diff --git a/CHANGES.md b/CHANGES.md index 637a7044..64bcb0f3 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,4 +1,90 @@ -* 2018-10-22 +## 2019-02-01 + +commit 6cc55ce8da94d380dadd7fd1f8f5f4c090bb83ad +Author: Jim Balhoff +Date: Thu Jan 31 09:53:31 2019 -0800 + + Roll back disjointness axiom in favor of SWRL rule. + +commit 689aa13a6c5c76d88a6f9e489d88f5da6a9eeef2 +Author: Jim Balhoff +Date: Thu Jan 31 09:51:47 2019 -0800 + + Make ‘causally downstream of’ also “disjoint” with overlaps. + +commit 2678ffea0d099151139562b47ba5cb542477b638 +Author: Jim Balhoff +Date: Thu Jan 31 09:45:59 2019 -0800 + + Convert disjoint properties to SWRL rule. + +commit 6886116c792b18adc01d31169104558aed39125c (origin/issue-298, issue-298) +Author: cmungall +Date: Thu Jan 17 20:26:17 2019 -0800 + + use odk robot + +commit 87c473aca97d89961e9b3567dba96f5406e78baa +Author: cmungall +Date: Wed Jan 16 13:54:55 2019 -0800 + + removing incorrect subPropertyOf, fixes #298 + +commit 0a1c6d318259e336e1659e613597986ac09fa558 +Author: Jim Balhoff +Date: Mon Dec 17 09:59:31 2018 -0500 + + Correct ‘directly develops from’ definition error. Fixes #292. + +commit d1b3b285d574431d06ffc5af908884bb0b8059f2 +Author: cmungall +Date: Thu Dec 13 12:31:10 2018 +0100 + + making enabled_by a subprop of has participant, fixes #249 + +commit eb0579c4c6d887803942a2cd0657561440c7f6d1 +Author: cmungall +Date: Thu Dec 13 12:29:31 2018 +0100 + + First pass at more specific has-input relations + See also #230 #244 + +commit f329dcf948b62042c80741c798e45f3b7263179e +Author: cmungall +Date: Tue Oct 23 09:32:18 2018 -0700 + + Added curator notes to grouping relations + Added property chain for disease-causes-dysfunction-of + Additional domain/range constraints + +commit 2d7a472622d93a75e5caebf3d94206935bb08fcd +Author: cmungall +Date: Tue Oct 23 08:16:29 2018 -0700 + + Adding more D+R constraints, adding irreflexivity axioms + +commit 3a0e8a9eab11323551695216b37925536c6a9c03 +Author: Chris Mungall +Date: Mon Oct 22 19:39:36 2018 -0700 + + Update README-editors.md + + Updated with more standard docs from ODK + +commit b3d0a62afb49e282ae0c97a416eb3a31e3616f72 +Author: cmungall +Date: Mon Oct 22 18:01:20 2018 -0700 + + updating docs + +commit 986574b436d47d9fd4e865afe81a50c08dd5eaae (tag: v2018-10-22) +Author: cmungall +Date: Mon Oct 22 17:53:26 2018 -0700 + + Adding missing imports + + +## 2018-10-22 Maintenance release - including missing file @@ -10,7 +96,7 @@ Date: Mon Oct 22 17:42:18 2018 -0700 -* 2018-10-19 +## 2018-10-19 This release contains stronger domain and range constraints for various relations. @@ -278,7 +364,7 @@ Date: Tue May 22 18:06:41 2018 +0100 -* 2017-07-19 Release +## 2017-07-19 Release commit 48d076312637419ed24dc77843b7dc84cfd33fcf Merge: 67d2257 3b74b3a @@ -345,7 +431,7 @@ Date: Fri Jun 30 13:30:46 2017 -0700 added exacerbates condition, consition exacerbated by, condition aameliorated by, and changed label of is preventative for condition to ameliorates condition. also made minor updates to text of definitions for causes or contributes to condition relations, as noted in #149 -* 2017-06-15 Release +## 2017-06-15 Release commit 7bf8fa406e90c8a849dd4acf65b3cd5f8b82e381 Author: Chris Mungall @@ -436,7 +522,7 @@ Date: Mon Jun 5 10:52:54 2017 -0700 gitowl ++ AnnotationAssertion(oboInOwl:created_by obo:RO_0002309 "cjm"^^xsd:string) gitowl || created_by "cjm"^^string -* 2017-05-29 Release +## 2017-05-29 Release commit https://github.com/oborel/obo-relations/commit/dd541eb02d08ab6e8a72c2c7fbcbe5db237fe444 Author: Chris Mungall diff --git a/generated-axioms.owl b/generated-axioms.owl index 1525959d..879f8439 100644 --- a/generated-axioms.owl +++ b/generated-axioms.owl @@ -1,8 +1,8 @@ @@ -148,5 +148,5 @@ - + diff --git a/ro-base.json b/ro-base.json index 2bc9998a..a1c12d86 100644 --- a/ro-base.json +++ b/ro-base.json @@ -146,7 +146,11 @@ "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", "xrefs" : [ ] - } + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] }, "type" : "PROPERTY", "lbl" : "attached to part of" @@ -1452,6 +1456,11 @@ "xrefs" : [ ] }, "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element", + "xrefs" : [ ] + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" @@ -1470,7 +1479,7 @@ } ] }, "type" : "PROPERTY", - "lbl" : "has fused element" + "lbl" : "derived from ancestral fusion of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", "meta" : { @@ -1852,6 +1861,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] @@ -2269,6 +2281,9 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002001", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { @@ -4183,16 +4198,13 @@ "basicPropertyValues" : [ { "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." - }, { - "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", - "lbl" : "helper property" + "lbl" : "helper property (not for use in curation)" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002585", "meta" : { @@ -4447,10 +4459,11 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - } ] + } ], + "deprecated" : true }, "type" : "PROPERTY", - "lbl" : "has active participant" + "lbl" : "obsolete has active participant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003306", "meta" : { @@ -4703,6 +4716,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" @@ -4879,6 +4895,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" } ] }, "type" : "PROPERTY", @@ -4893,6 +4912,9 @@ "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 a grouping relation." } ] }, "type" : "PROPERTY", @@ -5263,6 +5285,30 @@ }, "type" : "PROPERTY", "lbl" : "is direct form of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040042", + "meta" : { + "definition" : { + "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.", + "xrefs" : [ ] + }, + "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-10-21T19:46:34Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/164" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part-of is homeomorphic for independent continuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is homeomorphic for" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", "meta" : { @@ -5438,7 +5484,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002207", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y", + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", "xrefs" : [ ] }, "comments" : [ "TODO - add child relations from DOS" ], @@ -5467,6 +5513,10 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002328", "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.", + "xrefs" : [ ] + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -5902,6 +5952,26 @@ }, "type" : "PROPERTY", "lbl" : "symbiotically interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040035", + "meta" : { + "definition" : { + "val" : "This relation groups relations between diseases and any other kind of entity.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "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, in which the subject or object is a disease." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T00:00:32Z" + } ] + }, + "type" : "PROPERTY", + "lbl" : "disease relationship" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002561", "meta" : { @@ -5954,6 +6024,23 @@ }, "type" : "PROPERTY", "lbl" : "commensually interacts with" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "meta" : { + "definition" : { + "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T01:08:58Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has anatomical participant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002562", "meta" : { @@ -5977,6 +6064,9 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -6374,6 +6464,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -6580,6 +6673,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "involved in or reguates" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" } ] }, "type" : "PROPERTY", @@ -8337,6 +8433,12 @@ "lbl" : "has model" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + }, "type" : "PROPERTY", "lbl" : "related via evidence or inference to" }, { @@ -8986,10 +9088,68 @@ "basicPropertyValues" : [ { "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." + } ], + "deprecated" : true + }, + "type" : "PROPERTY", + "lbl" : "obsolete related via dependence to" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "meta" : { + "definition" : { + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Molecules of DNA are carriers of genetic information." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This hard drive is carrier of these data items." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This copy of *War and Peace* is carrier of the novel written by Tolstoy." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is carrier of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "meta" : { + "definition" : { + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.", + "xrefs" : [ ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "g-depends on", + "xrefs" : [ ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Genetic information generically depend on molecules of DNA." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The pattern shared by chess boards generically depends on any chess board." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This pdf file generically depends on this server." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The novel *War and Peace* generically depends on this copy of the novel." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The score of a symphony g-depends on a copy of the score." } ] }, "type" : "PROPERTY", - "lbl" : "related via dependence to" + "lbl" : "generically depends on" }, { "id" : "http://purl.obolibrary.org/obo/RO_HOM0000017", "meta" : { @@ -9776,8 +9936,17 @@ "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] } ], "basicPropertyValues" : [ { + "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_0000002" + }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add homeomorphy axiom" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" @@ -10690,6 +10859,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "part_of" + }, { + "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_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "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)" @@ -10699,12 +10877,21 @@ }, { "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/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { "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_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { "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'." @@ -10717,6 +10904,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "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." @@ -10968,7 +11158,8 @@ }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000060", "meta" : { - "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ] + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true }, "type" : "PROPERTY", "lbl" : "obsolete preceded by" @@ -11357,7 +11548,7 @@ } }, "type" : "PROPERTY", - "lbl" : "co-occurs" + "lbl" : "ecologically co-occurs with" }, { "id" : "http://purl.obolibrary.org/obo/RO_0008505", "meta" : { @@ -11428,6 +11619,10 @@ }, "type" : "CLASS", "lbl" : "obsolete dependent continuant" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000006", + "type" : "CLASS", + "lbl" : "spatial region" }, { "id" : "http://purl.obolibrary.org/obo/RO_0008504", "meta" : { @@ -11439,22 +11634,13 @@ }, "type" : "PROPERTY", "lbl" : "kleptoparasitized by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002088", - "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, - "type" : "PROPERTY", - "lbl" : "during which starts" }, { "id" : "http://purl.obolibrary.org/obo/RO_0004025", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" }, { @@ -11464,6 +11650,18 @@ }, "type" : "PROPERTY", "lbl" : "disease causes dysfunction of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + } ] + }, + "type" : "PROPERTY", + "lbl" : "during which starts" }, { "id" : "http://purl.obolibrary.org/obo/RO_0008503", "meta" : { @@ -11491,6 +11689,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" } ] }, "type" : "PROPERTY", @@ -11581,6 +11782,9 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:37:52Z" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" @@ -11622,6 +11826,9 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:29:32Z" }, { @@ -11640,9 +11847,6 @@ }, { "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 of which have a disease as the subject." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "After import upper level from OGMS, make domain more specific." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:50:54Z" @@ -11900,6 +12104,23 @@ }, "type" : "PROPERTY", "lbl" : "is causal gain of function germline mutation of in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004007", + "meta" : { + "definition" : { + "val" : "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has primary input or output" }, { "id" : "http://purl.obolibrary.org/obo/RO_0004006", "meta" : { @@ -11913,6 +12134,40 @@ }, "type" : "PROPERTY", "lbl" : "has partial material basis in germline mutation in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004009", + "meta" : { + "definition" : { + "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has primary input" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004008", + "meta" : { + "definition" : { + "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has primary output" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", "type" : "CLASS", @@ -12188,10 +12443,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002436", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002434" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002299", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002200", "pred" : "subPropertyOf", @@ -12224,6 +12475,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002083", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002081" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004007", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002334", "pred" : "subPropertyOf", @@ -12288,6 +12543,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002453", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002374", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002156" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002522", "pred" : "subPropertyOf", @@ -12296,10 +12555,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002584", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002595" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002585", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000141", "pred" : "is_a", @@ -12352,6 +12607,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004005", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0010001", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0010002" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002451", "pred" : "subPropertyOf", @@ -12420,10 +12679,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002120", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000302" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004029", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004023" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002338", "pred" : "subPropertyOf", @@ -12440,10 +12695,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002356", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002295" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002410", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002609" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002206", "pred" : "subPropertyOf", @@ -12528,6 +12779,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002106", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002112" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004029", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040035" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002437", "pred" : "subPropertyOf", @@ -12680,6 +12935,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002333", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002299", "pred" : "subPropertyOf", @@ -12776,10 +13035,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002315", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002105", "pred" : "inverseOf", @@ -12808,6 +13063,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002209", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004026", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040035" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004010", "pred" : "subPropertyOf", @@ -12896,14 +13155,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000056", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002630", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002212" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002331", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002217" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002630", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002212" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002509", "pred" : "subPropertyOf", @@ -12952,6 +13211,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002406", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002629" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002315", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002466", "pred" : "subPropertyOf", @@ -13248,10 +13511,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002229", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002230" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002592", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002533", "pred" : "is_a", @@ -13420,6 +13679,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004031", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002460", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002134", "pred" : "subPropertyOf", @@ -13428,6 +13691,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002101", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002592", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002439", "pred" : "inverseOf", @@ -13580,6 +13847,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002468", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002465" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002313", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002589", "pred" : "subPropertyOf", @@ -13640,6 +13911,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000075", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000006", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002211", "pred" : "subPropertyOf", @@ -13760,6 +14035,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002350", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002351" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004009", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002624", "pred" : "inverseOf", @@ -13813,13 +14092,13 @@ "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002627" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002530", + "sub" : "http://purl.obolibrary.org/obo/RO_0004008", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002515" + "obj" : "http://purl.obolibrary.org/obo/RO_0002234" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002610", + "sub" : "http://purl.obolibrary.org/obo/RO_0002530", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002609" + "obj" : "http://purl.obolibrary.org/obo/RO_0002515" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004030", "pred" : "subPropertyOf", @@ -13828,10 +14107,18 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000081", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000087" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002299", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000069", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004023", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040035" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008501", "pred" : "inverseOf", @@ -13856,10 +14143,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002373", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002567" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002460", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002459" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002264", "pred" : "subPropertyOf", @@ -13872,10 +14155,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000081", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000052" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002403", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002234" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", "pred" : "subPropertyOf", @@ -13900,10 +14179,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002219", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002221" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002296", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000025", "pred" : "subPropertyOf", @@ -14088,10 +14363,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002624", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002618" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002355", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "inverseOf", @@ -14112,10 +14383,18 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002618", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002585", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002623", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004008", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", @@ -14320,6 +14599,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002296", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002341", "pred" : "subPropertyOf", @@ -14416,6 +14699,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0009005", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0009001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0040036", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002243", "pred" : "subPropertyOf", @@ -14436,6 +14723,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000087", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002355", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002256", "pred" : "subPropertyOf", @@ -14452,10 +14743,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002570", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002343", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002636", "pred" : "inverseOf", @@ -14464,10 +14751,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002371", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002552", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002237", "pred" : "subPropertyOf", @@ -14508,10 +14791,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002640", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002634" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002565", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002342", "pred" : "subPropertyOf", @@ -14668,10 +14947,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002448", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002566" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002298", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002518", "pred" : "inverseOf", @@ -14692,10 +14967,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002515", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002527" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002374", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002320" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002104", "pred" : "subPropertyOf", @@ -14820,10 +15091,18 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002091", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002222" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002512", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002513" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000032", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000029" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002343", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002110", "pred" : "subPropertyOf", @@ -14848,6 +15127,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002552", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002208", "pred" : "inverseOf", @@ -14860,10 +15143,18 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004002", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004009", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002233" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002223", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002565", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000086", "pred" : "subPropertyOf", @@ -14872,10 +15163,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004014", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004010" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004026", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004023" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002257", "pred" : "subPropertyOf", @@ -14896,14 +15183,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002226", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002258" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002313", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002596", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002298", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002556", "pred" : "inverseOf", @@ -15009,13 +15296,19 @@ "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13]" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2]" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" @@ -15030,6 +15323,14 @@ "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009001", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002176", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { @@ -15039,17 +15340,36 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002572", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002452", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002573", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002574", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002332", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002179", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/CARO_0000006", + "pred" : "http://purl.obolibrary.org/obo/RO_0002179", + "obj" : "http://purl.obolibrary.org/obo/CARO_0000003" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002295", "domainClassIds" : [ "http://purl.obolibrary.org/obo/GO_0008150" ], @@ -15058,13 +15378,52 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002570", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0009003", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002571", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000300", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -15077,6 +15436,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002325", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002567", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002205", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -15089,12 +15452,23 @@ "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002200", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UPHENO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002322", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002437", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -15105,7 +15479,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002315", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -15114,6 +15488,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0003001", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -15135,7 +15513,7 @@ "rangeClassIds" : [ "http://xmlns.com/foaf/0.1/image" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002303", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/ENVO_01000254" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000085", @@ -15145,6 +15523,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000087", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002384", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000086", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] @@ -15154,14 +15536,33 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/R0_0009004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "pred" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002018", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -15190,8 +15591,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002254", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002375", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], @@ -15203,29 +15604,64 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002256", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002372", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002010", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002373", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002009", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004029", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001001" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002007", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0008505", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002121", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004027", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002244", "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002310" ] @@ -15239,16 +15675,20 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004026", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004023", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004022", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002514", "domainClassIds" : [ "http://purl.obolibrary.org/obo/RO_0002532" ], @@ -15265,6 +15705,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002356", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] @@ -15274,7 +15718,11 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004019", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002473", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001021", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] @@ -15285,6 +15733,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001022", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002111", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002232", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -15328,9 +15780,13 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002506", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002501", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -15352,7 +15808,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002222", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -15374,6 +15831,17 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002334", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002214", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002214", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/RO_0002214", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002215", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -15533,6 +16001,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002162" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000059", "http://purl.obolibrary.org/obo/RO_0000053" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] @@ -15563,6 +16034,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0009501", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000054", "http://purl.obolibrary.org/obo/RO_0002404" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0010001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/RO_0000058" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002314", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -15686,6 +16160,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002406", "http://purl.obolibrary.org/obo/RO_0002406" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "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" ] diff --git a/ro-base.obo b/ro-base.obo index 25695e10..1b2f03f5 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -4,9 +4,11 @@ subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 53 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 278 Logical Axioms: 58] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] ontology: ro/ro-base @@ -14,18 +16,23 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (is model of)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000002 ! part of continuant +relationship: RO:0002214 BFO:0000002 ! has prototype continuant +relationship: RO:HOM0000000 BFO:0000002 ! continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: BFO:0000050 BFO:0000003 ! part of occurrent +relationship: RO:HOM0000000 BFO:0000003 ! occurrent [Term] id: BFO:0000004 @@ -34,6 +41,7 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000004 ! part of independent continuant [Term] id: BFO:0000005 @@ -42,11 +50,17 @@ def: "A continuant that is either dependent on one or other independent continu is_a: ObsoleteClass ! Obsolete Class is_obsolete: true +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + [Term] id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] is_a: BFO:0000003 ! occurrent +relationship: RO:0002214 BFO:0000015 ! has prototype process [Term] id: BFO:0000016 @@ -60,11 +74,13 @@ 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: BFO:0000050 BFO:0000017 ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000019 ! part of quality [Term] id: BFO:0000020 @@ -72,6 +88,7 @@ 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 disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -84,6 +101,7 @@ id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] is_a: BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -102,6 +120,10 @@ id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant +[Term] +id: CARO:0000006 +relationship: RO:0002179 CARO:0000003 ! drains + [Term] id: GO:0004842 @@ -182,6 +204,13 @@ property_value: IAO:0000116 "Occurrents are not subject to change and so parthoo 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 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string @@ -239,6 +268,7 @@ id: BFO:0000060 name: obsolete preceded by comment: accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062 is_transitive: true +is_obsolete: true [Typedef] id: BFO:0000062 @@ -303,6 +333,8 @@ def: "'has consumer' is a relation between a material entity and an organism in property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: CARO:0001010 [Typedef] id: RO:0000052 @@ -468,6 +500,8 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (neural_circuit_path ?x ?y)\n (and\n (\"neuron ; CL_0000540\" ?x)\n (\"neuron ; CL_0000540\" ?y)\n (or \n (synapsed_by ?x ?y) \n (synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n (iff \n (neural_circuit_path ...s ?x ?y ?z)\n (and\n (neural_circuit_path ...s ?x ?y)\n (\"neuron ; CL_0000540\" ?z)\n (or \n (synapsed_by ?y ?z) \n (synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n (iff \n (in_neural_circuit_with ?x ?y)\n (exists (...s)\n (neural_circuit_path ?x ...s ?y)))) " xsd:string property_value: RO:0001900 RO:0001901 +domain: CL:0000540 +range: CL:0000540 is_transitive: true [Typedef] @@ -597,6 +631,8 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations 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:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant is_transitive: true [Typedef] @@ -618,6 +654,7 @@ inverse_of: RO:0002002 ! has 2D boundary id: RO:0002001 name: aligned with property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true @@ -650,6 +687,8 @@ id: RO:0002004 name: tracheates def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: RO:0001018 ! contained in [Typedef] @@ -657,6 +696,8 @@ id: RO:0002005 name: innervated_by property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +domain: CARO:0000003 +range: CARO:0001001 inverse_of: RO:0002134 ! innervates [Typedef] @@ -771,6 +812,8 @@ creation_date: 2017-05-24T09:44:33Z id: RO:0002018 name: has component process def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process is_a: RO:0002180 ! has component created_by: dos creation_date: 2017-05-24T09:49:21Z @@ -984,6 +1027,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: RO:0001900 RO:0001901 domain: CL:0000540 +range: CARO:0000003 is_a: RO:0002131 ! overlaps transitive_over: BFO:0000050 ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] @@ -1042,6 +1086,8 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "Lindsay Cowell" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 +domain: CARO:0000006 +range: CARO:0000006 is_a: BFO:0000051 ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -1131,6 +1177,8 @@ id: RO:0002111 name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 +range: BFO:0000040 ! material entity [Typedef] id: RO:0002112 @@ -1347,7 +1395,7 @@ property_value: IAO:0000117 "Jennifer Deegan" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: BFO:0000004 ! independent continuant +range: CARO:0001010 holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: results_in_developmental_progression_of RO:0002162 @@ -1401,8 +1449,9 @@ is_a: RO:0002323 ! mereotopologically related to id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 +range: CARO:0000003 holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -1442,7 +1491,7 @@ def: "A relationship that holds between a biological entity and a phenotype. Her subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000002 ! continuant +range: UPHENO:0001001 inverse_of: RO:0002201 ! phenotype of [Typedef] @@ -1519,7 +1568,7 @@ property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string domain: BFO:0000002 ! continuant -range: BFO:0000004 ! independent continuant +range: CARO:0000006 is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses transitive_over: BFO:0000050 ! part of @@ -1527,7 +1576,7 @@ transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002207 name: directly develops from -def: "Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y" [] +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1620,6 +1669,7 @@ property_value: IAO:0000112 "heart SubClassOf 'has prototype' some ('participate property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string +property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string [Typedef] @@ -1646,6 +1696,7 @@ 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" holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -1658,11 +1709,11 @@ def: "x actively participates in y if and only if x participates in y and x real property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "agent in" xsd:string is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 ! has active participant +inverse_of: RO:0002218 ! obsolete has active participant [Typedef] id: RO:0002218 -name: has active participant +name: obsolete has active participant def: "x has participant y if and only if x realizes some active role that inheres in y" [] subset: ro-eco property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string @@ -1671,6 +1722,7 @@ property_value: IAO:0000116 "This may be obsoleted and replaced by the original property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: RO:0000057 ! has participant +is_obsolete: true [Typedef] id: RO:0002219 @@ -1763,7 +1815,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000003 +domain: CARO:0000000 holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by @@ -1927,6 +1979,8 @@ def: "A relationship that holds between a substance and a chemical entity, if th synonym: "has active pharmaceutical ingredient" RELATED [] synonym: "has active substance" EXACT [] property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part inverse_of: RO:0002249 ! active ingredient in' @@ -1958,8 +2012,8 @@ def: "x has developmental contribution from y iff x has some part z such that z property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000004 ! independent continuant -range: CARO:0000003 +domain: CARO:0000000 +range: CARO:0000000 holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -2135,7 +2189,7 @@ property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Pier Buttigieg" xsd:string property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0000006 +domain: CARO:0001010 range: ENVO:01000254 is_a: RO:0002321 ! ecologically related to @@ -2180,8 +2234,8 @@ name: transports or maintains localization of def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "regulates localization of" xsd:string -is_a: RO:0000057 ! has participant is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! has anatomical participant transitive_over: BFO:0000051 ! has part [Typedef] @@ -2192,6 +2246,7 @@ property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub- property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 +property_value: seeAlso "defining-property-chains-involving-reflexivity" holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -2208,6 +2263,7 @@ id: RO:0002321 name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" 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 ecological interactions" xsd:string @@ -2218,6 +2274,7 @@ subset: ro-eco property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 is_a: RO:0002321 ! ecologically related to [Typedef] @@ -2281,6 +2338,7 @@ transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string @@ -2323,6 +2381,8 @@ property_value: IAO:0000112 "every cellular sphingolipid homeostasis process reg property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity is_a: RO:0002328 ! functionally related to [Typedef] @@ -2330,6 +2390,7 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to [Typedef] @@ -2365,6 +2426,7 @@ id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -2413,7 +2475,7 @@ name: results in growth of property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002344 @@ -2500,7 +2562,7 @@ name: results in structural organization of def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002356 @@ -2531,6 +2593,7 @@ name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to is_a: RO:0002177 ! attached to part of @@ -2542,6 +2605,7 @@ def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -2552,20 +2616,22 @@ def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that w property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to [Typedef] id: RO:0002374 -name: has fused element +name: derived from ancestral fusion of def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. +synonym: "has fused element" BROAD [] property_value: IAO:0000112 "false" xsd:boolean property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -is_a: RO:0002320 ! evolutionarily related to +is_a: RO:0002156 ! derived by descent from [Typedef] id: RO:0002375 @@ -2682,6 +2748,8 @@ name: has developmental potential involving def: "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)." [] property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: CARO:0000000 +range: CARO:0000000 is_a: RO:0002324 ! developmentally related to [Typedef] @@ -2753,7 +2821,6 @@ comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string holds_over_chain: RO:0002411 RO:0002402 -is_a: RO:0002234 ! has output is_obsolete: true [Typedef] @@ -2830,7 +2897,6 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002411 @@ -2955,6 +3021,7 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within @@ -3188,6 +3255,7 @@ id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: OGMS:0000031 is_a: RO:0002200 ! has phenotype [Typedef] @@ -3265,7 +3333,7 @@ id: RO:0002460 name: has vector subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002459 ! is vector for +is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 @@ -3290,8 +3358,7 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 -name: helper property -property_value: IAO:0000114 IAO:0000428 +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 @@ -3361,6 +3428,8 @@ property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part [Typedef] @@ -3658,6 +3727,7 @@ def: "x is the ribosomal translation of y if and only if a ribosome reads x thro property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to +inverse_of: RO:0002513 ! ribosomally translates to [Typedef] id: RO:0002513 @@ -3878,8 +3948,11 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string +domain: CARO:0000003 +range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true [Typedef] id: RO:0002552 @@ -3887,7 +3960,7 @@ name: results in ending of def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] property_value: IAO:0000117 "Chris Mungall" xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002553 @@ -3968,7 +4041,7 @@ 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 -is_a: RO:0002464 ! helper property +is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 @@ -3982,7 +4055,7 @@ name: results in movement of def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "" xsd:string -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002566 @@ -3999,6 +4072,8 @@ name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 +range: CARO:0000003 is_a: RO:0002328 ! functionally related to [Typedef] @@ -4058,6 +4133,7 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! specifically dependent continuant [Typedef] id: RO:0002574 @@ -4065,6 +4141,8 @@ name: participates in a biotic-biotic interaction with subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 +range: CARO:0001010 is_a: RO:0002437 ! biotically interacts with [Typedef] @@ -4109,7 +4187,7 @@ id: RO:0002585 name: results in closure of property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002586 @@ -4150,7 +4228,7 @@ is_a: RO:0002592 ! results in organization of id: RO:0002592 name: results in organization of def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: RO:0002593 @@ -4239,16 +4317,16 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002609 -name: related via dependence to +name: obsolete related via dependence to def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] 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 +is_obsolete: true [Typedef] id: RO:0002610 name: correlated with def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string -is_a: RO:0002609 ! related via dependence to [Typedef] id: RO:0002614 @@ -4267,6 +4345,7 @@ inverse_of: RO:0003301 ! is model of [Typedef] id: RO:0002616 name: related via evidence or inference to +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string [Typedef] id: RO:0002618 @@ -4452,6 +4531,7 @@ def: "Relation between a research artifact and an entity it is used to study, in comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string property_value: IAO:0000117 "Matthew Brush" xsd:string +is_asymmetric: true [Typedef] id: RO:0003302 @@ -4582,6 +4662,32 @@ inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to created_by: cjm creation_date: 2017-11-05T02:46:57Z +[Typedef] +id: RO:0004007 +name: has primary input or output +def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] +is_a: RO:0000057 ! has participant +created_by: cjm +creation_date: 2018-12-13T11:26:17Z + +[Typedef] +id: RO:0004008 +name: has primary output +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +is_a: RO:0002234 ! has output +is_a: RO:0004007 ! has primary input or output +created_by: cjm +creation_date: 2018-12-13T11:26:32Z + +[Typedef] +id: RO:0004009 +name: has primary input +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +is_a: RO:0002233 ! has input +is_a: RO:0004007 ! has primary input or output +created_by: cjm +creation_date: 2018-12-13T11:26:56Z + [Typedef] id: RO:0004010 name: is genetic basis for condition @@ -4663,7 +4769,7 @@ creation_date: 2017-11-05T03:20:29Z [Typedef] id: RO:0004019 name: disease has basis in -domain: BFO:0000016 ! disposition +domain: OGMS:0000031 is_a: RO:0004017 ! realizable has basis in is_a: RO:0004023 ! causal relationship with disease as subject created_by: cjm @@ -4673,7 +4779,8 @@ creation_date: 2017-11-05T03:26:47Z id: RO:0004020 name: disease has basis in dysfunction of def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] -range: BFO:0000040 ! material entity +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 is_a: RO:0004019 ! disease has basis in created_by: cjm creation_date: 2017-11-05T03:29:32Z @@ -4682,6 +4789,7 @@ creation_date: 2017-11-05T03:29:32Z id: RO:0004021 name: disease has basis in disruption of def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string range: BFO:0000015 ! process is_a: RO:0004019 ! disease has basis in created_by: cjm @@ -4691,6 +4799,7 @@ creation_date: 2017-11-05T03:37:52Z id: RO:0004022 name: disease has basis in feature def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] +domain: OGMS:0000031 is_a: RO:0002200 ! has phenotype is_a: RO:0004019 ! disease has basis in created_by: cjm @@ -4699,10 +4808,10 @@ creation_date: 2017-11-05T03:46:07Z [Typedef] id: RO:0004023 name: causal relationship with disease as subject -property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." 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 of which have a disease as the subject." xsd:string -domain: BFO:0000016 ! disposition +domain: OGMS:0000031 is_a: RO:0002410 ! causally related to +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-11-05T03:50:54Z @@ -4710,7 +4819,10 @@ creation_date: 2017-11-05T03:50:54Z id: RO:0004024 name: disease causes disruption of def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 range: BFO:0000015 ! process +holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: cjm @@ -4719,7 +4831,9 @@ creation_date: 2017-11-05T03:51:09Z [Typedef] id: RO:0004025 name: disease causes dysfunction of -range: BFO:0000004 ! independent continuant +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 +range: CARO:0000006 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: cjm @@ -4731,8 +4845,9 @@ name: disease has location def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 range: BFO:0000004 ! independent continuant -is_a: RO:0004023 ! causal relationship with disease as subject +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-11-05T04:06:02Z @@ -4740,6 +4855,8 @@ creation_date: 2017-11-05T04:06:02Z id: RO:0004027 name: disease has inflammation site def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] +domain: OGMS:0000031 +range: CARO:0000003 is_a: RO:0004026 ! disease has location created_by: cjm creation_date: 2017-12-26T19:37:31Z @@ -4759,7 +4876,8 @@ creation_date: 2017-12-26T19:45:49Z id: RO:0004029 name: disease has feature def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] -is_a: RO:0004023 ! causal relationship with disease as subject +domain: OGMS:0000031 +is_a: RO:0040035 ! disease relationship created_by: cjm creation_date: 2017-12-26T19:50:53Z @@ -4874,12 +4992,16 @@ is_a: RO:0002445 ! parasitized by id: RO:0008505 name: creates habitat for def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] +domain: CARO:0001010 +range: CARO:0001010 is_a: RO:0002321 ! ecologically related to [Typedef] id: RO:0008506 -name: co-occurs +name: ecologically co-occurs with def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +domain: CARO:0001010 +range: CARO:0001010 is_symmetric: true is_a: RO:0002321 ! ecologically related to @@ -4904,6 +5026,8 @@ property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xs property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009002 @@ -4912,6 +5036,8 @@ def: "\"has substance removed\" is a relation existing between two physical enti property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009003 @@ -4920,6 +5046,8 @@ def: "\"immersed in\" is a relation between a (physical) entity and a fluid subs property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity [Typedef] id: RO:0009005 @@ -4948,6 +5076,50 @@ range: BFO:0000015 ! process holds_over_chain: BFO:0000054 RO:0002404 is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + +[Typedef] +id: RO:0040035 +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: cjm +creation_date: 2018-09-26T00:00:32Z + +[Typedef] +id: RO:0040036 +name: has anatomical participant +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +is_a: RO:0000057 ! has participant +created_by: cjm +creation_date: 2018-09-26T01:08:58Z + [Typedef] id: RO:HOM0000000 name: in similarity relationship with @@ -4960,6 +5132,9 @@ xref: ECO:0000041 xref: SO:similar_to property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: IAO:0000116 "TODO: Add homeomorphy axiom" xsd:string +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 property_value: seeAlso HOM:0000000 is_symmetric: true @@ -5801,9 +5976,9 @@ def: "The relationship that links a specified entity with the process that resul property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string -range: CL:0000000 +range: CARO:0000003 is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_development_of @@ -5814,7 +5989,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_developmental_progression_of @@ -5859,7 +6034,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant [Typedef] id: results_in_morphogenesis_of @@ -5871,5 +6046,5 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: results_in_developmental_progression_of ! results in developmental progression of -is_a: RO:0000057 ! has participant +is_a: RO:0040036 ! has anatomical participant diff --git a/ro-base.owl b/ro-base.owl index c4cc98ee..df462a23 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -1,35 +1,36 @@ + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. + + OBO Relations Ontology + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 7] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>) VersionIRI(<null>))) [Axioms: 146 Logical Axioms: 45] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl>) VersionIRI(<null>))) [Axioms: 56 Logical Axioms: 13] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>) VersionIRI(<null>))) [Axioms: 6 Logical Axioms: 2] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/chemical.owl>) VersionIRI(<null>))) [Axioms: 9 Logical Axioms: 3] - Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] - https://github.com/oborel/obo-relations/ Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/core.owl>) VersionIRI(<null>))) [Axioms: 291 Logical Axioms: 62] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>) VersionIRI(<null>))) [Axioms: 6 Logical Axioms: 2] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/generated-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 9] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/rohom.owl>) VersionIRI(<null>))) [Axioms: 731 Logical Axioms: 148] - Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] - - OBO Relations Ontology + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>) VersionIRI(<null>))) [Axioms: 146 Logical Axioms: 45] + https://github.com/oborel/obo-relations/ @@ -739,6 +740,21 @@ Where we have an annotation assertion + + + + part-of is homeomorphic for independent continuants. + R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. + cjm + 2018-10-21T19:46:34Z + R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. + is homeomorphic for + + + + + + @@ -931,6 +947,13 @@ Where we have an annotation assertion 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 @@ -1106,6 +1129,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -1933,6 +1958,8 @@ AND t has_input y + + 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 @@ -2410,6 +2437,8 @@ Examples include: the relationship between two channels collected simultaneously + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -2551,6 +2580,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter releases neurotransmitter @@ -3234,7 +3264,23 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + + + + + + + + + @@ -3274,6 +3320,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + @@ -3310,7 +3364,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor @@ -3450,6 +3504,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. Chris Mungall has prototype @@ -3534,7 +3589,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Chris Mungall has agent - has active participant + obsolete has active participant + true @@ -3663,7 +3719,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + @@ -3920,6 +3976,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + Any portion of roundup 'has active ingredient' some glyphosate A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. has active substance @@ -3967,8 +4025,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - + + @@ -4665,6 +4723,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall @@ -4678,6 +4738,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of enables Chris Mungall @@ -4733,6 +4794,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization Chris Mungall + Do not use this relation directly. It is a grouping relation. related via localization to @@ -5227,6 +5289,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + 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 @@ -6076,6 +6140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + A relation that holds between a disease or an organism and a phenotype Chris Mungall has symptom @@ -6184,7 +6249,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Chris Mungall has vector @@ -6228,7 +6293,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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) @@ -6330,6 +6394,8 @@ the a supports either the existence of b, or the truth value of b. + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall @@ -6825,6 +6891,22 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + x is transcribed from y if and only if x is synthesized from template y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6850,6 +6932,23 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + + x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6862,6 +6961,22 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + inverse of ribosomal translation of Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -7153,6 +7268,10 @@ the a supports either the existence of b, or the truth value of b. + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. Chris Mungall @@ -7160,6 +7279,12 @@ the a supports either the existence of b, or the truth value of b.The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton + + + + + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. + @@ -7772,6 +7897,7 @@ the a supports either the existence of b, or the truth value of b. + Do not use this relation directly. It is a grouping relation. related via evidence or inference to @@ -8059,6 +8185,8 @@ the a supports either the existence of b, or the truth value of b. + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? Matthew Brush @@ -8280,6 +8408,64 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + cjm + 2018-12-13T11:26:17Z + has primary input or output + + + + + + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + cjm + 2018-12-13T11:26:32Z + has primary output + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + cjm + 2018-12-13T11:26:56Z + has primary input + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + @@ -8463,7 +8649,6 @@ Environmental exposures include those imposed by natural environments, experimen - After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm 2017-11-05T03:50:54Z @@ -8482,6 +8667,10 @@ Environmental exposures include those imposed by natural environments, experimen + + + + A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) cjm @@ -8972,6 +9161,9 @@ Environmental exposures include those imposed by natural environments, experimen Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + ECO:0000041 @@ -10636,6 +10828,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -10664,6 +10862,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -10686,6 +10890,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. @@ -10744,6 +10954,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + 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 @@ -10755,6 +10971,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + quality @@ -10764,6 +10986,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + 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 @@ -10785,6 +11013,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -10832,6 +11066,12 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + @@ -11167,6 +11407,12 @@ Environmental exposures include those imposed by natural environments, experimen /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + @@ -11221,6 +11467,61 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 @@ -12039,6 +12340,118 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + '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). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -12131,5 +12544,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/ro.json b/ro.json index f90d9220..7da61d65 100644 --- a/ro.json +++ b/ro.json @@ -119,6 +119,9 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002297", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { @@ -130,9 +133,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_formation_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" @@ -140,6 +140,20 @@ }, "type" : "PROPERTY", "lbl" : "results in formation of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] + }, + "type" : "PROPERTY", + "lbl" : "attached to part of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002298", "meta" : { @@ -148,9 +162,6 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_morphogenesis_of" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" }, { @@ -165,24 +176,13 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" } ] }, "type" : "PROPERTY", "lbl" : "results in morphogenesis of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - } ] - }, - "type" : "PROPERTY", - "lbl" : "attached to part of" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", "meta" : { @@ -300,14 +300,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_developmental_progression_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" @@ -367,14 +367,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_development_of" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -668,47 +668,47 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ancestral_stucture_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "evolutionarily_descended_from" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" } ] }, "type" : "PROPERTY", "lbl" : "derived by descent from" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "id" : "http://purl.obolibrary.org/obo/RO_0003003", "meta" : { "definition" : { - "val" : "inverse of derived by descent from", + "val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.", "xrefs" : [ ] }, - "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_0000116", + "val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in" } ] }, "type" : "PROPERTY", - "lbl" : "has derived by descendant" + "lbl" : "increases expression of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "id" : "http://purl.obolibrary.org/obo/RO_0002157", "meta" : { "definition" : { - "val" : "Holds between protein a (a transcription factor) and DNA element b if and only if a activates the process of transcription of b.", + "val" : "inverse of derived by descent from", "xrefs" : [ ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Logical axioms to be added after the relevant branch of GO is MIREOTed in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] }, "type" : "PROPERTY", - "lbl" : "increases expression of" + "lbl" : "has derived by descendant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002150", "meta" : { @@ -747,9 +747,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "proper overlaps" }, { @@ -758,6 +755,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -796,11 +796,11 @@ "xrefs" : [ "GOC:dos" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-07T12:58:06Z" - }, { "pred" : "ttp://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" } ] }, "type" : "PROPERTY", @@ -961,6 +961,20 @@ }, "type" : "PROPERTY", "lbl" : "acts upstream of or within" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "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" + } ] + }, + "type" : "PROPERTY", + "lbl" : "directly regulated by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", "meta" : { @@ -979,19 +993,22 @@ "type" : "PROPERTY", "lbl" : "has potential to developmentally contribute to" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "id" : "http://purl.obolibrary.org/obo/RO_0002386", "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." ], + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y", + "xrefs" : [ ] + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:24Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", - "lbl" : "directly regulated by" + "lbl" : "has potential to developmentally induce" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002023", "meta" : { @@ -1000,32 +1017,15 @@ "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" - } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulated by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002386", - "meta" : { - "definition" : { - "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y", - "xrefs" : [ ] - }, - "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://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" } ] }, "type" : "PROPERTY", - "lbl" : "has potential to developmentally induce" + "lbl" : "directly negatively regulated by" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002024", "meta" : { @@ -1096,11 +1096,11 @@ }, "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#creation_date", - "val" : "2017-09-22T14:14:36Z" - }, { "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" } ] }, "type" : "PROPERTY", @@ -1288,11 +1288,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" } ] }, "type" : "PROPERTY", @@ -1446,11 +1446,11 @@ "meta" : { "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:36:08Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" } ] }, "type" : "PROPERTY", @@ -1481,11 +1481,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:49:21Z" - }, { "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" } ] }, "type" : "PROPERTY", @@ -1632,6 +1632,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" @@ -1644,9 +1647,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" } ] }, "type" : "PROPERTY", @@ -1807,11 +1807,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:30:46Z" - }, { "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" } ] }, "type" : "PROPERTY", @@ -1887,24 +1887,6 @@ }, "type" : "PROPERTY", "lbl" : "developmentally induced by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", - "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.", - "xrefs" : [ ] - }, - "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" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has negative regulatory component activity" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002377", "meta" : { @@ -1936,6 +1918,24 @@ }, "type" : "PROPERTY", "lbl" : "distributary of" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "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.", + "xrefs" : [ ] + }, + "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#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has negative regulatory component activity" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", "meta" : { @@ -2187,6 +2187,16 @@ }, "type" : "PROPERTY", "lbl" : "existence starts during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.", + "xrefs" : [ ] + } + }, + "type" : "PROPERTY", + "lbl" : "under-expressed in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002004", "meta" : { @@ -2201,16 +2211,6 @@ }, "type" : "PROPERTY", "lbl" : "tracheates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002246", - "meta" : { - "definition" : { - "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "under-expressed in" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002005", "meta" : { @@ -4410,9 +4410,6 @@ "basicPropertyValues" : [ { "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." - }, { - "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" @@ -4674,10 +4671,11 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" - } ] + } ], + "deprecated" : true }, "type" : "PROPERTY", - "lbl" : "has active participant" + "lbl" : "obsolete has active participant" }, { "id" : "http://purl.obolibrary.org/obo/RO_0003306", "meta" : { @@ -4930,6 +4928,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" @@ -5123,6 +5124,9 @@ "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 a grouping relation." } ] }, "type" : "PROPERTY", @@ -5502,17 +5506,41 @@ "type" : "PROPERTY", "lbl" : "is direct form of" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "id" : "http://purl.obolibrary.org/obo/RO_0040042", "meta" : { "definition" : { - "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.", + "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.", "xrefs" : [ ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-10-21T19:46:34Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/164" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part-of is homeomorphic for independent continuants." + } ] + }, + "type" : "PROPERTY", + "lbl" : "is homeomorphic for" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "meta" : { + "definition" : { + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.", + "xrefs" : [ ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." }, { @@ -5676,7 +5704,7 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002207", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y", + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", "xrefs" : [ ] }, "comments" : [ "TODO - add child relations from DOS" ], @@ -6226,11 +6254,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "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, in which the subject or object is a disease." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-09-26T00:00:32Z" @@ -6910,9 +6938,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," @@ -6925,6 +6950,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/pull/173" @@ -7040,29 +7068,29 @@ "type" : "PROPERTY", "lbl" : "start, days post coitum" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "id" : "http://purl.obolibrary.org/obo/RO_0002426", "meta" : { - "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" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] }, "type" : "PROPERTY", - "lbl" : "causally upstream of, negative effect" + "lbl" : "differs in attribute" }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "id" : "http://purl.obolibrary.org/obo/RO_0002305", "meta" : { + "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" ], "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_0002411" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "cjm" } ] }, "type" : "PROPERTY", - "lbl" : "differs in attribute" + "lbl" : "causally upstream of, negative effect" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002427", "meta" : { @@ -7105,14 +7133,14 @@ }, "type" : "PROPERTY", "lbl" : "involved in regulation of" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "type" : "CLASS", - "lbl" : "biological_process" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002549", "type" : "PROPERTY", "lbl" : "start, weeks post birth" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "type" : "CLASS", + "lbl" : "biological_process" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", "meta" : { @@ -7294,15 +7322,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Marie Angelique Laporte" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-06-05T17:35:04Z" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Austin Meier" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Chris Mungall" @@ -8758,14 +8786,20 @@ }, "type" : "CLASS", "lbl" : "multicellular anatomical structure" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044419", - "type" : "CLASS", - "lbl" : "interspecies interaction between organisms" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + }, "type" : "PROPERTY", "lbl" : "related via evidence or inference to" + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044419", + "type" : "CLASS", + "lbl" : "interspecies interaction between organisms" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002610", "meta" : { @@ -8942,11 +8976,11 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "juvenification", + "val" : "pedomorphosis", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "pedomorphosis", + "val" : "juvenification", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9070,15 +9104,15 @@ }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(downstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_by ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(downstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(downstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_by ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(downstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(downstream_neural_circuit_path ?x ...s ?y)))) \n\t\t\t" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(downstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_by ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(downstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(downstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_by ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(downstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(downstream_neural_circuit_path ?x ...s ?y)))) \n\t\t\t" } ] }, "type" : "PROPERTY", @@ -9152,6 +9186,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(upstream_neural_circuit_path ?x ...s ?y))))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -9161,9 +9198,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(upstream_neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(synapsed_to ?x ?y))))\n\n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(upstream_neural_circuit_path ...s ?x ?y ?z )\n\t\t(and\n\t\t\t(upstream_neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(synapsed_to ?y ?z))))\n\t\t\t\n(forall (?x ?y) \n\t(iff \n\t\t(upstream_in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(upstream_neural_circuit_path ?x ...s ?y))))" } ] }, "type" : "PROPERTY", @@ -9209,6 +9243,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?x ?y) \n\t\t\t\t(synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(neural_circuit_path ...s ?x ?y ?z)\n\t\t(and\n\t\t\t(neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?y ?z) \n\t\t\t\t(synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n\t(iff \n\t\t(in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(neural_circuit_path ?x ...s ?y)))) " }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" @@ -9218,9 +9255,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(neural_circuit_path ?x ?y)\n\t\t(and\n\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t(\"neuron ; CL_0000540\" ?y)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?x ?y) \n\t\t\t\t(synapsed_to ?x ?y))))) \n\n(forall (...s ?x ?y ?z) \n\t(iff \n\t\t(neural_circuit_path ...s ?x ?y ?z)\n\t\t(and\n\t\t\t(neural_circuit_path ...s ?x ?y)\n\t\t\t(\"neuron ; CL_0000540\" ?z)\n\t\t\t(or \n\t\t\t\t(synapsed_by ?y ?z) \n\t\t\t\t(synapsed_to ?y ?z))))) \n\n(forall (?x ?y) \n\t(iff \n\t\t(in_neural_circuit_with ?x ?y)\n\t\t(exists (...s)\n\t\t\t(neural_circuit_path ?x ...s ?y)))) " } ] }, "type" : "PROPERTY", @@ -9274,15 +9308,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "many-to-many homology", + "val" : "many to many homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many:many homology ", + "val" : "many-to-many homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many to many homologous to", + "val" : "many:many homology ", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9358,14 +9392,14 @@ "pred" : "hasRelatedSynonym", "val" : "co-orthology", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "many to 1 orthology", - "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "1:many orthology", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "many to 1 orthology", + "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "1 to many orthologous to", @@ -9536,11 +9570,11 @@ }, "comments" : [ "The term is sometimes also used for anatomical structures." ], "xrefs" : [ { - "val" : "ECO:00000060" - }, { "val" : "SO:0000855" }, { "val" : "SO:0000858" + }, { + "val" : "ECO:00000060" }, { "val" : "SO:orthologous_to" } ], @@ -9627,13 +9661,13 @@ "val" : "SO:non_functional_homolog_of" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "non functional homologous to", - "xrefs" : [ ] - }, { "pred" : "hasBroadSynonym", "val" : "pseudogene", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "non functional homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/source", @@ -9657,15 +9691,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "1 to 1 homologous to", + "val" : "one-to-one homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "1:1 homology", + "val" : "1 to 1 homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "one-to-one homology", + "val" : "1:1 homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9690,15 +9724,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "1 to 1 orthologous to", + "val" : "one-to-one orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "1:1 orthology", + "val" : "1 to 1 orthologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "one-to-one orthology", + "val" : "1:1 orthology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9727,15 +9761,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "alloparalogy", + "val" : "out-paralogous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "outparalogy", + "val" : "alloparalogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "out-paralogous to", + "val" : "outparalogy", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9822,11 +9856,11 @@ "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "in-paralogous to", + "val" : "inparalogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "inparalogy", + "val" : "in-paralogous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -9854,18 +9888,18 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.014", "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000006", "ISBN:0123195837" ] }, "xrefs" : [ { - "val" : "ECO:0000071" - }, { "val" : "MI:2163" + }, { + "val" : "ECO:0000071" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "structural homologous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "idealistic homology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "structural homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -9888,43 +9922,43 @@ "xrefs" : [ "http://dx.doi.org/10.1016/S0169-5347(97)01125-7", "http://purl.obolibrary.org/obo/HOM_0000007", "ISBN:0123195837" ] }, "xrefs" : [ { + "val" : "SO:0000857" + }, { "val" : "SO:0000853" }, { - "val" : "SO:0000857" + "val" : "RO_proposed_relation:homologous_to" }, { - "val" : "SO:0000330" + "val" : "TAO:homologous_to" }, { "val" : "ECO:0000080" }, { - "val" : "SO:homologous_to" - }, { - "val" : "TAO:homologous_to" + "val" : "SO:0000330" }, { - "val" : "RO_proposed_relation:homologous_to" + "val" : "SO:homologous_to" } ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "historical homologous to", + "val" : "phylogenetic homology", "xrefs" : [ ] }, { - "pred" : "hasExactSynonym", - "val" : "taxic homology", + "pred" : "hasRelatedSynonym", + "val" : "true homology", "xrefs" : [ ] }, { - "pred" : "hasBroadSynonym", - "val" : "homology", + "pred" : "hasExactSynonym", + "val" : "historical homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "cladistic homology", + "val" : "taxic homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "phylogenetic homology", + "val" : "cladistic homology", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "true homology", + "pred" : "hasBroadSynonym", + "val" : "homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10033,10 +10067,6 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000009" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "rudiment", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "reversion", "xrefs" : [ ] @@ -10044,6 +10074,10 @@ "pred" : "hasExactSynonym", "val" : "atavism", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "rudiment", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10066,20 +10100,20 @@ "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000010", "MeSH:Synteny" ] }, "xrefs" : [ { - "val" : "SO:0005858" - }, { "val" : "SO:0000860" + }, { + "val" : "SO:0005858" }, { "val" : "MeSH:Synteny" } ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "syntenic homologous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "synteny", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "syntenic homologous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10128,31 +10162,31 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "fractional homology", + "val" : "partial homologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "segmental homology", + "val" : "fractional homology", "xrefs" : [ ] }, { - "pred" : "hasExactSynonym", - "val" : "partial homologous to", + "pred" : "hasRelatedSynonym", + "val" : "mixed homology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "partial correspondence", + "val" : "percent homology", "xrefs" : [ ] }, { - "pred" : "hasRelatedSynonym", - "val" : "mixed homology", + "pred" : "hasExactSynonym", + "val" : "segmental homology", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "modular homology", + "val" : "partial correspondence", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "percent homology", + "val" : "modular homology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10208,6 +10242,10 @@ "xrefs" : [ "http://dx.doi.org/10.1186/1471-213X-7-100", "http://purl.obolibrary.org/obo/HOM_0000012", "DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y" ] }, "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "duplicon", + "xrefs" : [ ] + }, { "pred" : "hasExactSynonym", "val" : "syntenic paralogous to", "xrefs" : [ ] @@ -10215,10 +10253,6 @@ "pred" : "hasRelatedSynonym", "val" : "paralogon", "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "duplicon", - "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -10241,13 +10275,13 @@ "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000002" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "analogy", - "xrefs" : [ ] - }, { "pred" : "hasExactSynonym", "val" : "homoplasous to", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "analogy", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/source", @@ -10304,25 +10338,34 @@ "val" : "SO:similar_to" } ], "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "similar to", + "xrefs" : [ ] + }, { "pred" : "hasExactSynonym", "val" : "sameness", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "correspondence", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] - }, { - "pred" : "hasExactSynonym", - "val" : "similar to", + "val" : "resemblance", "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "resemblance", - "xrefs" : [ ] + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] } ], "basicPropertyValues" : [ { + "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_0000002" + }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add homeomorphy axiom" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" @@ -10575,15 +10618,15 @@ }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "duplicate xenology", + "val" : "multiple xenology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "multiple xenology", + "val" : "paraxenologous to", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "paraxenologous to", + "val" : "duplicate xenology", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10674,15 +10717,15 @@ "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "apparent orthologous to", + "val" : "1:1 paralogy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "1:1 paralogy", + "val" : "apparent 1:1 orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "apparent 1:1 orthology", + "val" : "apparent orthologous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10732,16 +10775,12 @@ "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000048", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "many-to-many orthology", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", - "val" : "co-orthology", + "val" : "trans-homology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "many:many orthology", + "val" : "many-to-many orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", @@ -10749,12 +10788,16 @@ "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "trans-homology", + "val" : "co-orthology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "many to many orthologous to", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "many:many orthology", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10912,19 +10955,23 @@ "comments" : [ "Used for structures in closely related taxa." ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "re-awakening", + "val" : "homoiology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", "val" : "cryptic homology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "apomorphic tendency", + "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "homoplastic tendency", + "val" : "re-awakening", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "apomorphic tendency", + "val" : "underlying synapomorphy", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", @@ -10932,11 +10979,7 @@ "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", - "val" : "homoiology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "underlying synapomorphy", + "val" : "homoplastic tendency", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -10994,10 +11037,6 @@ "xrefs" : [ "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000055", "ISBN:978-0878932665" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "serial paralogy", - "xrefs" : [ ] - }, { "pred" : "hasExactSynonym", "val" : "tandem paralogous to", "xrefs" : [ ] @@ -11005,6 +11044,10 @@ "pred" : "hasRelatedSynonym", "val" : "iterative paralogy", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "serial paralogy", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -11086,13 +11129,13 @@ "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000042", "ISBN:978-0252068140" ] }, "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "synapomorphy", - "xrefs" : [ ] - }, { "pred" : "hasExactSynonym", "val" : "apomorphous to", "xrefs" : [ ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "synapomorphy", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11116,13 +11159,13 @@ }, "comments" : [ "This term is usually contrasted to apomorphy." ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "plesiomorphous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "symplesiomorphy", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "plesiomorphous to", + "xrefs" : [ ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", @@ -11209,20 +11252,20 @@ }, "comments" : [ "Used for structures in distantly related taxa." ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "deep homologous to", - "xrefs" : [ ] - }, { "pred" : "hasRelatedSynonym", "val" : "generative homology", "xrefs" : [ ] + }, { + "pred" : "hasExactSynonym", + "val" : "deep genetic homology", + "xrefs" : [ ] }, { "pred" : "hasRelatedSynonym", "val" : "homoiology", "xrefs" : [ ] }, { "pred" : "hasExactSynonym", - "val" : "deep genetic homology", + "val" : "deep homologous to", "xrefs" : [ ] } ], "basicPropertyValues" : [ { @@ -11277,6 +11320,15 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "part_of" + }, { + "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_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "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)" @@ -11286,12 +11338,21 @@ }, { "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/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { "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_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { "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'." @@ -11304,6 +11365,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "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." @@ -11458,11 +11522,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004050", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:24Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] }, "type" : "PROPERTY", @@ -11771,23 +11835,6 @@ }, "type" : "PROPERTY", "lbl" : "happens during" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004030", - "meta" : { - "definition" : { - "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:58:44Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "disease arises from structure" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002093", "meta" : { @@ -11806,6 +11853,23 @@ }, "type" : "PROPERTY", "lbl" : "ends during" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "disease arises from structure" }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "meta" : { @@ -11878,11 +11942,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004032", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002264" @@ -11971,11 +12035,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:50:53Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -11998,11 +12062,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:45:49Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" } ] }, "type" : "PROPERTY", @@ -12108,12 +12172,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes dysfunction of (disease to anatomical entity)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:58:20Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" } ] }, "type" : "PROPERTY", @@ -12152,11 +12216,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:51:09Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease causes disruption of (disease to process)" @@ -12213,12 +12277,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T04:06:02Z" @@ -12250,12 +12314,12 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:37:52Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -12315,9 +12379,6 @@ }, { "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 of which have a disease as the subject." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "After import upper level from OGMS, make domain more specific." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T03:50:54Z" @@ -12469,11 +12530,11 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317344" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:57:07Z" @@ -12491,12 +12552,12 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:56:40Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317343" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" } ] }, "type" : "PROPERTY", @@ -12565,14 +12626,14 @@ "xrefs" : [ ] }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410295" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:56:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -12601,6 +12662,23 @@ }, "type" : "PROPERTY", "lbl" : "is causal gain of function germline mutation of in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004007", + "meta" : { + "definition" : { + "val" : "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.", + "xrefs" : [ ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has primary input or output" }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002124", "type" : "CLASS", @@ -12618,6 +12696,40 @@ }, "type" : "PROPERTY", "lbl" : "has partial material basis in germline mutation in" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004009", + "meta" : { + "definition" : { + "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:56Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has primary input" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004008", + "meta" : { + "definition" : { + "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:32Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" + } ] + }, + "type" : "PROPERTY", + "lbl" : "has primary output" }, { "id" : "http://purl.obolibrary.org/obo/GO_0016881", "type" : "CLASS", @@ -12675,11 +12787,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004003", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317343" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:54Z" @@ -12717,11 +12829,11 @@ "id" : "http://purl.obolibrary.org/obo/RO_0004004", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:46:07Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "cjm" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:07Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_317344" @@ -12735,15 +12847,15 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "cjm" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410296" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.orpha.net/ORDO/Orphanet_410295" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "cjm" } ] }, "type" : "PROPERTY", @@ -12957,6 +13069,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002083", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002081" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004007", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002334", "pred" : "subPropertyOf", @@ -13409,14 +13525,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002287", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002286" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002440", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004004", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002440", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002291", "pred" : "subPropertyOf", @@ -13453,6 +13569,10 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002333", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002299", "pred" : "subPropertyOf", @@ -13782,17 +13902,17 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0040036" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002466", + "sub" : "http://purl.obolibrary.org/obo/RO_0002455", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002465" + "obj" : "http://purl.obolibrary.org/obo/RO_0002442" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002252", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002375" }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002455", + "sub" : "http://purl.obolibrary.org/obo/RO_0002466", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002442" + "obj" : "http://purl.obolibrary.org/obo/RO_0002465" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002263", "pred" : "subPropertyOf", @@ -13945,14 +14065,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002430", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002428" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002113", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002114", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002120" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002113", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002130" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002379", "pred" : "subPropertyOf", @@ -14289,6 +14409,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004031", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002328" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002460", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002134", "pred" : "subPropertyOf", @@ -14509,14 +14633,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002245", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002206" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002231", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002479" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002180", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002231", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002479" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002230", "pred" : "subPropertyOf", @@ -14525,14 +14649,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002088", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002091" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0004012", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002007", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004012", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004010" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004024", "pred" : "subPropertyOf", @@ -14597,14 +14721,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002458", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002438" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002476", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002258" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002458", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002233", "pred" : "subPropertyOf", @@ -14645,14 +14769,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002000", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002002" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002495", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002494" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002216", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002500" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002495", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002494" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", "pred" : "subPropertyOf", @@ -14669,6 +14793,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002350", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002351" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004009", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002624", "pred" : "inverseOf", @@ -14729,6 +14857,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002626", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002627" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004008", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002234" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002530", "pred" : "subPropertyOf", @@ -14773,10 +14905,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0003302", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002410" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002460", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002459" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002373", "pred" : "subPropertyOf", @@ -14809,14 +14937,14 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0000001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002588", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002297" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0004034", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002588", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002297" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000141", "pred" : "is_a", @@ -14965,14 +15093,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002444", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002454" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002246", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002206" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002461", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000056" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002246", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002206" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002232", "pred" : "subPropertyOf", @@ -15033,14 +15161,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0000079", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000085" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002090", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002159", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002320" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002090", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", "pred" : "subPropertyOf", @@ -15057,6 +15185,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002623", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004008", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0004007" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0008508", "pred" : "subPropertyOf", @@ -15237,14 +15369,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002459", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002574" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0003305", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0003304" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002177", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002323" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0003305", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0003304" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002551", "pred" : "inverseOf", @@ -15281,14 +15413,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000016", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000006" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002349", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002349", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002295" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002445", "pred" : "subPropertyOf", @@ -15357,14 +15489,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002331", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002431" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002026", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002286", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002384" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002026", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002323" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "inverseOf", @@ -15753,14 +15885,14 @@ "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000065", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000000" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002297", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002295" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000065", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000000" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0051705", "pred" : "is_a", @@ -15797,6 +15929,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002326", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002329" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002512", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002513" }, { "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000032", "pred" : "subPropertyOf", @@ -15853,6 +15989,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0004002", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0004000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0004009", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002233" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002223", "pred" : "subPropertyOf", @@ -15993,62 +16133,65 @@ "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/description", "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://obofoundry.org/ro" + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7]" + "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" + "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 56 Logical Axioms: 13]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]" - }, { - "pred" : "http://xmlns.com/foaf/0.1/homepage", - "val" : " https://github.com/oborel/obo-relations/" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 61 Logical Axioms: 0]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 110 Logical Axioms: 27]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://obofoundry.org/ro" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6]" }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "OBO Relations Ontology" + "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148]" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", - "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 110 Logical Axioms: 27]" + "val" : "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45]" + }, { + "pred" : "http://xmlns.com/foaf/0.1/homepage", + "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2018-10-19/ro.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl" }, "equivalentNodesSets" : [ ], "logicalDefinitionAxioms" : [ ], @@ -16070,6 +16213,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002572", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002452", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], @@ -16086,6 +16232,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002332", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002179", "allValuesFromEdges" : [ { @@ -16127,6 +16277,37 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000300", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000003", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -16191,6 +16372,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0003001", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002150", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -16235,6 +16420,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/R0_0009004", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002258", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -16254,6 +16443,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002414", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002018", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], @@ -16327,6 +16520,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0008506", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002248", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002007", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] @@ -16406,6 +16603,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004019", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OGMS_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002473", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001021", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] @@ -16418,7 +16619,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002111", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002232", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], @@ -16462,6 +16664,10 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002506", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002104", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002226", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000000" ] @@ -16512,13 +16718,13 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002214", "allValuesFromEdges" : [ { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", - "pred" : "http://purl.obolibrary.org/obo/RO_0002214", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" - }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000002", "pred" : "http://purl.obolibrary.org/obo/RO_0002214", "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "http://purl.obolibrary.org/obo/RO_0002214", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002215", @@ -16838,6 +17044,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002406", "http://purl.obolibrary.org/obo/RO_0002406" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "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" ] diff --git a/ro.obo b/ro.obo index 0b0d4d01..7f758b6d 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2018-10-19 +data-version: releases/2019-02-02 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] @@ -10,6 +10,7 @@ remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] @@ -22,13 +23,14 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (is model of)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000002 ! part of continuant relationship: RO:0002214 BFO:0000002 ! has prototype continuant relationship: RO:HOM0000000 BFO:0000002 ! continuant @@ -36,6 +38,7 @@ relationship: RO:HOM0000000 BFO:0000002 ! continuant id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: BFO:0000050 BFO:0000003 ! part of occurrent relationship: RO:HOM0000000 BFO:0000003 ! occurrent [Term] @@ -45,6 +48,7 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000004 ! part of independent continuant [Term] id: BFO:0000005 @@ -77,11 +81,13 @@ 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: BFO:0000050 BFO:0000017 ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000019 ! part of quality [Term] id: BFO:0000020 @@ -89,6 +95,7 @@ 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 disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -101,6 +108,7 @@ id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] is_a: BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -521,6 +529,13 @@ property_value: IAO:0000116 "Occurrents are not subject to change and so parthoo 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 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string @@ -643,6 +658,8 @@ def: "'has consumer' is a relation between a material entity and an organism in property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: CARO:0001010 ! organism or virus or viroid [Typedef] id: RO:0000052 @@ -1120,6 +1137,8 @@ creation_date: 2017-05-24T09:44:33Z id: RO:0002018 name: has component process def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process is_a: RO:0002180 ! has component created_by: dos creation_date: 2017-05-24T09:49:21Z @@ -1392,6 +1411,8 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "Lindsay Cowell" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 +domain: CARO:0000006 ! material anatomical entity +range: CARO:0000006 ! material anatomical entity is_a: BFO:0000051 ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -1482,6 +1503,7 @@ name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string domain: CARO:0000003 ! connected anatomical structure +range: BFO:0000040 ! material entity [Typedef] id: RO:0002112 @@ -1879,7 +1901,7 @@ transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002207 name: directly develops from -def: "Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y" [] +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1972,6 +1994,7 @@ property_value: IAO:0000112 "heart SubClassOf 'has prototype' some ('participate property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string +property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string [Typedef] @@ -2011,11 +2034,11 @@ def: "x actively participates in y if and only if x participates in y and x real property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "agent in" xsd:string is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 ! has active participant +inverse_of: RO:0002218 ! obsolete has active participant [Typedef] id: RO:0002218 -name: has active participant +name: obsolete has active participant def: "x has participant y if and only if x realizes some active role that inheres in y" [] subset: ro-eco property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string @@ -2024,6 +2047,7 @@ property_value: IAO:0000116 "This may be obsoleted and replaced by the original property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: RO:0000057 ! has participant +is_obsolete: true [Typedef] id: RO:0002219 @@ -2280,6 +2304,8 @@ def: "A relationship that holds between a substance and a chemical entity, if th synonym: "has active pharmaceutical ingredient" RELATED [] synonym: "has active substance" EXACT [] property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part inverse_of: RO:0002249 ! active ingredient in' @@ -2680,6 +2706,8 @@ property_value: IAO:0000112 "every cellular sphingolipid homeostasis process reg property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity is_a: RO:0002328 ! functionally related to [Typedef] @@ -2687,6 +2715,7 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to [Typedef] @@ -2722,6 +2751,7 @@ id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -3550,6 +3580,7 @@ id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: OGMS:0000031 ! disease is_a: RO:0002200 ! has phenotype [Typedef] @@ -3627,7 +3658,7 @@ id: RO:0002460 name: has vector subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002459 ! is vector for +is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 @@ -3653,7 +3684,6 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000114 IAO:0000428 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 @@ -3723,6 +3753,8 @@ property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part [Typedef] @@ -4020,6 +4052,7 @@ def: "x is the ribosomal translation of y if and only if a ribosome reads x thro property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to +inverse_of: RO:0002513 ! ribosomally translates to [Typedef] id: RO:0002513 @@ -4240,8 +4273,11 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true [Typedef] id: RO:0002552 @@ -4634,6 +4670,7 @@ inverse_of: RO:0003301 ! is model of [Typedef] id: RO:0002616 name: related via evidence or inference to +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string [Typedef] id: RO:0002618 @@ -4819,6 +4856,7 @@ def: "Relation between a research artifact and an entity it is used to study, in comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string property_value: IAO:0000117 "Matthew Brush" xsd:string +is_asymmetric: true [Typedef] id: RO:0003302 @@ -4949,6 +4987,32 @@ inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to created_by: cjm creation_date: 2017-11-05T02:46:57Z +[Typedef] +id: RO:0004007 +name: has primary input or output +def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] +is_a: RO:0000057 ! has participant +created_by: cjm +creation_date: 2018-12-13T11:26:17Z + +[Typedef] +id: RO:0004008 +name: has primary output +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +is_a: RO:0002234 ! has output +is_a: RO:0004007 ! has primary input or output +created_by: cjm +creation_date: 2018-12-13T11:26:32Z + +[Typedef] +id: RO:0004009 +name: has primary input +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +is_a: RO:0002233 ! has input +is_a: RO:0004007 ! has primary input or output +created_by: cjm +creation_date: 2018-12-13T11:26:56Z + [Typedef] id: RO:0004010 name: is genetic basis for condition @@ -5069,7 +5133,6 @@ creation_date: 2017-11-05T03:46:07Z [Typedef] id: RO:0004023 name: causal relationship with disease as subject -property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." 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 of which have a disease as the subject." xsd:string domain: OGMS:0000031 ! disease is_a: RO:0002410 ! causally related to @@ -5084,6 +5147,7 @@ def: "A relationship between a disease and a process where the disease process d property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string domain: OGMS:0000031 ! disease range: BFO:0000015 ! process +holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: cjm @@ -5393,6 +5457,9 @@ xref: ECO:0000041 xref: SO:similar_to property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: IAO:0000116 "TODO: Add homeomorphy axiom" xsd:string +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 property_value: seeAlso HOM:0000000 is_symmetric: true diff --git a/ro.owl b/ro.owl index 9d59e0e3..754e3b5f 100644 --- a/ro.owl +++ b/ro.owl @@ -1,40 +1,41 @@ + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> - + - - - - - - - + + + + + + + + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] - https://github.com/oborel/obo-relations/ - Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] + https://github.com/oborel/obo-relations/ @@ -676,6 +677,21 @@ Where we have an annotation assertion + + + + part-of is homeomorphic for independent continuants. + R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. + cjm + 2018-10-21T19:46:34Z + R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. + is homeomorphic for + + + + + + @@ -758,6 +774,13 @@ Where we have an annotation assertion + + + + + + + @@ -804,6 +827,8 @@ Where we have an annotation assertion + + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -1314,6 +1339,8 @@ AND t has_input y + + 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 @@ -1663,6 +1690,8 @@ Examples include: the relationship between two channels collected simultaneously + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1804,6 +1833,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter releases neurotransmitter @@ -2487,7 +2517,23 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + + + + + + + + + @@ -2527,6 +2573,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + @@ -2563,7 +2617,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor @@ -2703,6 +2757,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. Chris Mungall has prototype @@ -2787,7 +2842,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Chris Mungall has agent - has active participant + obsolete has active participant + true @@ -3143,6 +3199,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + Any portion of roundup 'has active ingredient' some glyphosate A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. has active substance @@ -3876,6 +3934,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall @@ -3889,6 +3949,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of enables Chris Mungall @@ -3944,6 +4005,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization Chris Mungall + Do not use this relation directly. It is a grouping relation. related via localization to @@ -5260,6 +5322,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + A relation that holds between a disease or an organism and a phenotype Chris Mungall has symptom @@ -5368,7 +5431,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Chris Mungall has vector @@ -5412,7 +5475,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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) @@ -5514,6 +5576,8 @@ the a supports either the existence of b, or the truth value of b. + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall @@ -6009,6 +6073,22 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + x is transcribed from y if and only if x is synthesized from template y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6034,6 +6114,23 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + + x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6046,6 +6143,22 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + inverse of ribosomal translation of Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6337,6 +6450,10 @@ the a supports either the existence of b, or the truth value of b. + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. Chris Mungall @@ -6344,6 +6461,12 @@ the a supports either the existence of b, or the truth value of b.The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton + + + + + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. + @@ -6956,6 +7079,7 @@ the a supports either the existence of b, or the truth value of b. + Do not use this relation directly. It is a grouping relation. related via evidence or inference to @@ -7243,6 +7367,8 @@ the a supports either the existence of b, or the truth value of b. + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? Matthew Brush @@ -7464,6 +7590,64 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + cjm + 2018-12-13T11:26:17Z + has primary input or output + + + + + + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + cjm + 2018-12-13T11:26:32Z + has primary output + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + cjm + 2018-12-13T11:26:56Z + has primary input + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + @@ -7647,7 +7831,6 @@ Environmental exposures include those imposed by natural environments, experimen - After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm 2017-11-05T03:50:54Z @@ -7666,6 +7849,10 @@ Environmental exposures include those imposed by natural environments, experimen + + + + A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) cjm @@ -8151,6 +8338,16 @@ Environmental exposures include those imposed by natural environments, experimen + + + + TODO: Add homeomorphy axiom + + + + + + @@ -8564,6 +8761,12 @@ Environmental exposures include those imposed by natural environments, experimen /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + @@ -8618,6 +8821,61 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 @@ -9163,9 +9421,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -9174,9 +9432,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -9436,6 +9694,118 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + '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). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -9528,5 +9898,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 8ddb5e2c..5b6ec1dd 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -2,7 +2,8 @@ OBO=http://purl.obolibrary.org/obo SRC=ro-edit.owl ROBOT=robot -ONTS= ro.obo ro.owl ro.json ro-base.owl ro-base.obo ro-base.json chemical.owl annotations.owl other_import.owl core.owl go-biotic.owl pato_import.owl temporal-intervals.owl bfo-axioms.owl bfo-classes-minimal.owl el-constraints.owl go_mf_import.owl go_cc_import.owl rohom.owl generated-axioms.owl +ONTS_TO_BUILD= ro.obo ro.owl ro.json ro-base.owl ro-base.obo ro-base.json chemical.owl annotations.owl other_import.owl core.owl go-biotic.owl pato_import.owl temporal-intervals.owl bfo-axioms.owl bfo-classes-minimal.owl el-constraints.owl go_mf_import.owl go_cc_import.owl generated-axioms.owl +ONTS= $(ONTS_TO_BUILD) rohom.owl # ======================================== # PRODUCTION @@ -12,7 +13,7 @@ all: build build: ro.owl ro.obo ro.json all_subsets -release: +release: $(ONTS_TO_BUILD) cp -pr catalog-v001.xml $(ONTS) subsets ../.. # fairly dump release process whilst waiting for Oort - check than versionIRI has been entered manually. @@ -136,6 +137,8 @@ build-using-oort: ro-edit.owl ontology-release-runner --catalog-xml catalog-v001.xml --outdir build --simple --allow-overwrite --reasoner hermit ro-edit.owl touch $@ +hom.obo: + wget $(OBO)/hom.obo -O $@.tmp && mv $@.tmp $@ hom-fixed.obo: hom.obo obo-grep.pl --neg -r is_obsolete: $< > $@.tmp && mv $@.tmp $@ diff --git a/src/ontology/generated-axioms.owl b/src/ontology/generated-axioms.owl index 1525959d..879f8439 100644 --- a/src/ontology/generated-axioms.owl +++ b/src/ontology/generated-axioms.owl @@ -1,8 +1,8 @@ @@ -148,5 +148,5 @@ - + diff --git a/src/ontology/ro.obo b/src/ontology/ro.obo index 20157e1c..7f758b6d 100644 --- a/src/ontology/ro.obo +++ b/src/ontology/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2018-10-22 +data-version: releases/2019-02-02 subsetdef: ro-eco "" subsetdef: RO:0002259 "" remark: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] @@ -10,6 +10,7 @@ remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 291 Logical Axioms: 62] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 42 Logical Axioms: 16] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 14] remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] @@ -22,13 +23,14 @@ property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations O property_value: http://purl.org/dc/elements/1.1/source http://obofoundry.org/ro property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (is model of)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has anatomical participant)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (symbiosis, encompassing mutualism through parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (parasitism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (mutualism)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: (commensalism)\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.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())))\nDLSafeRule(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())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"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\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(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())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000002 ! part of continuant relationship: RO:0002214 BFO:0000002 ! has prototype continuant relationship: RO:HOM0000000 BFO:0000002 ! continuant @@ -36,6 +38,7 @@ relationship: RO:HOM0000000 BFO:0000002 ! continuant id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: BFO:0000050 BFO:0000003 ! part of occurrent relationship: RO:HOM0000000 BFO:0000003 ! occurrent [Term] @@ -45,6 +48,7 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000004 ! part of independent continuant [Term] id: BFO:0000005 @@ -77,11 +81,13 @@ 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: BFO:0000050 BFO:0000017 ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000019 ! part of quality [Term] id: BFO:0000020 @@ -89,6 +95,7 @@ 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 disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -101,6 +108,7 @@ id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] is_a: BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -521,6 +529,13 @@ property_value: IAO:0000116 "Occurrents are not subject to change and so parthoo 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 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string @@ -643,6 +658,8 @@ def: "'has consumer' is a relation between a material entity and an organism in property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +domain: BFO:0000040 ! material entity +range: CARO:0001010 ! organism or virus or viroid [Typedef] id: RO:0000052 @@ -1120,6 +1137,8 @@ creation_date: 2017-05-24T09:44:33Z id: RO:0002018 name: has component process def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process is_a: RO:0002180 ! has component created_by: dos creation_date: 2017-05-24T09:49:21Z @@ -1392,6 +1411,8 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 "Lindsay Cowell" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 +domain: CARO:0000006 ! material anatomical entity +range: CARO:0000006 ! material anatomical entity is_a: BFO:0000051 ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] @@ -1482,6 +1503,7 @@ name: releases neurotransmitter property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000118 "has neurotransmitter" xsd:string domain: CARO:0000003 ! connected anatomical structure +range: BFO:0000040 ! material entity [Typedef] id: RO:0002112 @@ -1879,7 +1901,7 @@ transitive_over: BFO:0000050 ! part of [Typedef] id: RO:0002207 name: directly develops from -def: "Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y" [] +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -1972,6 +1994,7 @@ property_value: IAO:0000112 "heart SubClassOf 'has prototype' some ('participate property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string +property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string [Typedef] @@ -2011,11 +2034,11 @@ def: "x actively participates in y if and only if x participates in y and x real property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "agent in" xsd:string is_a: RO:0000056 ! participates in -inverse_of: RO:0002218 ! has active participant +inverse_of: RO:0002218 ! obsolete has active participant [Typedef] id: RO:0002218 -name: has active participant +name: obsolete has active participant def: "x has participant y if and only if x realizes some active role that inheres in y" [] subset: ro-eco property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string @@ -2024,6 +2047,7 @@ property_value: IAO:0000116 "This may be obsoleted and replaced by the original property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has agent" xsd:string is_a: RO:0000057 ! has participant +is_obsolete: true [Typedef] id: RO:0002219 @@ -2280,6 +2304,8 @@ def: "A relationship that holds between a substance and a chemical entity, if th synonym: "has active pharmaceutical ingredient" RELATED [] synonym: "has active substance" EXACT [] property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part inverse_of: RO:0002249 ! active ingredient in' @@ -2680,6 +2706,8 @@ property_value: IAO:0000112 "every cellular sphingolipid homeostasis process reg property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity is_a: RO:0002328 ! functionally related to [Typedef] @@ -2687,6 +2715,7 @@ id: RO:0002333 name: enabled by def: "inverse of enables" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to [Typedef] @@ -2722,6 +2751,7 @@ id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -3550,6 +3580,7 @@ id: RO:0002452 name: has symptom def: "A relation that holds between a disease or an organism and a phenotype" [] property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: OGMS:0000031 ! disease is_a: RO:0002200 ! has phenotype [Typedef] @@ -3627,7 +3658,7 @@ id: RO:0002460 name: has vector subset: ro-eco property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002459 ! is vector for +is_a: RO:0002574 ! participates in a biotic-biotic interaction with [Typedef] id: RO:0002461 @@ -3653,7 +3684,6 @@ is_a: RO:0002461 ! partner in [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000114 IAO:0000428 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 @@ -3723,6 +3753,8 @@ property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity is_a: BFO:0000051 ! has part [Typedef] @@ -4020,6 +4052,7 @@ def: "x is the ribosomal translation of y if and only if a ribosome reads x thro property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI is_a: RO:0002330 ! genomically related to +inverse_of: RO:0002513 ! ribosomally translates to [Typedef] id: RO:0002513 @@ -4240,8 +4273,11 @@ property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb ske property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity is_a: BFO:0000051 ! has part inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true [Typedef] id: RO:0002552 @@ -4634,6 +4670,7 @@ inverse_of: RO:0003301 ! is model of [Typedef] id: RO:0002616 name: related via evidence or inference to +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string [Typedef] id: RO:0002618 @@ -4819,6 +4856,7 @@ def: "Relation between a research artifact and an entity it is used to study, in comment: The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. property_value: IAO:0000116 "To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader?" xsd:string property_value: IAO:0000117 "Matthew Brush" xsd:string +is_asymmetric: true [Typedef] id: RO:0003302 @@ -4949,6 +4987,32 @@ inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to created_by: cjm creation_date: 2017-11-05T02:46:57Z +[Typedef] +id: RO:0004007 +name: has primary input or output +def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] +is_a: RO:0000057 ! has participant +created_by: cjm +creation_date: 2018-12-13T11:26:17Z + +[Typedef] +id: RO:0004008 +name: has primary output +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +is_a: RO:0002234 ! has output +is_a: RO:0004007 ! has primary input or output +created_by: cjm +creation_date: 2018-12-13T11:26:32Z + +[Typedef] +id: RO:0004009 +name: has primary input +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +is_a: RO:0002233 ! has input +is_a: RO:0004007 ! has primary input or output +created_by: cjm +creation_date: 2018-12-13T11:26:56Z + [Typedef] id: RO:0004010 name: is genetic basis for condition @@ -5069,7 +5133,6 @@ creation_date: 2017-11-05T03:46:07Z [Typedef] id: RO:0004023 name: causal relationship with disease as subject -property_value: IAO:0000116 "After import upper level from OGMS, make domain more specific." 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 of which have a disease as the subject." xsd:string domain: OGMS:0000031 ! disease is_a: RO:0002410 ! causally related to @@ -5084,6 +5147,7 @@ def: "A relationship between a disease and a process where the disease process d property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string domain: OGMS:0000031 ! disease range: BFO:0000015 ! process +holds_over_chain: RO:0004025 RO:0002215 is_a: RO:0004023 ! causal relationship with disease as subject transitive_over: BFO:0000050 ! part of created_by: cjm @@ -5393,6 +5457,9 @@ xref: ECO:0000041 xref: SO:similar_to property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: IAO:0000116 "TODO: Add homeomorphy axiom" xsd:string +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 property_value: seeAlso HOM:0000000 is_symmetric: true diff --git a/src/ontology/ro.owl b/src/ontology/ro.owl index 5be90084..754e3b5f 100644 --- a/src/ontology/ro.owl +++ b/src/ontology/ro.owl @@ -1,40 +1,41 @@ + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:swrl="http://www.w3.org/2003/11/swrl#" + xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" + xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" + xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:oboInOwl1="ttp://www.geneontology.org/formats/oboInOwl#"> - + - - - - - - - + + + + + + + + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] - https://github.com/oborel/obo-relations/ - Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] OBO Relations Ontology + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] + Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0] + https://github.com/oborel/obo-relations/ @@ -826,6 +827,8 @@ Where we have an annotation assertion + + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -1336,6 +1339,8 @@ AND t has_input y + + 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 @@ -1685,6 +1690,8 @@ Examples include: the relationship between two channels collected simultaneously + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. @@ -1826,6 +1833,7 @@ Examples include: the relationship between two channels collected simultaneously + has neurotransmitter releases neurotransmitter @@ -2509,7 +2517,23 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + + + + + + + + + @@ -2549,6 +2573,14 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + @@ -2585,7 +2617,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from 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, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor @@ -2725,6 +2757,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. Chris Mungall has prototype @@ -2809,7 +2842,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.Chris Mungall has agent - has active participant + obsolete has active participant + true @@ -3165,6 +3199,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + Any portion of roundup 'has active ingredient' some glyphosate A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. has active substance @@ -3898,6 +3934,8 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall @@ -3911,6 +3949,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + inverse of enables Chris Mungall @@ -3966,6 +4005,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds via some process of localization Chris Mungall + Do not use this relation directly. It is a grouping relation. related via localization to @@ -5282,6 +5322,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + A relation that holds between a disease or an organism and a phenotype Chris Mungall has symptom @@ -5390,7 +5431,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Chris Mungall has vector @@ -5434,7 +5475,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - 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) @@ -5536,6 +5576,8 @@ the a supports either the existence of b, or the truth value of b. + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. Chris Mungall @@ -6031,6 +6073,22 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + x is transcribed from y if and only if x is synthesized from template y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6056,6 +6114,23 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + + x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6068,6 +6143,22 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + + + + + + + + + + inverse of ribosomal translation of Chris Mungall http://www.ncbi.nlm.nih.gov/pubmed/20226267 @@ -6359,6 +6450,10 @@ the a supports either the existence of b, or the truth value of b. + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. Chris Mungall @@ -6366,6 +6461,12 @@ the a supports either the existence of b, or the truth value of b.The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). has skeleton + + + + + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. + @@ -6978,6 +7079,7 @@ the a supports either the existence of b, or the truth value of b. + Do not use this relation directly. It is a grouping relation. related via evidence or inference to @@ -7265,6 +7367,8 @@ the a supports either the existence of b, or the truth value of b. + + Relation between a research artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. To Do: decide on scope of this relation - inclusive of computational models in domain, or only physical models? Restricted to linking biological systems and phenomena? Inclusive of only diseases in range, or broader? Matthew Brush @@ -7486,6 +7590,64 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + cjm + 2018-12-13T11:26:17Z + has primary input or output + + + + + + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + cjm + 2018-12-13T11:26:32Z + has primary output + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + cjm + 2018-12-13T11:26:56Z + has primary input + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + @@ -7669,7 +7831,6 @@ Environmental exposures include those imposed by natural environments, experimen - After import upper level from OGMS, make domain more specific. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. cjm 2017-11-05T03:50:54Z @@ -7688,6 +7849,10 @@ Environmental exposures include those imposed by natural environments, experimen + + + + A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) cjm @@ -8176,6 +8341,7 @@ Environmental exposures include those imposed by natural environments, experimen + TODO: Add homeomorphy axiom @@ -8595,6 +8761,12 @@ Environmental exposures include those imposed by natural environments, experimen /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + @@ -8649,6 +8821,61 @@ Environmental exposures include those imposed by natural environments, experimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 @@ -9467,6 +9694,118 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + + '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). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -9559,5 +9898,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - +