nematode - nematodes - roundworm - roundworms - ncbi_taxonomy - Nemata - nematodes - NCBITaxon:6231 - Nematoda - - - - - nematode - - - - - - nematodes - - - - - - roundworm - - - - - - roundworms - - - - - - Nemata - - - - - - nematodes - - - - - - - - - - - NCBITaxon:33251 - GC_ID:1 - ncbi_taxonomy - NCBITaxon:6236 - Rhabditida - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:6237 - Caenorhabditis - - - - - - - - - - GC_ID:1 - roundworm - ncbi_taxonomy - Rhabditis elegans - NCBITaxon:6239 - Caenorhabditis elegans - - - - - roundworm - - - - - - Rhabditis elegans - - - - - - - - - - - NCBITaxon:54603 - GC_ID:1 - ncbi_taxonomy - NCBITaxon:6243 - Rhabditidae - - - - - - - - - - GC_ID:1 - chordates - ncbi_taxonomy - chordates - NCBITaxon:7711 - Chordata - - - - - chordates - - - - - - chordates - - - - - - - - - - - GC_ID:1 - Vertebrata - vertebrates - ncbi_taxonomy - vertebrates - NCBITaxon:7742 - Vertebrata <vertebrates> - - - - - Vertebrata - - - - - - vertebrates - - - - - - vertebrates - - - - - - - - - - - GC_ID:1 - Gnathostomata - jawed vertebrates - ncbi_taxonomy - NCBITaxon:7776 - Gnathostomata <vertebrates> - - - - - Gnathostomata - - - - - - jawed vertebrates - - - - - - - - - - - GC_ID:1 - fish - fishes - ray-finned fishes - ncbi_taxonomy - Actinopterygi - Osteichthyes - bony fishes - NCBITaxon:7898 - Actinopterygii - - - - - fish - - - - - - fishes - - - - - - ray-finned fishes - - - - - - Actinopterygi - - - - - - Osteichthyes - - - - - - bony fishes - - - - - - - - - - - GC_ID:1 - carps and others - ncbi_taxonomy - NCBITaxon:7952 - Cypriniformes - - - - - carps and others - - - - - - - - - - - NCBITaxon:46777 - NCBITaxon:487617 - GC_ID:1 - ncbi_taxonomy - Brachydanio - Celestichthys - NCBITaxon:7954 - Danio - - - - - Brachydanio - - - - - - Celestichthys - - - - - - - - - - - NCBITaxon:27702 - NCBITaxon:37966 - GC_ID:1 - leopard danio - zebra danio - zebra fish - zebrafish - ncbi_taxonomy - Brachydanio rerio - Brachydanio rerio frankei - Cyprinus rerio - Danio frankei - Danio rerio frankei - NCBITaxon:7955 - Danio rerio - - - - - leopard danio - - - - - - zebra danio - - - - - - zebra fish - - - - - - zebrafish - - - - - - Brachydanio rerio - - - - - - Brachydanio rerio frankei - - - - - - Cyprinus rerio - - - - - - Danio frankei - - - - - - Danio rerio frankei - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:8287 - Sarcopterygii - - - - - - - - - - GC_ID:1 - Mus - ncbi_taxonomy - NCBITaxon:862507 - Mus <subgenus> - - - - - Mus - - - - - - - - - - - GC_ID:1 - Craniata - ncbi_taxonomy - NCBITaxon:89593 - Craniata <chordates> - - - - - Craniata - - - - - - - - - - - GC_ID:1 - eutherian mammals - placental mammals - placentals - ncbi_taxonomy - Placentalia - placentals - NCBITaxon:9347 - Eutheria - - - - - eutherian mammals - - - - - - placental mammals - - - - - - placentals - - - - - - Placentalia - - - - - - placentals - - - - - - - - - - - GC_ID:1 - primate - ncbi_taxonomy - Primata - primates - NCBITaxon:9443 - Primates - - - - - primate - - - - - - Primata - - - - - - primates - - - - - - - - - - - GC_ID:1 - ncbi_taxonomy - NCBITaxon:9526 - Catarrhini - - - - - - - - - - GC_ID:1 - great apes - ncbi_taxonomy - Pongidae - NCBITaxon:9604 - Hominidae - - - - - great apes - - - - - - Pongidae - - - - - - - - - - - GC_ID:1 - humans - ncbi_taxonomy - NCBITaxon:9605 - Homo - - - - - humans - - - - - - - - - - - GC_ID:1 - human - man - ncbi_taxonomy - NCBITaxon:9606 - Homo sapiens - - - - - human - - - - - - man - - - - - - - - - - - GC_ID:1 - rodent - ncbi_taxonomy - rodents - NCBITaxon:9989 - Rodentia - - - - - rodent - - - - - - rodents - - - - - - - - +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2023-02-19"^^xsd:string) + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion(rdfs:label "has_broad_synonym") + + + +############################ +# Classes +############################ + +# Class: (root) + +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "all") +AnnotationAssertion( "NCBITaxon:1") +AnnotationAssertion(rdfs:label "root") + +# Class: (Muridae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:15371245") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:10066") +AnnotationAssertion(rdfs:label "Muridae") +SubClassOf( ) + +# Class: (Mus ) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Mus") +AnnotationAssertion(Annotation( ) "mice") +AnnotationAssertion(Annotation( ) "mouse") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:10088") +AnnotationAssertion(rdfs:label "Mus ") +SubClassOf( ) + +# Class: (Mus musculus) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:85055") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "house mouse") +AnnotationAssertion(Annotation( ) "mouse") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:10090") +AnnotationAssertion(rdfs:label "Mus musculus") +SubClassOf( ) + +# Class: (Rattus) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "rat") +AnnotationAssertion(Annotation( ) "rats") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:10114") +AnnotationAssertion(rdfs:label "Rattus") +SubClassOf( ) + +# Class: (Rattus norvegicus) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:36465") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Norway rat") +AnnotationAssertion(Annotation( ) "brown rat") +AnnotationAssertion(Annotation( ) "rat") +AnnotationAssertion(Annotation( ) "rats") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:10116") +AnnotationAssertion(rdfs:label "Rattus norvegicus") +SubClassOf( ) + +# Class: (Teleostomi) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:117570") +AnnotationAssertion(rdfs:label "Teleostomi") +SubClassOf( ) + +# Class: (Euteleostomi) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:40673") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "bony vertebrates") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:117571") +AnnotationAssertion(rdfs:label "Euteleostomi") +SubClassOf( ) + +# Class: (Chromadorea) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:27837") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Adenophorea") +AnnotationAssertion( "NCBITaxon:119089") +AnnotationAssertion(rdfs:label "Chromadorea") +SubClassOf( ) + +# Class: (Ecdysozoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:1206794") +AnnotationAssertion(rdfs:label "Ecdysozoa") +SubClassOf( ) + +# Class: (cellular organisms) + +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "biota") +AnnotationAssertion( "NCBITaxon:131567") +AnnotationAssertion(rdfs:label "cellular organisms") +SubClassOf( ) + +# Class: (Archelosauria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:22839753") +AnnotationAssertion( "PMID:25450099") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Archosauria-Testudines") +AnnotationAssertion(Annotation( ) "Testudines + Archosauria group") +AnnotationAssertion( "NCBITaxon:1329799") +AnnotationAssertion(rdfs:label "Archelosauria") +SubClassOf( ) + +# Class: (Dipnotetrapodomorpha) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:1338369") +AnnotationAssertion(rdfs:label "Dipnotetrapodomorpha") +SubClassOf( ) + +# Class: (Boreoeutheria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:11743200") +AnnotationAssertion( "PMID:11791233") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Boreotheria") +AnnotationAssertion( "NCBITaxon:1437010") +AnnotationAssertion(rdfs:label "Boreoeutheria") +SubClassOf( ) + +# Class: (Galloanserae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Galloanseri") +AnnotationAssertion(Annotation( ) "ducks, geese, chickens, fowl, quail, currasows and allies") +AnnotationAssertion( "NCBITaxon:1549675") +AnnotationAssertion(rdfs:label "Galloanserae") +SubClassOf( ) + +# Class: (Myomorpha) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "mice and others") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Sciurognathi") +AnnotationAssertion( "NCBITaxon:1963758") +AnnotationAssertion(rdfs:label "Myomorpha") +SubClassOf( ) + +# Class: (Homininae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Homo/Pan/Gorilla group") +AnnotationAssertion( "NCBITaxon:207598") +AnnotationAssertion(rdfs:label "Homininae") +SubClassOf( ) + +# Class: (Rhabditina) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:2301116") +AnnotationAssertion(rdfs:label "Rhabditina") +SubClassOf( ) + +# Class: (Rhabditomorpha) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:2301119") +AnnotationAssertion(rdfs:label "Rhabditomorpha") +SubClassOf( ) + +# Class: (Eukaryota) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:23020233") +AnnotationAssertion( "PMID:30257078") +AnnotationAssertion(Annotation( ) "eucaryotes") +AnnotationAssertion(Annotation( ) "eukaryotes") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Eucarya") +AnnotationAssertion(Annotation( ) "Eucaryotae") +AnnotationAssertion(Annotation( ) "Eukarya") +AnnotationAssertion(Annotation( ) "Eukaryotae") +AnnotationAssertion(Annotation( ) "eukaryotes") +AnnotationAssertion( "NCBITaxon:2759") +AnnotationAssertion(rdfs:label "Eukaryota") +SubClassOf( ) + +# Class: (Euarchontoglires) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:11214319") +AnnotationAssertion( "PMID:12082125") +AnnotationAssertion( "PMID:12878460") +AnnotationAssertion( "PMID:15522813") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:314146") +AnnotationAssertion(rdfs:label "Euarchontoglires") +SubClassOf( ) + +# Class: (Glires) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:11214319") +AnnotationAssertion( "PMID:12082125") +AnnotationAssertion( "PMID:15522813") +AnnotationAssertion(Annotation( ) "Rodents and rabbits") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:314147") +AnnotationAssertion(rdfs:label "Glires") +SubClassOf( ) + +# Class: (Simiiformes) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Anthropoidea") +AnnotationAssertion( "NCBITaxon:314293") +AnnotationAssertion(rdfs:label "Simiiformes") +SubClassOf( ) + +# Class: (Hominoidea) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "ape") +AnnotationAssertion(Annotation( ) "apes") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:314295") +AnnotationAssertion(rdfs:label "Hominoidea") +SubClassOf( ) + +# Class: (Tetrapoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "tetrapods") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:32523") +AnnotationAssertion(rdfs:label "Tetrapoda") +SubClassOf( ) + +# Class: (Amniota) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "amniotes") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:32524") +AnnotationAssertion(rdfs:label "Amniota") +SubClassOf( ) + +# Class: (Theria ) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Theria") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:32525") +AnnotationAssertion(rdfs:label "Theria ") +SubClassOf( ) + +# Class: (Sauria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "diapsids") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Diapsida") +AnnotationAssertion( "NCBITaxon:32561") +AnnotationAssertion(rdfs:label "Sauria") +SubClassOf( ) + +# Class: (Opisthokonta) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Fungi/Metazoa group") +AnnotationAssertion(Annotation( ) "opisthokonts") +AnnotationAssertion( "NCBITaxon:33154") +AnnotationAssertion(rdfs:label "Opisthokonta") +SubClassOf( ) + +# Class: (Metazoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "metazoans") +AnnotationAssertion(Annotation( ) "multicellular animals") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Animalia") +AnnotationAssertion(Annotation( ) "animals") +AnnotationAssertion( "NCBITaxon:33208") +AnnotationAssertion(rdfs:label "Metazoa") +SubClassOf( ) + +# Class: (Bilateria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:33213") +AnnotationAssertion(rdfs:label "Bilateria") +SubClassOf( ) + +# Class: (Protostomia) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:33317") +AnnotationAssertion(rdfs:label "Protostomia") +SubClassOf( ) + +# Class: (Deuterostomia) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "deuterostomes") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:33511") +AnnotationAssertion(rdfs:label "Deuterostomia") +SubClassOf( ) + +# Class: (Muroidea) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:15019624") +AnnotationAssertion( "PMID:15371245") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:337687") +AnnotationAssertion(rdfs:label "Muroidea") +SubClassOf( ) + +# Class: (Haplorrhini) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:376913") +AnnotationAssertion(rdfs:label "Haplorrhini") +SubClassOf( ) + +# Class: (Murinae) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:109679") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:39107") +AnnotationAssertion(rdfs:label "Murinae") +SubClassOf( ) + +# Class: (Mammalia) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "mammals") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "mammals") +AnnotationAssertion( "NCBITaxon:40674") +AnnotationAssertion(rdfs:label "Mammalia") +SubClassOf( ) + +# Class: (Dinosauria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "dinosaur") +AnnotationAssertion(Annotation( ) "dinosaurs") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:436486") +AnnotationAssertion(rdfs:label "Dinosauria") +SubClassOf( ) + +# Class: (Saurischia) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:436489") +AnnotationAssertion(rdfs:label "Saurischia") +SubClassOf( ) + +# Class: (Theropoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:436491") +AnnotationAssertion(rdfs:label "Theropoda") +SubClassOf( ) + +# Class: (Coelurosauria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:436492") +AnnotationAssertion(rdfs:label "Coelurosauria") +SubClassOf( ) + +# Class: (Rhabditoidea) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:55879") +AnnotationAssertion(rdfs:label "Rhabditoidea") +SubClassOf( ) + +# Class: (Peloderinae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:55885") +AnnotationAssertion(rdfs:label "Peloderinae") +SubClassOf( ) + +# Class: (Eumetazoa) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6072") +AnnotationAssertion(rdfs:label "Eumetazoa") +SubClassOf( ) + +# Class: (Nematoda) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "nematode") +AnnotationAssertion(Annotation( ) "nematodes") +AnnotationAssertion(Annotation( ) "roundworm") +AnnotationAssertion(Annotation( ) "roundworms") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Nemata") +AnnotationAssertion(Annotation( ) "nematodes") +AnnotationAssertion( "NCBITaxon:6231") +AnnotationAssertion(rdfs:label "Nematoda") +SubClassOf( ) + +# Class: (Rhabditida) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:33251") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6236") +AnnotationAssertion(rdfs:label "Rhabditida") +SubClassOf( ) + +# Class: (Caenorhabditis) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6237") +AnnotationAssertion(rdfs:label "Caenorhabditis") +SubClassOf( ) + +# Class: (Caenorhabditis elegans) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Rhabditis elegans") +AnnotationAssertion( "NCBITaxon:6239") +AnnotationAssertion(rdfs:label "Caenorhabditis elegans") +SubClassOf( ) + +# Class: (Rhabditidae) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:54603") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6243") +AnnotationAssertion(rdfs:label "Rhabditidae") +SubClassOf( ) + +# Class: (Chordata) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "chordates") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "chordates") +AnnotationAssertion( "NCBITaxon:7711") +AnnotationAssertion(rdfs:label "Chordata") +SubClassOf( ) + +# Class: (Vertebrata ) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Vertebrata") +AnnotationAssertion(Annotation( ) "vertebrates") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "vertebrates") +AnnotationAssertion( "NCBITaxon:7742") +AnnotationAssertion(rdfs:label "Vertebrata ") +SubClassOf( ) + +# Class: (Gnathostomata ) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Gnathostomata") +AnnotationAssertion(Annotation( ) "jawed vertebrates") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:7776") +AnnotationAssertion(rdfs:label "Gnathostomata ") +SubClassOf( ) + +# Class: (Sarcopterygii) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:8287") +AnnotationAssertion(rdfs:label "Sarcopterygii") +SubClassOf( ) + +# Class: (Sauropsida) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "sauropsids") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:8457") +AnnotationAssertion(rdfs:label "Sauropsida") +SubClassOf( ) + +# Class: (Archosauria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:8492") +AnnotationAssertion(rdfs:label "Archosauria") +SubClassOf( ) + +# Class: (Mus ) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Mus") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:862507") +AnnotationAssertion(rdfs:label "Mus ") +SubClassOf( ) + +# Class: (Aves) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "birds") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "avian") +AnnotationAssertion(Annotation( ) "birds") +AnnotationAssertion( "NCBITaxon:8782") +AnnotationAssertion(rdfs:label "Aves") +SubClassOf( ) + +# Class: (Neognathae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:8825") +AnnotationAssertion(rdfs:label "Neognathae") +SubClassOf( ) + +# Class: (Craniata ) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Craniata") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:89593") +AnnotationAssertion(rdfs:label "Craniata ") +SubClassOf( ) + +# Class: (Galliformes) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "landfowls") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:8976") +AnnotationAssertion(rdfs:label "Galliformes") +SubClassOf( ) + +# Class: (Phasianidae) + +AnnotationAssertion( ) +AnnotationAssertion( "NCBITaxon:9099") +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "turkeys") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:9005") +AnnotationAssertion(rdfs:label "Phasianidae") +SubClassOf( ) + +# Class: (Gallus) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:9030") +AnnotationAssertion(rdfs:label "Gallus") +SubClassOf( ) + +# Class: (Gallus gallus) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "Gallus domesticus") +AnnotationAssertion(Annotation( ) "bantam") +AnnotationAssertion(Annotation( ) "chicken") +AnnotationAssertion(Annotation( ) "chickens") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Gallus gallus domesticus") +AnnotationAssertion(Annotation( ) "Phasianus gallus") +AnnotationAssertion( "NCBITaxon:9031") +AnnotationAssertion(rdfs:label "Gallus gallus") +SubClassOf( ) + +# Class: (Phasianinae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:9072") +AnnotationAssertion(rdfs:label "Phasianinae") +SubClassOf( ) + +# Class: (Eutheria) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "eutherian mammals") +AnnotationAssertion(Annotation( ) "placental mammals") +AnnotationAssertion(Annotation( ) "placentals") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Placentalia") +AnnotationAssertion(Annotation( ) "placentals") +AnnotationAssertion( "NCBITaxon:9347") +AnnotationAssertion(rdfs:label "Eutheria") +SubClassOf( ) + +# Class: (Primates) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "primate") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Primata") +AnnotationAssertion(Annotation( ) "primates") +AnnotationAssertion( "NCBITaxon:9443") +AnnotationAssertion(rdfs:label "Primates") +SubClassOf( ) + +# Class: (Catarrhini) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:9526") +AnnotationAssertion(rdfs:label "Catarrhini") +SubClassOf( ) + +# Class: (Hominidae) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "great apes") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "Pongidae") +AnnotationAssertion( "NCBITaxon:9604") +AnnotationAssertion(rdfs:label "Hominidae") +SubClassOf( ) + +# Class: (Homo) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "humans") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:9605") +AnnotationAssertion(rdfs:label "Homo") +SubClassOf( ) + +# Class: (Homo sapiens) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "human") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:9606") +AnnotationAssertion(rdfs:label "Homo sapiens") +SubClassOf( ) + +# Class: (Rodentia) + +AnnotationAssertion( ) +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion(Annotation( ) "rodent") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion(Annotation( ) "rodents") +AnnotationAssertion( "NCBITaxon:9989") +AnnotationAssertion(rdfs:label "Rodentia") +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 36bdb46..e2f95fc 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -1,3402 +1,1742 @@ - - - - - - 2021-06-16 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - has_broad_synonym - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2023-02-19"^^xsd:string) + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:comment)) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (is a defining property chain axiom) + +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL") +AnnotationAssertion(rdfs:label "is a defining property chain axiom") + +# Annotation Property: (is a defining property chain axiom where second argument is reflexive) + +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.") +AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion(rdfs:label "has_broad_synonym") + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "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'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "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'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (preceded by) + +AnnotationAssertion( "preceded by"@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "is preceded by"@en) +AnnotationAssertion( "preceded_by"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (precedes) + +AnnotationAssertion( "precedes"@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "precedes"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility is a characteristic of this vase"@en) +AnnotationAssertion( "this red color is a characteristic of this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") +AnnotationAssertion(rdfs:label "characteristic of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +FunctionalObjectProperty() + +# Object Property: (has characteristic) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has characteristic"@en) +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) +AnnotationAssertion( "this input material (or this output material) participates in this process"@en) +AnnotationAssertion( "this investigator participates in this investigation"@en) +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion(rdfs:label "participates in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has participant) + +AnnotationAssertion( "has participant"@en) +AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) +AnnotationAssertion( "this investigation has participant this investigator"@en) +AnnotationAssertion( "this process has participant this input material (or this output material)"@en) +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion(rdfs:label "has participant"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion(rdfs:label "has quality"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion( "inverse of has disposition") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) + +# Object Property: (has regulatory component activity) + +AnnotationAssertion( "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.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has negative regulatory component activity) + +AnnotationAssertion( "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.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs: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'.") +AnnotationAssertion(rdfs:label "has negative regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has positive regulatory component activity) + +AnnotationAssertion( "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.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs: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'.") +AnnotationAssertion(rdfs:label "has positive regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has component activity) + +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") +AnnotationAssertion(rdfs:label "has component activity") +SubObjectPropertyOf( ) + +# Object Property: (has component process) + +AnnotationAssertion( "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.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has component process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulated by) + +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) rdfs: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.") +AnnotationAssertion(rdfs:label "directly regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly negatively regulated by) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "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.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly negatively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly positively regulated by) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "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.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly positively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has effector activity) + +AnnotationAssertion(Annotation( "GOC:dos"^^xsd:string) "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.") +AnnotationAssertion( "dos") +AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") +AnnotationAssertion(rdfs:label "has effector activity") +SubObjectPropertyOf( ) +FunctionalObjectProperty() + +# Object Property: (ends after) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) +AnnotationAssertion(rdfs:label "ends after"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately preceded by) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "starts_at_end_of") +AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately precedes) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "ends_at_start_of") +AnnotationAssertion( "meets") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately precedes"@en) +SubObjectPropertyOf( ) + +# Object Property: (overlaps) + +AnnotationAssertion( ) +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "overlaps"@en) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (in taxon) + +AnnotationAssertion( ) +AnnotationAssertion( "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.") +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion( "Jennifer Deegan") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Connects a biological entity to its taxon of origin.") +AnnotationAssertion(rdfs:label "in taxon") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has component) + +AnnotationAssertion( ) +AnnotationAssertion( "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.") +AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") +AnnotationAssertion( "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."@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has component"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (develops from) + +AnnotationAssertion( ) +AnnotationAssertion( "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion( "David Osumi-Sutherland"@en) +AnnotationAssertion( "Melissa Haendel") +AnnotationAssertion( "Terry Meehan"@en) +AnnotationAssertion(rdfs:comment "This is the transitive form of the develops from relation") +AnnotationAssertion(rdfs:label "develops from"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (develops into) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of develops from") +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion( "David Osumi-Sutherland"@en) +AnnotationAssertion( "Terry Meehan"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "develops into"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (regulates) + +AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "David Hill") +AnnotationAssertion( "Tanya Berardini") +AnnotationAssertion( ) +AnnotationAssertion( "GO") +AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") +AnnotationAssertion( "regulates (processual)") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulates) + +AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion( ) +AnnotationAssertion( "negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (positively regulates) + +AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion( ) +AnnotationAssertion( "positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (capable of) + +AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") +AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") +AnnotationAssertion( "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. ") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "has function realized in") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "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)\".") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of part of) + +AnnotationAssertion( "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.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "has function in") +AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (temporally related to) + +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "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.") +AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") +AnnotationAssertion(rdfs:label "temporally related to"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has input) + +AnnotationAssertion( ) +AnnotationAssertion( "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.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "consumes") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has input"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (has developmental contribution from) + +AnnotationAssertion( "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]") +AnnotationAssertion( ) +AnnotationAssertion( "x has developmental contribution from y iff x has some part z such that z develops from y"@en) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "has developmental contribution from"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (developmentally contributes to) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of has developmental contribution from") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "developmentally contributes to"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (developmentally preceded by) + +AnnotationAssertion( ) +AnnotationAssertion( "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "In general you should not use this relation to make assertions - use one of the more specific relations below this one") +AnnotationAssertion(rdfs:comment "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from") +AnnotationAssertion(rdfs:label "developmentally preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (acts upstream of) + +AnnotationAssertion( "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.") +AnnotationAssertion( "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.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within) + +AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") +AnnotationAssertion( "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.") +AnnotationAssertion( "affects") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (developmentally succeeded by) + +AnnotationAssertion( ) +AnnotationAssertion( "Inverse of developmentally preceded by") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "developmentally succeeded by"@en) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, positive effect) + +AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs: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") +AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, negative effect) + +AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (characteristic of part of) + +AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") +AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "inheres in part of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "characteristic of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (evolutionarily related to) + +AnnotationAssertion( "A relationship that holds via some environmental process") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.") +AnnotationAssertion(rdfs:label "evolutionarily related to"@en) + +# Object Property: (mereotopologically related to) + +AnnotationAssertion( "A mereological relationship or a topological relationship") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mereotopologically related to"@en) + +# Object Property: (developmentally related to) + +AnnotationAssertion( "A relationship that holds between entities participating in some developmental process (GO:0032502)") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development") +AnnotationAssertion(rdfs:label "developmentally related to"@en) + +# Object Property: (enables) + +AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") +AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "catalyzes") +AnnotationAssertion( "executes") +AnnotationAssertion( "has") +AnnotationAssertion( "is catalyzing") +AnnotationAssertion( "is executing") +AnnotationAssertion( "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.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enables"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (functionally related to) + +AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") +AnnotationAssertion(rdfs:label "functionally related to"@en) + +# Object Property: (part of structure that is capable of) + +AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) +SubObjectPropertyOf( ) + +# Object Property: (involved in) + +AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "actively involved in") +AnnotationAssertion( "enables part of") +AnnotationAssertion(rdfs:label "involved in"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (enabled by) + +AnnotationAssertion( "inverse of enables") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enabled by"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (regulated by) + +AnnotationAssertion( "inverse of regulates") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "regulated by (processual)") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulated by"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulated by) + +AnnotationAssertion( "inverse of negatively regulates") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (positively regulated by) + +AnnotationAssertion( "inverse of positively regulates") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (input of) + +AnnotationAssertion( "inverse of has input") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "input of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has developmental potential involving) + +AnnotationAssertion( ) +AnnotationAssertion( "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)."@en) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "has developmental potential involving"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has potential to developmentally contribute to) + +AnnotationAssertion( ) +AnnotationAssertion( "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y"@en) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "has potential to developmentally contribute to"@en) +SubObjectPropertyOf( ) + +# Object Property: (has potential to develop into) + +AnnotationAssertion( ) +AnnotationAssertion( "x has the potential to develop into y iff x develops into y or if x is capable of developing into y"@en) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "has potential to develop into"@en) +SubObjectPropertyOf( ) + +# Object Property: (has potential to directly develop into) + +AnnotationAssertion( ) +AnnotationAssertion( "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y"@en) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "has potential to directly develop into"@en) +SubObjectPropertyOf( ) + +# Object Property: (causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of upstream of") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (indirectly positively regulates) + +AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "indirectly activates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (indirectly negatively regulates) + +AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "indirectly inhibits") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (causally related to) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") +AnnotationAssertion( "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. +To define causal relations in an activity-flow type network, we make use of 3 primitives: - + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? - - +The 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. +For 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. - +For 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. - +Each of these 3 primitives can be composed to yield a cross-product of different relation types.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causally related to"@en) + +# Object Property: (causally upstream of) + +AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately causally upstream of) + +AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within) + +AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") +AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "influences (processual)") +AnnotationAssertion( "affects") +AnnotationAssertion(rdfs:label "causally upstream of or within") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (causally downstream of or within) + +AnnotationAssertion( "inverse of causally upstream of or within") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally downstream of or within") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (involved in regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (involved in positive regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in positive regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in negative regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in negative regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in or involved in regulation of) + +AnnotationAssertion( "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") +AnnotationAssertion( "OWL does not allow defining object properties via a Union") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "involved in or reguates") +AnnotationAssertion(rdfs:label "involved in or involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (interacts with) + +AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion( "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.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "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.") +AnnotationAssertion( "in pairwise interaction with") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interacts with") +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) +SymmetricObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (molecularly interacts with) + +AnnotationAssertion( "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.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "binds") +AnnotationAssertion( "molecularly binds with") +AnnotationAssertion(rdfs:label "molecularly interacts with") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (phosphorylates) + +AnnotationAssertion( "Axiomatization to GO to be added later") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") +AnnotationAssertion(rdfs:label "phosphorylates") +SubObjectPropertyOf( ) + +# Object Property: (directly regulates activity of) + +AnnotationAssertion( "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. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion( "molecularly controls") +AnnotationAssertion(rdfs:label "directly regulates activity of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly negatively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion( "directly inhibits") +AnnotationAssertion( "molecularly decreases activity of") +AnnotationAssertion(rdfs:label "directly negatively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly positively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion( "directly activates") +AnnotationAssertion( "molecularly increases activity of") +AnnotationAssertion(rdfs:label "directly positively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (helper property (not for use in curation)) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") +AnnotationAssertion(rdfs:label "helper property (not for use in curation)") + +# Object Property: (is kinase activity) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "is kinase activity") +SubObjectPropertyOf( ) + +# Object Property: (causal agent in process) + +AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal agent in process") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causal relation between processes) + +AnnotationAssertion( "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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between processes") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (depends on) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "depends on") +AnnotationAssertion(rdfs:seeAlso ) + +# Object Property: (causal relation between entities) + +AnnotationAssertion( "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") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between entities") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causally influenced by) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "causally influenced by (entity-centric)") +AnnotationAssertion(rdfs:label "causally influenced by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (interaction relation helper property) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "interaction relation helper property") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (molecular interaction relation helper property) + +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "molecular interaction relation helper property") +SubObjectPropertyOf( ) + +# Object Property: (causally influences) + +AnnotationAssertion( "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).") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion( ) +AnnotationAssertion( "causally influences (entity-centric)") +AnnotationAssertion(rdfs:label "causally influences") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulates) + +AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion( "directly regulates (processual)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has part structure that is capable of) + +AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") +AnnotationAssertion( "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") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion(rdfs:label "has part structure that is capable of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causal relation between material entity and a process) + +AnnotationAssertion( "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.") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal relation between material entity and a process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of regulating) + +AnnotationAssertion( "pyrethroid -> growth") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of negatively regulating) + +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of negatively regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of positively regulating) + +AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of positively regulating") +SubObjectPropertyOf( ) + +# Object Property: (process has causal agent) + +AnnotationAssertion( "Inverse of 'causal agent in process'") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "process has causal agent") +SubObjectPropertyOf( ) + +# Object Property: (directly positively regulates) + +AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly positively regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (directly negatively regulates) + +AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly negatively regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (enables subfunction) + +AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "enables subfunction") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, positive effect) + +AnnotationAssertion( "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") +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, negative effect) + +AnnotationAssertion( "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") +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( "cjm") +AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +SubObjectPropertyOf( ) + +# Object Property: (regulates activity of) + +AnnotationAssertion( "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.") +AnnotationAssertion( "Vasundra Touré") +AnnotationAssertion(rdfs:label "regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (indirectly causally upstream of) + +AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) +SubObjectPropertyOf( ) + +# Object Property: (indirectly regulates) + +AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") +AnnotationAssertion( "pg") +AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (device utilizes material) + +AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") +AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") +AnnotationAssertion( "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion( "https://orcid.org/0000-0003-2620-0345") +AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") +AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "utilizes") +AnnotationAssertion(rdfs:label "device utilizes material"@en) +# Object Property: (regulates characteristic) - +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates characteristic") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) - - - - - 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.) +# Object Property: (positively regulates characteristic) -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 - - - - - - - - - - - - - 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) - 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 - - - - - has part - - - - - - - - - - - - - - - - - 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. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - 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. - - precedes - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - site of - [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 - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - 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. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - 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 - - - - - - - - - - dos - 2017-09-17T13:52:24Z - 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. - directly regulated by - - - - - 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. - GOC:dos - - - - - - - - - - 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. - dos - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - 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 - - - - - - - - - - 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. - dos - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - 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 - - - - - - - - - - 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 - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan - - - - Connects a biological entity to its taxon of origin. - in taxon - - - - - - - - - - - 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 - - - - - - - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan - This is the transitive form of the develops from relation - develops from - - - - - - - - - - - - - inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan - - develops into - - - - - - - - - - - - - - - - - - - - - - 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. - 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 - Chris Mungall - David Hill - Tanya Berardini - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - - - - regulates - - - - - - - - - - - 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. - Chris Mungall - - negatively regulates (process to process) - - - - - negatively regulates - - - - - - - - - - - - - - - - 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. - Chris Mungall - - positively regulates (process to process) - - - - - positively regulates - - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - 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. - Chris Mungall - has function realized 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)". - - capable of - - - - - - - - - - - - - - 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 - capable of part of - - - - - - - - - - true - - - - - - - - - - - Chris Mungall - - 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. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - - x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall - has developmental contribution from - - - - - - - - - - - - - - - inverse of has developmental contribution from - Chris Mungall - - developmentally contributes to - - - - - - - - - - - - - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false - Chris Mungall - In general you should not use this relation to make assertions - use one of the more specific relations below this one - This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - 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 - - - - - - - - - - - Inverse of developmentally preceded by - Chris Mungall - developmentally succeeded by - - - - - - - - - - - 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 - - - - - - - - - - - cjm - 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 - causally upstream of, negative effect - - - - - - - - A relationship that holds via some environmental process - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. - evolutionarily related to - - - - - - - - A mereological relationship or a topological relationship - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - mereotopologically related to - - - - - - - - A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development - developmentally related to - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - Chris Mungall - catalyzes - executes - has - is catalyzing - 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 - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall - This is a grouping relation that collects relations used for the purpose of connecting structure and function - functionally related to - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall - actively involved in - enables part of - involved in - - - - - - - - - - - inverse of enables - Chris Mungall - - enabled by - - - - - - - - - - - - inverse of regulates - Chris Mungall - regulated by (processual) - - regulated by - - - - - - - - - inverse of negatively regulates - Chris Mungall - - negatively regulated by - - - - - - - - - inverse of positively regulates - Chris Mungall - - positively regulated by - - - - - - - - - - inverse of has input - Chris Mungall - - - input of - - - - - - - - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall - has developmental potential involving - - - - - - - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall - has potential to developmentally contribute to - - - - - - - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall - has potential to develop into - - - - - - - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall - has potential to directly develop into - - - - - - - - - - - - inverse of upstream of - Chris Mungall - causally downstream of - - - - - - - - - - - - Chris Mungall - immediately causally downstream of - - - - - - - - - This relation groups causal relations between material entities and causal relations between processes - 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. +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulates characteristic") +SubObjectPropertyOf( ) -To define causal relations in an activity-flow type network, we make use of 3 primitives: +# Object Property: (negatively regulates characteristic) - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulates characteristic") +SubObjectPropertyOf( ) -The 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. -For 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. -For 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. +############################ +# Classes +############################ -Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causally related to - - - - - - - - - - - - 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 - - - - - - - - - - - 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. - Chris Mungall - - immediately causally upstream of - - - - - - - - - - - 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. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall - influences (processual) - affects - causally upstream of or within - - - - - - - - - - inverse of causally upstream of or within - Chris Mungall - - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall - - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall - - involved in negative regulation of - - - - - - - - - - - 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 - OWL does not allow defining object properties via a Union - Chris Mungall - involved in or reguates - involved in or involved in regulation of - - - - - - - - - - - - - - A protein that enables activity in a cytosol. - 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. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - 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 - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' - 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. - Chris Mungall - 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. - in pairwise interaction with - - interacts with - http://purl.obolibrary.org/obo/MI_0914 - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - - 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. - Chris Mungall - binds - molecularly binds with - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - Axiomatization to GO to be added later - Chris Mungall - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - phosphorylates - - - - - - - - - - - - - - - - - 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. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré - molecularly controls - directly regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré - directly inhibits - molecularly decreases activity of - directly negatively regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré - directly activates - molecularly increases activity of - directly positively regulates activity of - - - - - - - - Chris Mungall - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property (not for use in curation) - - - - - - - - - - - - - - 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 - - - - - - - - - Chris Mungall - is kinase activity - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - causal agent in process - - - - - - - - - - - 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. - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between processes - - - - - - - - - - - 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 - Chris Mungall - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between entities - - - - - - - - - - Chris Mungall - - causally influenced by (entity-centric) - causally influenced by - - - - - - - - - Chris Mungall - interaction relation helper property - - https://github.com/oborel/obo-relations/wiki/InteractionRelations - - - - - - - - - Chris Mungall - molecular interaction relation helper property - - - - - - - - - - - - - - - - - - - - - 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). - Chris Mungall - Vasundra Touré - - causally influences (entity-centric) - causally influences - - - - - - - - - - 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. - Chris Mungall - - directly regulates (processual) - - - - - directly regulates - - - - - - - - - - - - - - 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 - has part structure that is capable of - - - - - - - - - - - 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. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - capable of negatively regulating - - - - - - - - - - - - - renin -> arteriolar smooth muscle contraction - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - capable of positively regulating - - - - - - - - - Inverse of 'causal agent in process' - - process has causal agent - - - - - - - - - - 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. - - directly positively regulates (process to process) - - - - - directly positively regulates - - - - - - - - - - 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. - - directly negatively regulates (process to process) - - - - - directly negatively regulates - - - - - - - - - - - - - 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 - enables subfunction - - - - - - - - - - - - - - cjm - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - - - - - - - - - - - - - - - cjm - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect - - - - - - - - - - - - - - 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 - - cjm - 2018-01-26T23:53:14Z - - acts upstream of, positive effect - - - - - - - - - - - - - - - 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 - - cjm - 2018-01-26T23:53:22Z - - acts upstream of, negative effect - - - - - - - - - - - cjm - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect - - - - - - - - - - cjm - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect - - - - - - - - - - - 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. - Vasundra Touré - regulates activity of - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - independent continuant - - +# Class: (continuant) +AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) - +# Class: (occurrent) - - - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - process - - +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) +# Class: (independent continuant) - +AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - +# Class: (process) - - - - anatomical entity - - +AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) +# Class: (disposition) - +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) - - - - connected anatomical structure - - +# Class: (realizable entity) +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) - +# Class: (quality) - - - - - material anatomical entity - - +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +# Class: (specifically dependent continuant) - +AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) - - - organism or virus or viroid - - +# Class: (role) +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) - +# Class: (function) - - - biological entity - - +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) +# Class: (material entity) - +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) - - - molecular process - molecular_function - - +# Class: (anatomical entity) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "anatomical entity"@en) +SubClassOf( ) - +# Class: (organism or virus or viroid) - - - catalytic activity - - - - - - - - - - nucleus - - +AnnotationAssertion(rdfs:label "organism or virus or viroid") +SubClassOf( ) +# Class: (biological entity) - - - - - biological_process - - - - - - - - - - - - true - - - kinase activity - - - - - - - - - transferase activity - - - - - - - - - transferase activity, transferring phosphorus-containing groups - - - - - - - - - - cell part - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +AnnotationAssertion(rdfs:label "biological entity") +SubClassOf( ) +# Class: (molecular_function) + +AnnotationAssertion( "molecular process") +AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) + +# Class: (catalytic activity) + +AnnotationAssertion(rdfs:label "catalytic activity") +SubClassOf( ) + +# Class: (nucleus) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "nucleus"@en) + +# Class: (biological_process) + +AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) + +# Class: (kinase activity) + +AnnotationAssertion(rdfs:label "kinase activity") +SubClassOf( ) +SubClassOf( ObjectHasSelf()) + +# Class: (transferase activity) + +AnnotationAssertion(rdfs:label "transferase activity") +SubClassOf( ) + +# Class: (transferase activity, transferring phosphorus-containing groups) + +AnnotationAssertion(rdfs:label "transferase activity, transferring phosphorus-containing groups") +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion( "quality (PATO)") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + + +SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(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()))) +DLSafeRule(Annotation(rdfs:comment "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'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "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'"^^xsd:string) Annotation(rdfs:label "involved in BP"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "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.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(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()))) +DLSafeRule(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()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +) \ No newline at end of file diff --git a/src/ontology/imports/so_import.owl b/src/ontology/imports/so_import.owl index 3059a88..dbb9811 100644 --- a/src/ontology/imports/so_import.owl +++ b/src/ontology/imports/so_import.owl @@ -1,14 +1,26 @@ - - - - - - +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2023-02-19"^^xsd:string) + +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion(rdfs:label "has_broad_synonym") + + + +) \ No newline at end of file diff --git a/src/ontology/reports/chr-edit.owl-obo-report.tsv b/src/ontology/reports/chr-edit.owl-obo-report.tsv index c168f0d..2067cbe 100644 --- a/src/ontology/reports/chr-edit.owl-obo-report.tsv +++ b/src/ontology/reports/chr-edit.owl-obo-report.tsv @@ -946,32 +946,6 @@ WARN missing_definition chromosome IV (C elegans) IAO:0000115 WARN missing_definition chromosome M (C elegans) IAO:0000115 WARN missing_definition chromosome V (C elegans) IAO:0000115 WARN missing_definition chromosome X (C elegans) IAO:0000115 -WARN missing_definition chromosome 1 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 10 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 11 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 12 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 13 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 14 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 15 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 16 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 17 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 18 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 19 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 2 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 20 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 21 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 22 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 23 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 24 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 25 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 3 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 4 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 5 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 6 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 7 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 8 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome 9 (Danio rerio) IAO:0000115 -WARN missing_definition chromosome M (Danio rerio) IAO:0000115 WARN missing_definition chromosome 1 (Chicken) IAO:0000115 WARN missing_definition chromosome 10 (Chicken) IAO:0000115 WARN missing_definition 10cen (Chicken) IAO:0000115