diff --git a/core.json b/core.json index e47d77c8..cbd70634 100644 --- a/core.json +++ b/core.json @@ -3,16 +3,16 @@ "id" : "http://purl.obolibrary.org/obo/ro/core.json", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/license", + "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-28" + "val" : "2023-08-18" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : "https://github.com/oborel/obo-relations/wiki/ROCore" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/core.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/core.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -406,7 +406,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -692,7 +692,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" } ] } diff --git a/core.obo b/core.obo index d7d7cf5a..5ef0e65d 100644 --- a/core.obo +++ b/core.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: ro/releases/2023-06-28/core.owl +data-version: ro/releases/2023-08-18/core.owl ontology: ro/core -property_value: http://purl.org/dc/elements/1.1/license https://creativecommons.org/publicdomain/zero/1.0/ +property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage "https://github.com/oborel/obo-relations/wiki/ROCore" xsd:anyURI -property_value: owl:versionInfo "2023-06-28" xsd:string +property_value: owl:versionInfo "2023-08-18" xsd:string [Term] id: BFO:0000002 @@ -222,7 +222,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -373,7 +373,7 @@ inverse_of: RO:0001025 ! located in id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string diff --git a/core.owl b/core.owl index fde746bf..5604e8b3 100644 --- a/core.owl +++ b/core.owl @@ -1,7 +1,6 @@ + xmlns:terms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - 2023-06-28 + + + 2023-08-18 https://github.com/oborel/obo-relations/wiki/ROCore @@ -86,21 +86,15 @@ - - - - - - - + - + - + - + @@ -304,7 +298,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -533,7 +527,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in diff --git a/ro-base.json b/ro-base.json index ceb40ecc..f82d0759 100644 --- a/ro-base.json +++ b/ro-base.json @@ -16,12 +16,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-28" + "val" : "2023-08-18" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro-base.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -321,7 +321,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -515,7 +515,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -854,10 +854,9 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "lbl" : "contained in", + "lbl" : "obsolete contained in", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contained in" @@ -867,30 +866,28 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained_in" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "lbl" : "contains", + "lbl" : "obsolete contains", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contains" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001020", @@ -967,7 +964,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -10928,7 +10925,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" @@ -11527,10 +11524,10 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11552,10 +11549,10 @@ "val" : "homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11579,10 +11576,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11607,10 +11604,10 @@ "val" : "ECO:0000075" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11632,10 +11629,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11657,10 +11654,10 @@ "val" : "parallel evolution" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11689,10 +11686,10 @@ "val" : "MI:2163" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11743,10 +11740,10 @@ "val" : "TAO:homologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11774,10 +11771,10 @@ "val" : "ECO:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11804,10 +11801,10 @@ "val" : "reversion" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11838,10 +11835,10 @@ "val" : "SO:0005858" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11869,10 +11866,10 @@ "val" : "SO:paralogous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11899,10 +11896,10 @@ "val" : "paralogon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11923,10 +11920,10 @@ "val" : "syntenic orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11965,10 +11962,10 @@ "val" : "percent homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -11992,10 +11989,10 @@ "val" : "MeSH:Structural_Homology,_Protein" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12022,10 +12019,10 @@ "val" : "SO:non_functional_homolog_of" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12056,10 +12053,10 @@ "val" : "SO:orthologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12081,10 +12078,10 @@ "val" : "xenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12111,10 +12108,10 @@ "val" : "one-to-one homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12141,10 +12138,10 @@ "val" : "one-to-one orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12168,10 +12165,10 @@ "val" : "homoeology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12198,10 +12195,10 @@ "val" : "symparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12228,10 +12225,10 @@ "val" : "outparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12252,10 +12249,10 @@ "val" : "pro-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12277,10 +12274,10 @@ "val" : "semi-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12304,10 +12301,10 @@ "val" : "homonomy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12331,10 +12328,10 @@ "val" : "heterochrony" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12358,10 +12355,10 @@ "val" : "pedomorphosis" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12378,10 +12375,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000030" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12398,10 +12395,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12425,10 +12422,10 @@ "val" : "neotenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12449,10 +12446,10 @@ "val" : "mimicrous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12485,10 +12482,10 @@ "val" : "many to 1 orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12515,10 +12512,10 @@ "val" : "many:many homology " } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12545,10 +12542,10 @@ "val" : "1:many homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12572,10 +12569,10 @@ "val" : "synapomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12600,10 +12597,10 @@ "val" : "symplesiomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12634,10 +12631,10 @@ "val" : "homoiology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12658,10 +12655,10 @@ "val" : "hemiplasous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12682,10 +12679,10 @@ "val" : "gametologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12709,10 +12706,10 @@ "val" : "MeSH:Chromosome_Pairing" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12748,10 +12745,10 @@ "val" : "trans-homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12772,10 +12769,10 @@ "val" : "within-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12797,10 +12794,10 @@ "val" : "between-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12821,10 +12818,10 @@ "val" : "post-displacement" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12841,10 +12838,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000052", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12865,10 +12862,10 @@ "val" : "synologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12892,10 +12889,10 @@ "val" : "ECO:0000080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12922,10 +12919,10 @@ "val" : "serial paralogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12965,10 +12962,10 @@ "val" : "re-awakening" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12993,10 +12990,10 @@ "val" : "syngenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13027,10 +13024,10 @@ "val" : "pseudoorthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13052,10 +13049,10 @@ "val" : "pseudoparalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13077,10 +13074,10 @@ "val" : "equivalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13101,10 +13098,10 @@ "val" : "interologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13125,10 +13122,10 @@ "val" : "functional similarity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13149,10 +13146,10 @@ "val" : "iterative homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13179,10 +13176,10 @@ "val" : "paraxenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13204,10 +13201,10 @@ "val" : "plerologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13229,10 +13226,10 @@ "val" : "homotopous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13253,10 +13250,10 @@ "val" : "heterotopy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13278,10 +13275,10 @@ "val" : "homoeologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13302,10 +13299,10 @@ "val" : "axis paramorphism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13326,10 +13323,10 @@ "val" : "regulogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13606,7 +13603,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001018" + "obj" : "http://purl.obolibrary.org/obo/RO_0001025" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "subPropertyOf", @@ -16335,10 +16332,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0001015", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001018", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", @@ -16840,10 +16833,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001020", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] @@ -17422,9 +17411,6 @@ }, { "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_0001018", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro-base.obo b/ro-base.obo index 8dc953e6..8efea67c 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2023-06-28/ro-base.owl +data-version: ro/releases/2023-08-18/ro-base.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -12,7 +12,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-06-28" xsd:string +property_value: owl:versionInfo "2023-08-18" xsd:string [Term] id: BFO:0000002 @@ -263,7 +263,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -363,7 +363,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -488,7 +488,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -500,7 +499,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -512,7 +510,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -554,25 +551,20 @@ inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 -name: contained in -subset: ro-eco +name: obsolete contained in property_value: IAO:0000111 "contained in" xsd:string property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000118 "contained_in" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001019 -name: contains -subset: ro-eco +name: obsolete contains property_value: IAO:0000111 "contains" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001020 @@ -611,7 +603,7 @@ id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string @@ -680,7 +672,7 @@ def: "The relationship that holds between a trachea or tracheole and an antomica property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: UBERON:0000061 range: UBERON:0000061 -is_a: RO:0001018 ! contained in +is_a: RO:0001025 ! located in [Typedef] id: RO:0002005 @@ -5832,7 +5824,7 @@ property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -5865,7 +5857,6 @@ name: positively correlated with def: "A relation between entities in which one increases or decreases as the other does the same." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 property_value: IAO:0000118 "directly correlated with" xsd:string -is_reflexive: true is_symmetric: true is_a: RO:0002610 ! correlated with @@ -6108,8 +6099,8 @@ synonym: "sameness" EXACT [] synonym: "similar to" EXACT [] 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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/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 @@ -6122,8 +6113,8 @@ name: in homology relationship with def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] comment: This broad definition encompasses all the working definitions proposed so far in the literature. synonym: "homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000001 is_symmetric: true is_a: RO:0002158 ! shares ancestor with @@ -6136,8 +6127,8 @@ name: in homoplasy relationship with def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] synonym: "analogy" RELATED [] synonym: "homoplasous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000002 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with @@ -6149,8 +6140,8 @@ def: "Similarity that is characterized by the organization of anatomical structu comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. synonym: "homocracous to" EXACT [] xref: ECO:0000075 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000003 is_symmetric: true is_a: RO:0002320 ! evolutionarily related to @@ -6162,8 +6153,8 @@ name: in convergence relationship with def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] comment: Convergence usually implies a notion of adaptation. synonym: "analogy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000004 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6174,8 +6165,8 @@ name: in parallelism relationship with def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. synonym: "parallel evolution" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000005 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6188,8 +6179,8 @@ synonym: "idealistic homology" RELATED [] synonym: "structural homologous to" EXACT [] xref: ECO:0000071 xref: MI:2163 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000006 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6211,8 +6202,8 @@ xref: SO:0000853 xref: SO:0000857 xref: SO:homologous_to xref: TAO:homologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000007 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6225,8 +6216,8 @@ comment: Applicable only to morphology. A certain degree of ambiguity is accepte synonym: "biological homologous to" EXACT [] synonym: "transformational homology" RELATED [] xref: ECO:0000067 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000008 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6238,8 +6229,8 @@ def: "Homoplasy that involves phenotypes similar to those seen in ancestors with synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000009 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6253,8 +6244,8 @@ synonym: "synteny" RELATED [] xref: MeSH:Synteny xref: SO:0000860 xref: SO:0005858 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000010 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6267,8 +6258,8 @@ synonym: "paralogous to" EXACT [] xref: SO:0000854 xref: SO:0000859 xref: SO:paralogous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000011 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6281,8 +6272,8 @@ def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20 synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] synonym: "syntenic paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000012 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with @@ -6293,8 +6284,8 @@ id: RO:HOM0000013 name: in syntenic orthology relationship with def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] synonym: "syntenic orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000013 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with @@ -6310,8 +6301,8 @@ synonym: "partial correspondence" RELATED [] synonym: "partial homologous to" EXACT [] synonym: "percent homology" RELATED [] synonym: "segmental homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000014 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6322,8 +6313,8 @@ name: in protein structural homology relationship with def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] synonym: "protein structural homologous to" EXACT [] xref: MeSH:Structural_Homology\,_Protein -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000015 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6335,8 +6326,8 @@ def: "Structural homology that involves a pseudogenic feature and its functional synonym: "non functional homologous to" EXACT [] synonym: "pseudogene" BROAD [] xref: SO:non_functional_homolog_of -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000016 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6352,8 +6343,8 @@ xref: ECO:00000060 xref: SO:0000855 xref: SO:0000858 xref: SO:orthologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000017 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6364,8 +6355,8 @@ name: in xenology relationship with def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). synonym: "xenologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000018 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6377,8 +6368,8 @@ def: "Historical homology that involves two members sharing no other homologs in synonym: "1 to 1 homologous to" EXACT [] synonym: "1:1 homology" EXACT [] synonym: "one-to-one homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000019 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6390,8 +6381,8 @@ def: "Orthology that involves two genes that did not experience any duplication synonym: "1 to 1 orthologous to" EXACT [] synonym: "1:1 orthology" EXACT [] synonym: "one-to-one orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000020 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -6403,8 +6394,8 @@ name: in ohnology relationship with def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] synonym: "homoeology" RELATED [] synonym: "ohnologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000022 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6416,8 +6407,8 @@ def: "Paralogy that results from a lineage-specific duplication subsequent to a synonym: "in-paralogous to" EXACT [] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000023 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6430,8 +6421,8 @@ def: "Paralogy that results from a duplication preceding a given speciation even synonym: "alloparalogy" EXACT [] synonym: "out-paralogous to" EXACT [] synonym: "outparalogy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000024 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6441,8 +6432,8 @@ id: RO:HOM0000025 name: in pro-orthology relationship with def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] synonym: "pro-orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000025 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with @@ -6453,8 +6444,8 @@ name: in semi-orthology relationship with def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] comment: The converse of pro-orthologous. synonym: "semi-orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000026 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with @@ -6465,8 +6456,8 @@ name: in serial homology relationship with def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] synonym: "homonomy" RELATED [] synonym: "serial homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000027 is_symmetric: true is_a: RO:HOM0000066 ! in iterative homology relationship with @@ -6477,8 +6468,8 @@ name: in heterochronous homology relationship with def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] synonym: "heterochronous homologous to" EXACT [] synonym: "heterochrony" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000028 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -6489,8 +6480,8 @@ name: in paedomorphorsis relationship with def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000029 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with @@ -6500,8 +6491,8 @@ disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with id: RO:HOM0000030 name: in peramorphosis relationship with def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000030 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with @@ -6510,8 +6501,8 @@ is_a: RO:HOM0000028 ! in heterochronous homology relationship with id: RO:HOM0000031 name: in progenesis relationship with def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000031 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -6522,8 +6513,8 @@ name: in neoteny relationship with def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] synonym: "juvenilization" EXACT [] synonym: "neotenous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000032 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -6533,8 +6524,8 @@ id: RO:HOM0000033 name: in mimicry relationship with def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] synonym: "mimicrous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000033 is_symmetric: true is_a: RO:HOM0000004 ! in convergence relationship with @@ -6548,8 +6539,8 @@ synonym: "1:many orthology" EXACT [] synonym: "co-orthology" RELATED [] synonym: "many to 1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000034 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -6562,8 +6553,8 @@ def: "Historical homology that involves two members of a larger set of homologs. synonym: "many to many homologous to" EXACT [] synonym: "many-to-many homology" EXACT [] synonym: "many:many homology " EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000036 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6575,8 +6566,8 @@ def: "Historical homology that involves a structure that has no other homologs i synonym: "1 to many homologous to" EXACT [] synonym: "1:many homology" RELATED [] synonym: "one-to-many homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000037 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6587,8 +6578,8 @@ name: in apomorphy relationship with def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] synonym: "apomorphous to" EXACT [] synonym: "synapomorphy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000042 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6601,8 +6592,8 @@ def: "Historical homology that is based on distant shared ancestry." [http://pur comment: This term is usually contrasted to apomorphy. synonym: "plesiomorphous to" EXACT [] synonym: "symplesiomorphy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000043 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6616,8 +6607,8 @@ synonym: "deep genetic homology" EXACT [] synonym: "deep homologous to" EXACT [] synonym: "generative homology" RELATED [] synonym: "homoiology" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000044 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -6628,8 +6619,8 @@ id: RO:HOM0000045 name: in hemiplasy relationship with def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] synonym: "hemiplasous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000045 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6639,8 +6630,8 @@ id: RO:HOM0000046 name: in gametology relationship with def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] synonym: "gametologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000046 is_symmetric: true is_a: RO:HOM0000047 ! in chromosomal homology relationship with @@ -6651,8 +6642,8 @@ name: in chromosomal homology relationship with def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] synonym: "chromosomal homologous to" EXACT [] xref: MeSH:Chromosome_Pairing -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000047 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6667,8 +6658,8 @@ synonym: "many-to-many orthology" EXACT [] synonym: "many:many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000048 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -6679,8 +6670,8 @@ id: RO:HOM0000049 name: in within-species paralogy relationship with def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "within-species paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000049 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6692,8 +6683,8 @@ name: in between-species paralogy relationship with def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] comment: The genes have diverged before a speciation event. synonym: "between-species paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000050 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6703,8 +6694,8 @@ id: RO:HOM0000051 name: in postdisplacement relationship with def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] synonym: "post-displacement" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000051 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -6713,8 +6704,8 @@ is_a: RO:HOM0000029 ! in paedomorphorsis relationship with id: RO:HOM0000052 name: in hypermorphosis relationship with def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000052 is_symmetric: true is_a: RO:HOM0000030 ! in peramorphosis relationship with @@ -6724,8 +6715,8 @@ id: RO:HOM0000053 name: in synology relationship with def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] synonym: "synologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000053 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -6736,8 +6727,8 @@ name: in isoorthology relationship with def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] synonym: "isoorthologous to" EXACT [] xref: ECO:0000080 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000054 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -6750,8 +6741,8 @@ def: "Paralogy that is characterized by duplication of adjacent sequences on a c synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] synonym: "tandem paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000055 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6768,8 +6759,8 @@ synonym: "homoplastic tendency" RELATED [] synonym: "latent homologous to" EXACT [] synonym: "re-awakening" RELATED [] synonym: "underlying synapomorphy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000057 is_symmetric: true is_a: RO:HOM0000005 ! in parallelism relationship with @@ -6782,8 +6773,8 @@ def: "Homocracy that involves recognizably corresponding characters that occurs comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. synonym: "generative homology" EXACT [] synonym: "syngenous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000058 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -6797,8 +6788,8 @@ synonym: "1:1 paralogy" EXACT [] synonym: "apparent 1:1 orthology" EXACT [] synonym: "apparent orthologous to" EXACT [] synonym: "pseudoorthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000060 is_symmetric: true is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with @@ -6810,8 +6801,8 @@ name: in pseudoparalogy relationship with def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] comment: These genes may come out as paralogs in a single-genome analysis. synonym: "pseudoparalogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000061 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -6822,8 +6813,8 @@ name: in equivalogy relationship with def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] comment: This may include examples of orthology, paralogy and xenology. synonym: "equivalogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000062 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6834,8 +6825,8 @@ id: RO:HOM0000063 name: in interology relationship with def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] synonym: "interologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000063 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6845,8 +6836,8 @@ id: RO:HOM0000065 name: in functional equivalence relationship with def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] synonym: "functional similarity" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000065 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with @@ -6856,8 +6847,8 @@ id: RO:HOM0000066 name: in iterative homology relationship with def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] synonym: "iterative homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000066 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -6869,8 +6860,8 @@ def: "Xenology that is characterized by multiple horizontal transfer events, res synonym: "duplicate xenology" EXACT [] synonym: "multiple xenology" EXACT [] synonym: "paraxenologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000068 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -6881,8 +6872,8 @@ name: in plerology relationship with def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] comment: This phenomenon is usually due to gene conversion process. synonym: "plerologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000069 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6893,8 +6884,8 @@ name: in homotopy relationship with def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. synonym: "homotopous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000071 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6905,8 +6896,8 @@ id: RO:HOM0000072 name: in homeosis relationship with def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] synonym: "heterotopy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000072 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -6917,8 +6908,8 @@ name: in homoeology relationship with def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. synonym: "homoeologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000073 is_symmetric: true is_a: RO:HOM0000022 ! in ohnology relationship with @@ -6929,8 +6920,8 @@ id: RO:HOM0000074 name: in paramorphism relationship with def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] synonym: "axis paramorphism" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000074 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -6941,8 +6932,8 @@ id: RO:HOM0000075 name: in regulogy relationship with def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] synonym: "regulogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000075 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with diff --git a/ro-base.owl b/ro-base.owl index 578d6094..f6602b63 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -18,12 +18,12 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://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 - 2023-06-28 + 2023-08-18 https://github.com/oborel/obo-relations/ @@ -917,24 +917,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - @@ -1293,7 +1275,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1439,7 +1421,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1593,7 +1575,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. @@ -1609,7 +1590,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. @@ -1625,7 +1605,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. @@ -1690,24 +1669,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - contained_in - - - contained in + obsolete contained in + + true @@ -1716,9 +1684,9 @@ range: spatial region or site (immaterial continuant) contains - - - contains + obsolete contains + + true @@ -1809,7 +1777,7 @@ range: spatial region or site (immaterial continuant) Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in @@ -1896,7 +1864,7 @@ range: spatial region or site (immaterial continuant) - + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). @@ -10210,7 +10178,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10244,7 +10212,7 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10256,7 +10224,6 @@ For example, protein A (transcription factor) indirectly increases by expression - A relation between entities in which one increases or decreases as the other does the same. directly correlated with @@ -10681,8 +10648,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu TODO: Add homeomorphy axiom - - + + ECO:0000041 SO:similar_to sameness @@ -10716,8 +10683,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from common evolutionary origin. - - + + homologous to This broad definition encompasses all the working definitions proposed so far in the literature. in homology relationship with @@ -10741,8 +10708,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - - + + homoplasous to analogy in homoplasy relationship with @@ -10765,8 +10732,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - + + ECO:0000075 homocracous to Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. @@ -10791,8 +10758,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - - + + analogy Convergence usually implies a notion of adaptation. in convergence relationship with @@ -10814,8 +10781,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - - + + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. in parallelism relationship with @@ -10837,8 +10804,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - - + + ECO:0000071 MI:2163 structural homologous to @@ -10864,8 +10831,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - - + + homology ECO:0000080 RO_proposed_relation:homologous_to @@ -10899,8 +10866,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - + + ECO:0000067 biological homologous to transformational homology @@ -10925,8 +10892,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - + + atavism rudiment reversion @@ -10949,8 +10916,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - - + + MeSH:Synteny SO:0000860 SO:0005858 @@ -10976,8 +10943,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - - + + SO:0000854 SO:0000859 SO:paralogous_to @@ -11004,8 +10971,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - - + + syntenic paralogous to duplicon paralogon @@ -11029,8 +10996,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - - + + syntenic orthologous to in syntenic orthology relationship with @@ -11051,8 +11018,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - + + fractional homology partial homologous to segmental homology @@ -11080,8 +11047,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - + + MeSH:Structural_Homology,_Protein protein structural homologous to in protein structural homology relationship with @@ -11104,8 +11071,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - - + + pseudogene SO:non_functional_homolog_of non functional homologous to @@ -11128,8 +11095,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - - + + ECO:00000060 SO:0000855 SO:0000858 @@ -11158,8 +11125,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - + + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). in xenology relationship with @@ -11182,8 +11149,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - - + + 1 to 1 homologous to 1:1 homology one-to-one homology @@ -11207,8 +11174,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - + + 1 to 1 orthologous to 1:1 orthology one-to-one orthology @@ -11232,8 +11199,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - - + + ohnologous to homoeology in ohnology relationship with @@ -11256,8 +11223,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - + + in-paralogous to inparalogy symparalogy @@ -11280,8 +11247,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - - + + alloparalogy out-paralogous to outparalogy @@ -11304,8 +11271,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - + + pro-orthologous to in pro-orthology relationship with @@ -11327,8 +11294,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - + + semi-orthologous to The converse of pro-orthologous. in semi-orthology relationship with @@ -11351,8 +11318,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - - + + serial homologous to homonomy in serial homology relationship with @@ -11374,8 +11341,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - + + heterochronous homologous to heterochrony in heterochronous homology relationship with @@ -11398,8 +11365,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - + + juvenification pedomorphosis in paedomorphorsis relationship with @@ -11422,8 +11389,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - + + in peramorphosis relationship with @@ -11443,8 +11410,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - + + in progenesis relationship with @@ -11465,8 +11432,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - - + + juvenilization neotenous to in neoteny relationship with @@ -11489,8 +11456,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - - + + mimicrous to in mimicry relationship with @@ -11512,8 +11479,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - + + 1 to many orthologous to 1:many orthology one-to-many orthology @@ -11539,8 +11506,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - - + + many to many homologous to many-to-many homology many:many homology @@ -11563,8 +11530,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - + + 1 to many homologous to one-to-many homology 1:many homology @@ -11588,8 +11555,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - + + apomorphous to synapomorphy in apomorphy relationship with @@ -11611,8 +11578,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - - + + plesiomorphous to symplesiomorphy This term is usually contrasted to apomorphy. @@ -11636,8 +11603,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - + + deep genetic homology deep homologous to generative homology @@ -11663,8 +11630,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - + + hemiplasous to in hemiplasy relationship with @@ -11685,8 +11652,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - + + gametologous to in gametology relationship with @@ -11707,8 +11674,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - + + MeSH:Chromosome_Pairing chromosomal homologous to in chromosomal homology relationship with @@ -11731,8 +11698,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - + + many to many orthologous to many-to-many orthology many:many orthology @@ -11760,8 +11727,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - - + + within-species paralogous to in within-species paralogy relationship with @@ -11782,8 +11749,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - - + + between-species paralogous to The genes have diverged before a speciation event. in between-species paralogy relationship with @@ -11805,8 +11772,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - + + post-displacement in postdisplacement relationship with @@ -11827,8 +11794,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - - + + in hypermorphosis relationship with @@ -11849,8 +11816,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - + + synologous to in synology relationship with @@ -11873,8 +11840,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - - + + ECO:0000080 isoorthologous to in isoorthology relationship with @@ -11896,8 +11863,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - + + tandem paralogous to iterative paralogy serial paralogy @@ -11922,8 +11889,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - + + apomorphic tendency cryptic homology latent homologous to @@ -11954,8 +11921,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - + + generative homology syngenous to Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. @@ -11980,8 +11947,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - + + 1:1 paralogy apparent 1:1 orthology apparent orthologous to @@ -12007,8 +11974,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - + + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. in pseudoparalogy relationship with @@ -12031,8 +11998,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - - + + equivalogous to This may include examples of orthology, paralogy and xenology. in equivalogy relationship with @@ -12054,8 +12021,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - + + interologous to in interology relationship with @@ -12077,8 +12044,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - - + + functional similarity in functional equivalence relationship with @@ -12100,8 +12067,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - - + + iterative homologous to in iterative homology relationship with @@ -12122,8 +12089,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - + + duplicate xenology multiple xenology paraxenologous to @@ -12146,8 +12113,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - + + plerologous to This phenomenon is usually due to gene conversion process. in plerology relationship with @@ -12170,8 +12137,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - - + + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. in homotopy relationship with @@ -12195,8 +12162,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - - + + heterotopy in homeosis relationship with @@ -12219,8 +12186,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - - + + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. in homoeology relationship with @@ -12243,8 +12210,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - + + axis paramorphism in paramorphism relationship with @@ -12266,8 +12233,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - + + regulogous to in regulogy relationship with diff --git a/ro-full.json b/ro-full.json index 98ff4f25..ecabec35 100644 --- a/ro-full.json +++ b/ro-full.json @@ -13,12 +13,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-28" + "val" : "2023-08-18" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro-full.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -384,7 +384,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -2482,6 +2482,36 @@ "val" : "https://orcid.org/0000-0003-4423-4370" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003008", + "lbl" : "previous name", + "meta" : { + "definition" : { + "val" : "A synonym type for names that have been used as primary labels in the past." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003009", + "lbl" : "legal name", + "meta" : { + "definition" : { + "val" : "A synonym type for the legal entity name" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -2649,7 +2679,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -2988,10 +3018,9 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "lbl" : "contained in", + "lbl" : "obsolete contained in", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contained in" @@ -3001,30 +3030,28 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained_in" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "lbl" : "contains", + "lbl" : "obsolete contains", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contains" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001020", @@ -3101,7 +3128,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13062,7 +13089,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" @@ -13661,10 +13688,10 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13686,10 +13713,10 @@ "val" : "homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13713,10 +13740,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13741,10 +13768,10 @@ "val" : "ECO:0000075" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13766,10 +13793,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13791,10 +13818,10 @@ "val" : "parallel evolution" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13823,10 +13850,10 @@ "val" : "MI:2163" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13877,10 +13904,10 @@ "val" : "TAO:homologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13908,10 +13935,10 @@ "val" : "ECO:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13938,10 +13965,10 @@ "val" : "reversion" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13972,10 +13999,10 @@ "val" : "SO:0005858" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14003,10 +14030,10 @@ "val" : "SO:paralogous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14033,10 +14060,10 @@ "val" : "paralogon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14057,10 +14084,10 @@ "val" : "syntenic orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14099,10 +14126,10 @@ "val" : "percent homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14126,10 +14153,10 @@ "val" : "MeSH:Structural_Homology,_Protein" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14156,10 +14183,10 @@ "val" : "SO:non_functional_homolog_of" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14190,10 +14217,10 @@ "val" : "SO:orthologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14215,10 +14242,10 @@ "val" : "xenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14245,10 +14272,10 @@ "val" : "one-to-one homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14275,10 +14302,10 @@ "val" : "one-to-one orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14302,10 +14329,10 @@ "val" : "homoeology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14332,10 +14359,10 @@ "val" : "symparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14362,10 +14389,10 @@ "val" : "outparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14386,10 +14413,10 @@ "val" : "pro-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14411,10 +14438,10 @@ "val" : "semi-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14438,10 +14465,10 @@ "val" : "homonomy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14465,10 +14492,10 @@ "val" : "heterochrony" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14492,10 +14519,10 @@ "val" : "pedomorphosis" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14512,10 +14539,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000030" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14532,10 +14559,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14559,10 +14586,10 @@ "val" : "neotenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14583,10 +14610,10 @@ "val" : "mimicrous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14619,10 +14646,10 @@ "val" : "many to 1 orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14649,10 +14676,10 @@ "val" : "many:many homology " } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14679,10 +14706,10 @@ "val" : "1:many homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14706,10 +14733,10 @@ "val" : "synapomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14734,10 +14761,10 @@ "val" : "symplesiomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14768,10 +14795,10 @@ "val" : "homoiology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14792,10 +14819,10 @@ "val" : "hemiplasous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14816,10 +14843,10 @@ "val" : "gametologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14843,10 +14870,10 @@ "val" : "MeSH:Chromosome_Pairing" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14882,10 +14909,10 @@ "val" : "trans-homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14906,10 +14933,10 @@ "val" : "within-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14931,10 +14958,10 @@ "val" : "between-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14955,10 +14982,10 @@ "val" : "post-displacement" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14975,10 +15002,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000052", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14999,10 +15026,10 @@ "val" : "synologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15026,10 +15053,10 @@ "val" : "ECO:0000080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15056,10 +15083,10 @@ "val" : "serial paralogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15099,10 +15126,10 @@ "val" : "re-awakening" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15127,10 +15154,10 @@ "val" : "syngenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15161,10 +15188,10 @@ "val" : "pseudoorthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15186,10 +15213,10 @@ "val" : "pseudoparalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15211,10 +15238,10 @@ "val" : "equivalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15235,10 +15262,10 @@ "val" : "interologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15259,10 +15286,10 @@ "val" : "functional similarity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15283,10 +15310,10 @@ "val" : "iterative homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15313,10 +15340,10 @@ "val" : "paraxenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15338,10 +15365,10 @@ "val" : "plerologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15363,10 +15390,10 @@ "val" : "homotopous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15387,10 +15414,10 @@ "val" : "heterotopy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15412,10 +15439,10 @@ "val" : "homoeologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15436,10 +15463,10 @@ "val" : "axis paramorphism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15460,10 +15487,10 @@ "val" : "regulogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -16301,7 +16328,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001018" + "obj" : "http://purl.obolibrary.org/obo/RO_0001025" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "subPropertyOf", @@ -19030,10 +19057,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0001015", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001018", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", @@ -19535,10 +19558,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001020", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] @@ -20117,9 +20136,6 @@ }, { "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_0001018", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro-full.obo b/ro-full.obo index 40c54a4c..6879f323 100644 --- a/ro-full.obo +++ b/ro-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: ro/releases/2023-06-28/ro-full.owl +data-version: ro/releases/2023-08-18/ro-full.owl subsetdef: common_anatomy "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -13,7 +13,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-06-28" xsd:string +property_value: owl:versionInfo "2023-08-18" xsd:string [Term] id: BFO:0000002 @@ -711,7 +711,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -816,7 +816,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -941,7 +941,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -953,7 +952,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -965,7 +963,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -1007,25 +1004,20 @@ inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 -name: contained in -subset: ro-eco +name: obsolete contained in property_value: IAO:0000111 "contained in" xsd:string property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000118 "contained_in" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001019 -name: contains -subset: ro-eco +name: obsolete contains property_value: IAO:0000111 "contains" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001020 @@ -1064,7 +1056,7 @@ id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string @@ -1133,7 +1125,7 @@ def: "The relationship that holds between a trachea or tracheole and an antomica property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: RO:0001018 ! contained in +is_a: RO:0001025 ! located in [Typedef] id: RO:0002005 @@ -6285,7 +6277,7 @@ property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -6318,7 +6310,6 @@ name: positively correlated with def: "A relation between entities in which one increases or decreases as the other does the same." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 property_value: IAO:0000118 "directly correlated with" xsd:string -is_reflexive: true is_symmetric: true is_a: RO:0002610 ! correlated with @@ -6561,8 +6552,8 @@ synonym: "sameness" EXACT [] synonym: "similar to" EXACT [] 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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/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 @@ -6575,8 +6566,8 @@ name: in homology relationship with def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] comment: This broad definition encompasses all the working definitions proposed so far in the literature. synonym: "homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000001 is_symmetric: true is_a: RO:0002158 ! shares ancestor with @@ -6589,8 +6580,8 @@ name: in homoplasy relationship with def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] synonym: "analogy" RELATED [] synonym: "homoplasous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000002 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with @@ -6602,8 +6593,8 @@ def: "Similarity that is characterized by the organization of anatomical structu comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. synonym: "homocracous to" EXACT [] xref: ECO:0000075 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000003 is_symmetric: true is_a: RO:0002320 ! evolutionarily related to @@ -6615,8 +6606,8 @@ name: in convergence relationship with def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] comment: Convergence usually implies a notion of adaptation. synonym: "analogy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000004 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6627,8 +6618,8 @@ name: in parallelism relationship with def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. synonym: "parallel evolution" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000005 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6641,8 +6632,8 @@ synonym: "idealistic homology" RELATED [] synonym: "structural homologous to" EXACT [] xref: ECO:0000071 xref: MI:2163 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000006 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6664,8 +6655,8 @@ xref: SO:0000853 xref: SO:0000857 xref: SO:homologous_to xref: TAO:homologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000007 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6678,8 +6669,8 @@ comment: Applicable only to morphology. A certain degree of ambiguity is accepte synonym: "biological homologous to" EXACT [] synonym: "transformational homology" RELATED [] xref: ECO:0000067 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000008 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6691,8 +6682,8 @@ def: "Homoplasy that involves phenotypes similar to those seen in ancestors with synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000009 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6706,8 +6697,8 @@ synonym: "synteny" RELATED [] xref: MeSH:Synteny xref: SO:0000860 xref: SO:0005858 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000010 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6720,8 +6711,8 @@ synonym: "paralogous to" EXACT [] xref: SO:0000854 xref: SO:0000859 xref: SO:paralogous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000011 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6734,8 +6725,8 @@ def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20 synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] synonym: "syntenic paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000012 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with @@ -6746,8 +6737,8 @@ id: RO:HOM0000013 name: in syntenic orthology relationship with def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] synonym: "syntenic orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000013 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with @@ -6763,8 +6754,8 @@ synonym: "partial correspondence" RELATED [] synonym: "partial homologous to" EXACT [] synonym: "percent homology" RELATED [] synonym: "segmental homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000014 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6775,8 +6766,8 @@ name: in protein structural homology relationship with def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] synonym: "protein structural homologous to" EXACT [] xref: MeSH:Structural_Homology\,_Protein -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000015 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6788,8 +6779,8 @@ def: "Structural homology that involves a pseudogenic feature and its functional synonym: "non functional homologous to" EXACT [] synonym: "pseudogene" BROAD [] xref: SO:non_functional_homolog_of -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000016 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6805,8 +6796,8 @@ xref: ECO:00000060 xref: SO:0000855 xref: SO:0000858 xref: SO:orthologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000017 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6817,8 +6808,8 @@ name: in xenology relationship with def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). synonym: "xenologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000018 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6830,8 +6821,8 @@ def: "Historical homology that involves two members sharing no other homologs in synonym: "1 to 1 homologous to" EXACT [] synonym: "1:1 homology" EXACT [] synonym: "one-to-one homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000019 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6843,8 +6834,8 @@ def: "Orthology that involves two genes that did not experience any duplication synonym: "1 to 1 orthologous to" EXACT [] synonym: "1:1 orthology" EXACT [] synonym: "one-to-one orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000020 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -6856,8 +6847,8 @@ name: in ohnology relationship with def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] synonym: "homoeology" RELATED [] synonym: "ohnologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000022 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6869,8 +6860,8 @@ def: "Paralogy that results from a lineage-specific duplication subsequent to a synonym: "in-paralogous to" EXACT [] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000023 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6883,8 +6874,8 @@ def: "Paralogy that results from a duplication preceding a given speciation even synonym: "alloparalogy" EXACT [] synonym: "out-paralogous to" EXACT [] synonym: "outparalogy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000024 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6894,8 +6885,8 @@ id: RO:HOM0000025 name: in pro-orthology relationship with def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] synonym: "pro-orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000025 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with @@ -6906,8 +6897,8 @@ name: in semi-orthology relationship with def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] comment: The converse of pro-orthologous. synonym: "semi-orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000026 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with @@ -6918,8 +6909,8 @@ name: in serial homology relationship with def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] synonym: "homonomy" RELATED [] synonym: "serial homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000027 is_symmetric: true is_a: RO:HOM0000066 ! in iterative homology relationship with @@ -6930,8 +6921,8 @@ name: in heterochronous homology relationship with def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] synonym: "heterochronous homologous to" EXACT [] synonym: "heterochrony" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000028 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -6942,8 +6933,8 @@ name: in paedomorphorsis relationship with def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000029 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with @@ -6953,8 +6944,8 @@ disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with id: RO:HOM0000030 name: in peramorphosis relationship with def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000030 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with @@ -6963,8 +6954,8 @@ is_a: RO:HOM0000028 ! in heterochronous homology relationship with id: RO:HOM0000031 name: in progenesis relationship with def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000031 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -6975,8 +6966,8 @@ name: in neoteny relationship with def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] synonym: "juvenilization" EXACT [] synonym: "neotenous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000032 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -6986,8 +6977,8 @@ id: RO:HOM0000033 name: in mimicry relationship with def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] synonym: "mimicrous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000033 is_symmetric: true is_a: RO:HOM0000004 ! in convergence relationship with @@ -7001,8 +6992,8 @@ synonym: "1:many orthology" EXACT [] synonym: "co-orthology" RELATED [] synonym: "many to 1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000034 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -7015,8 +7006,8 @@ def: "Historical homology that involves two members of a larger set of homologs. synonym: "many to many homologous to" EXACT [] synonym: "many-to-many homology" EXACT [] synonym: "many:many homology " EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000036 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7028,8 +7019,8 @@ def: "Historical homology that involves a structure that has no other homologs i synonym: "1 to many homologous to" EXACT [] synonym: "1:many homology" RELATED [] synonym: "one-to-many homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000037 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7040,8 +7031,8 @@ name: in apomorphy relationship with def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] synonym: "apomorphous to" EXACT [] synonym: "synapomorphy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000042 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7054,8 +7045,8 @@ def: "Historical homology that is based on distant shared ancestry." [http://pur comment: This term is usually contrasted to apomorphy. synonym: "plesiomorphous to" EXACT [] synonym: "symplesiomorphy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000043 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7069,8 +7060,8 @@ synonym: "deep genetic homology" EXACT [] synonym: "deep homologous to" EXACT [] synonym: "generative homology" RELATED [] synonym: "homoiology" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000044 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -7081,8 +7072,8 @@ id: RO:HOM0000045 name: in hemiplasy relationship with def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] synonym: "hemiplasous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000045 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7092,8 +7083,8 @@ id: RO:HOM0000046 name: in gametology relationship with def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] synonym: "gametologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000046 is_symmetric: true is_a: RO:HOM0000047 ! in chromosomal homology relationship with @@ -7104,8 +7095,8 @@ name: in chromosomal homology relationship with def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] synonym: "chromosomal homologous to" EXACT [] xref: MeSH:Chromosome_Pairing -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000047 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7120,8 +7111,8 @@ synonym: "many-to-many orthology" EXACT [] synonym: "many:many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000048 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -7132,8 +7123,8 @@ id: RO:HOM0000049 name: in within-species paralogy relationship with def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "within-species paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000049 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7145,8 +7136,8 @@ name: in between-species paralogy relationship with def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] comment: The genes have diverged before a speciation event. synonym: "between-species paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000050 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7156,8 +7147,8 @@ id: RO:HOM0000051 name: in postdisplacement relationship with def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] synonym: "post-displacement" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000051 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -7166,8 +7157,8 @@ is_a: RO:HOM0000029 ! in paedomorphorsis relationship with id: RO:HOM0000052 name: in hypermorphosis relationship with def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000052 is_symmetric: true is_a: RO:HOM0000030 ! in peramorphosis relationship with @@ -7177,8 +7168,8 @@ id: RO:HOM0000053 name: in synology relationship with def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] synonym: "synologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000053 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -7189,8 +7180,8 @@ name: in isoorthology relationship with def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] synonym: "isoorthologous to" EXACT [] xref: ECO:0000080 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000054 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -7203,8 +7194,8 @@ def: "Paralogy that is characterized by duplication of adjacent sequences on a c synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] synonym: "tandem paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000055 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7221,8 +7212,8 @@ synonym: "homoplastic tendency" RELATED [] synonym: "latent homologous to" EXACT [] synonym: "re-awakening" RELATED [] synonym: "underlying synapomorphy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000057 is_symmetric: true is_a: RO:HOM0000005 ! in parallelism relationship with @@ -7235,8 +7226,8 @@ def: "Homocracy that involves recognizably corresponding characters that occurs comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. synonym: "generative homology" EXACT [] synonym: "syngenous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000058 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -7250,8 +7241,8 @@ synonym: "1:1 paralogy" EXACT [] synonym: "apparent 1:1 orthology" EXACT [] synonym: "apparent orthologous to" EXACT [] synonym: "pseudoorthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000060 is_symmetric: true is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with @@ -7263,8 +7254,8 @@ name: in pseudoparalogy relationship with def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] comment: These genes may come out as paralogs in a single-genome analysis. synonym: "pseudoparalogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000061 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -7275,8 +7266,8 @@ name: in equivalogy relationship with def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] comment: This may include examples of orthology, paralogy and xenology. synonym: "equivalogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000062 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7287,8 +7278,8 @@ id: RO:HOM0000063 name: in interology relationship with def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] synonym: "interologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000063 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7298,8 +7289,8 @@ id: RO:HOM0000065 name: in functional equivalence relationship with def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] synonym: "functional similarity" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000065 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with @@ -7309,8 +7300,8 @@ id: RO:HOM0000066 name: in iterative homology relationship with def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] synonym: "iterative homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000066 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -7322,8 +7313,8 @@ def: "Xenology that is characterized by multiple horizontal transfer events, res synonym: "duplicate xenology" EXACT [] synonym: "multiple xenology" EXACT [] synonym: "paraxenologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000068 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -7334,8 +7325,8 @@ name: in plerology relationship with def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] comment: This phenomenon is usually due to gene conversion process. synonym: "plerologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000069 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7346,8 +7337,8 @@ name: in homotopy relationship with def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. synonym: "homotopous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000071 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -7358,8 +7349,8 @@ id: RO:HOM0000072 name: in homeosis relationship with def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] synonym: "heterotopy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000072 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -7370,8 +7361,8 @@ name: in homoeology relationship with def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. synonym: "homoeologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000073 is_symmetric: true is_a: RO:HOM0000022 ! in ohnology relationship with @@ -7382,8 +7373,8 @@ id: RO:HOM0000074 name: in paramorphism relationship with def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] synonym: "axis paramorphism" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000074 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -7394,8 +7385,8 @@ id: RO:HOM0000075 name: in regulogy relationship with def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] synonym: "regulogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000075 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with diff --git a/ro-full.owl b/ro-full.owl index ff2f151d..6795b17f 100644 --- a/ro-full.owl +++ b/ro-full.owl @@ -21,11 +21,11 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://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 - 2023-06-28 + 2023-08-18 https://github.com/oborel/obo-relations/ @@ -1164,12 +1164,6 @@ Where we have an annotation assertion - - - - - - @@ -1647,7 +1641,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1802,7 +1796,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1956,7 +1950,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. @@ -1972,7 +1965,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. @@ -1988,7 +1980,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. @@ -2053,24 +2044,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - contained_in - - - contained in + obsolete contained in + + true @@ -2079,9 +2059,9 @@ range: spatial region or site (immaterial continuant) contains - - - contains + obsolete contains + + true @@ -2172,7 +2152,7 @@ range: spatial region or site (immaterial continuant) Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in @@ -2259,7 +2239,7 @@ range: spatial region or site (immaterial continuant) - + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). @@ -10573,7 +10553,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10607,7 +10587,7 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10619,7 +10599,6 @@ For example, protein A (transcription factor) indirectly increases by expression - A relation between entities in which one increases or decreases as the other does the same. directly correlated with @@ -11044,8 +11023,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu TODO: Add homeomorphy axiom - - + + ECO:0000041 SO:similar_to sameness @@ -11079,8 +11058,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from common evolutionary origin. - - + + homologous to This broad definition encompasses all the working definitions proposed so far in the literature. in homology relationship with @@ -11104,8 +11083,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - - + + homoplasous to analogy in homoplasy relationship with @@ -11128,8 +11107,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - + + ECO:0000075 homocracous to Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. @@ -11154,8 +11133,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - - + + analogy Convergence usually implies a notion of adaptation. in convergence relationship with @@ -11177,8 +11156,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - - + + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. in parallelism relationship with @@ -11200,8 +11179,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - - + + ECO:0000071 MI:2163 structural homologous to @@ -11227,8 +11206,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - - + + homology ECO:0000080 RO_proposed_relation:homologous_to @@ -11262,8 +11241,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - + + ECO:0000067 biological homologous to transformational homology @@ -11288,8 +11267,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - + + atavism rudiment reversion @@ -11312,8 +11291,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - - + + MeSH:Synteny SO:0000860 SO:0005858 @@ -11339,8 +11318,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - - + + SO:0000854 SO:0000859 SO:paralogous_to @@ -11367,8 +11346,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - - + + syntenic paralogous to duplicon paralogon @@ -11392,8 +11371,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - - + + syntenic orthologous to in syntenic orthology relationship with @@ -11414,8 +11393,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - + + fractional homology partial homologous to segmental homology @@ -11443,8 +11422,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - + + MeSH:Structural_Homology,_Protein protein structural homologous to in protein structural homology relationship with @@ -11467,8 +11446,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - - + + pseudogene SO:non_functional_homolog_of non functional homologous to @@ -11491,8 +11470,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - - + + ECO:00000060 SO:0000855 SO:0000858 @@ -11521,8 +11500,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - + + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). in xenology relationship with @@ -11545,8 +11524,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - - + + 1 to 1 homologous to 1:1 homology one-to-one homology @@ -11570,8 +11549,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - + + 1 to 1 orthologous to 1:1 orthology one-to-one orthology @@ -11595,8 +11574,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - - + + ohnologous to homoeology in ohnology relationship with @@ -11619,8 +11598,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - + + in-paralogous to inparalogy symparalogy @@ -11643,8 +11622,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - - + + alloparalogy out-paralogous to outparalogy @@ -11667,8 +11646,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - + + pro-orthologous to in pro-orthology relationship with @@ -11690,8 +11669,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - + + semi-orthologous to The converse of pro-orthologous. in semi-orthology relationship with @@ -11714,8 +11693,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - - + + serial homologous to homonomy in serial homology relationship with @@ -11737,8 +11716,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - + + heterochronous homologous to heterochrony in heterochronous homology relationship with @@ -11761,8 +11740,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - + + juvenification pedomorphosis in paedomorphorsis relationship with @@ -11785,8 +11764,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - + + in peramorphosis relationship with @@ -11806,8 +11785,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - + + in progenesis relationship with @@ -11828,8 +11807,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - - + + juvenilization neotenous to in neoteny relationship with @@ -11852,8 +11831,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - - + + mimicrous to in mimicry relationship with @@ -11875,8 +11854,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - + + 1 to many orthologous to 1:many orthology one-to-many orthology @@ -11902,8 +11881,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - - + + many to many homologous to many-to-many homology many:many homology @@ -11926,8 +11905,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - + + 1 to many homologous to one-to-many homology 1:many homology @@ -11951,8 +11930,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - + + apomorphous to synapomorphy in apomorphy relationship with @@ -11974,8 +11953,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - - + + plesiomorphous to symplesiomorphy This term is usually contrasted to apomorphy. @@ -11999,8 +11978,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - + + deep genetic homology deep homologous to generative homology @@ -12026,8 +12005,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - + + hemiplasous to in hemiplasy relationship with @@ -12048,8 +12027,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - + + gametologous to in gametology relationship with @@ -12070,8 +12049,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - + + MeSH:Chromosome_Pairing chromosomal homologous to in chromosomal homology relationship with @@ -12094,8 +12073,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - + + many to many orthologous to many-to-many orthology many:many orthology @@ -12123,8 +12102,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - - + + within-species paralogous to in within-species paralogy relationship with @@ -12145,8 +12124,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - - + + between-species paralogous to The genes have diverged before a speciation event. in between-species paralogy relationship with @@ -12168,8 +12147,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - + + post-displacement in postdisplacement relationship with @@ -12190,8 +12169,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - - + + in hypermorphosis relationship with @@ -12212,8 +12191,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - + + synologous to in synology relationship with @@ -12236,8 +12215,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - - + + ECO:0000080 isoorthologous to in isoorthology relationship with @@ -12259,8 +12238,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - + + tandem paralogous to iterative paralogy serial paralogy @@ -12285,8 +12264,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - + + apomorphic tendency cryptic homology latent homologous to @@ -12317,8 +12296,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - + + generative homology syngenous to Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. @@ -12343,8 +12322,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - + + 1:1 paralogy apparent 1:1 orthology apparent orthologous to @@ -12370,8 +12349,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - + + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. in pseudoparalogy relationship with @@ -12394,8 +12373,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - - + + equivalogous to This may include examples of orthology, paralogy and xenology. in equivalogy relationship with @@ -12417,8 +12396,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - + + interologous to in interology relationship with @@ -12440,8 +12419,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - - + + functional similarity in functional equivalence relationship with @@ -12463,8 +12442,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - - + + iterative homologous to in iterative homology relationship with @@ -12485,8 +12464,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - + + duplicate xenology multiple xenology paraxenologous to @@ -12509,8 +12488,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - + + plerologous to This phenomenon is usually due to gene conversion process. in plerology relationship with @@ -12533,8 +12512,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - - + + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. in homotopy relationship with @@ -12558,8 +12537,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - - + + heterotopy in homeosis relationship with @@ -12582,8 +12561,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - - + + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. in homoeology relationship with @@ -12606,8 +12585,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - + + axis paramorphism in paramorphism relationship with @@ -12629,8 +12608,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - + + regulogous to in regulogy relationship with @@ -15452,6 +15431,18 @@ No imports misnomer + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + previous name + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + legal name + diff --git a/ro.json b/ro.json index f43bfa61..e0aadc9d 100644 --- a/ro.json +++ b/ro.json @@ -13,12 +13,12 @@ "val" : "OBO Relations Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-28" + "val" : "2023-08-18" }, { "pred" : "http://xmlns.com/foaf/0.1/homepage", "val" : " https://github.com/oborel/obo-relations/" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro.json" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -384,7 +384,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -2482,6 +2482,36 @@ "val" : "https://orcid.org/0000-0003-4423-4370" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003008", + "lbl" : "previous name", + "meta" : { + "definition" : { + "val" : "A synonym type for names that have been used as primary labels in the past." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003009", + "lbl" : "legal name", + "meta" : { + "definition" : { + "val" : "A synonym type for the legal entity name" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -2649,7 +2679,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -2988,10 +3018,9 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "lbl" : "contained in", + "lbl" : "obsolete contained in", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contained in" @@ -3001,30 +3030,28 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained_in" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "lbl" : "contains", + "lbl" : "obsolete contains", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contains" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001020", @@ -3101,7 +3128,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13062,7 +13089,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" @@ -13661,10 +13688,10 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13686,10 +13713,10 @@ "val" : "homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13713,10 +13740,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13741,10 +13768,10 @@ "val" : "ECO:0000075" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13766,10 +13793,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13791,10 +13818,10 @@ "val" : "parallel evolution" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13823,10 +13850,10 @@ "val" : "MI:2163" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13877,10 +13904,10 @@ "val" : "TAO:homologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13908,10 +13935,10 @@ "val" : "ECO:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13938,10 +13965,10 @@ "val" : "reversion" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13972,10 +13999,10 @@ "val" : "SO:0005858" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14003,10 +14030,10 @@ "val" : "SO:paralogous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14033,10 +14060,10 @@ "val" : "paralogon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14057,10 +14084,10 @@ "val" : "syntenic orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14099,10 +14126,10 @@ "val" : "percent homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14126,10 +14153,10 @@ "val" : "MeSH:Structural_Homology,_Protein" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14156,10 +14183,10 @@ "val" : "SO:non_functional_homolog_of" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14190,10 +14217,10 @@ "val" : "SO:orthologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14215,10 +14242,10 @@ "val" : "xenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14245,10 +14272,10 @@ "val" : "one-to-one homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14275,10 +14302,10 @@ "val" : "one-to-one orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14302,10 +14329,10 @@ "val" : "homoeology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14332,10 +14359,10 @@ "val" : "symparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14362,10 +14389,10 @@ "val" : "outparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14386,10 +14413,10 @@ "val" : "pro-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14411,10 +14438,10 @@ "val" : "semi-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14438,10 +14465,10 @@ "val" : "homonomy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14465,10 +14492,10 @@ "val" : "heterochrony" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14492,10 +14519,10 @@ "val" : "pedomorphosis" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14512,10 +14539,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000030" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14532,10 +14559,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14559,10 +14586,10 @@ "val" : "neotenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14583,10 +14610,10 @@ "val" : "mimicrous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14619,10 +14646,10 @@ "val" : "many to 1 orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14649,10 +14676,10 @@ "val" : "many:many homology " } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14679,10 +14706,10 @@ "val" : "1:many homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14706,10 +14733,10 @@ "val" : "synapomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14734,10 +14761,10 @@ "val" : "symplesiomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14768,10 +14795,10 @@ "val" : "homoiology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14792,10 +14819,10 @@ "val" : "hemiplasous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14816,10 +14843,10 @@ "val" : "gametologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14843,10 +14870,10 @@ "val" : "MeSH:Chromosome_Pairing" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14882,10 +14909,10 @@ "val" : "trans-homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14906,10 +14933,10 @@ "val" : "within-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14931,10 +14958,10 @@ "val" : "between-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14955,10 +14982,10 @@ "val" : "post-displacement" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14975,10 +15002,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000052", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14999,10 +15026,10 @@ "val" : "synologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15026,10 +15053,10 @@ "val" : "ECO:0000080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15056,10 +15083,10 @@ "val" : "serial paralogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15099,10 +15126,10 @@ "val" : "re-awakening" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15127,10 +15154,10 @@ "val" : "syngenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15161,10 +15188,10 @@ "val" : "pseudoorthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15186,10 +15213,10 @@ "val" : "pseudoparalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15211,10 +15238,10 @@ "val" : "equivalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15235,10 +15262,10 @@ "val" : "interologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15259,10 +15286,10 @@ "val" : "functional similarity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15283,10 +15310,10 @@ "val" : "iterative homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15313,10 +15340,10 @@ "val" : "paraxenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15338,10 +15365,10 @@ "val" : "plerologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15363,10 +15390,10 @@ "val" : "homotopous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15387,10 +15414,10 @@ "val" : "heterotopy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15412,10 +15439,10 @@ "val" : "homoeologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15436,10 +15463,10 @@ "val" : "axis paramorphism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -15460,10 +15487,10 @@ "val" : "regulogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -16301,7 +16328,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001018" + "obj" : "http://purl.obolibrary.org/obo/RO_0001025" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "subPropertyOf", @@ -19030,10 +19057,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0001015", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001018", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", @@ -19535,10 +19558,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0001018", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001020", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ] @@ -20117,9 +20136,6 @@ }, { "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_0001018", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/ro.obo b/ro.obo index 0b1695dd..9cd84f7c 100644 --- a/ro.obo +++ b/ro.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2023-06-28 +data-version: releases/2023-08-18 subsetdef: common_anatomy "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -13,7 +13,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-06-28" xsd:string +property_value: owl:versionInfo "2023-08-18" xsd:string [Term] id: BFO:0000002 @@ -711,7 +711,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -816,7 +816,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -941,7 +941,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -953,7 +952,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -965,7 +963,6 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.n property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: RO:0001900 RO:0001901 -is_transitive: true is_obsolete: true [Typedef] @@ -1007,25 +1004,20 @@ inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 -name: contained in -subset: ro-eco +name: obsolete contained in property_value: IAO:0000111 "contained in" xsd:string property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000118 "contained_in" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001019 -name: contains -subset: ro-eco +name: obsolete contains property_value: IAO:0000111 "contains" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001020 @@ -1064,7 +1056,7 @@ id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string @@ -1133,7 +1125,7 @@ def: "The relationship that holds between a trachea or tracheole and an antomica property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: RO:0001018 ! contained in +is_a: RO:0001025 ! located in [Typedef] id: RO:0002005 @@ -6285,7 +6277,7 @@ property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease @@ -6318,7 +6310,6 @@ name: positively correlated with def: "A relation between entities in which one increases or decreases as the other does the same." [] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1909-9269 property_value: IAO:0000118 "directly correlated with" xsd:string -is_reflexive: true is_symmetric: true is_a: RO:0002610 ! correlated with @@ -6561,8 +6552,8 @@ synonym: "sameness" EXACT [] synonym: "similar to" EXACT [] 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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/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 @@ -6575,8 +6566,8 @@ name: in homology relationship with def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] comment: This broad definition encompasses all the working definitions proposed so far in the literature. synonym: "homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000001 is_symmetric: true is_a: RO:0002158 ! shares ancestor with @@ -6589,8 +6580,8 @@ name: in homoplasy relationship with def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] synonym: "analogy" RELATED [] synonym: "homoplasous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000002 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with @@ -6602,8 +6593,8 @@ def: "Similarity that is characterized by the organization of anatomical structu comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. synonym: "homocracous to" EXACT [] xref: ECO:0000075 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000003 is_symmetric: true is_a: RO:0002320 ! evolutionarily related to @@ -6615,8 +6606,8 @@ name: in convergence relationship with def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] comment: Convergence usually implies a notion of adaptation. synonym: "analogy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000004 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6627,8 +6618,8 @@ name: in parallelism relationship with def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. synonym: "parallel evolution" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000005 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6641,8 +6632,8 @@ synonym: "idealistic homology" RELATED [] synonym: "structural homologous to" EXACT [] xref: ECO:0000071 xref: MI:2163 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000006 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6664,8 +6655,8 @@ xref: SO:0000853 xref: SO:0000857 xref: SO:homologous_to xref: TAO:homologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000007 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6678,8 +6669,8 @@ comment: Applicable only to morphology. A certain degree of ambiguity is accepte synonym: "biological homologous to" EXACT [] synonym: "transformational homology" RELATED [] xref: ECO:0000067 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000008 is_symmetric: true is_a: RO:HOM0000001 ! in homology relationship with @@ -6691,8 +6682,8 @@ def: "Homoplasy that involves phenotypes similar to those seen in ancestors with synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000009 is_symmetric: true is_a: RO:HOM0000002 ! in homoplasy relationship with @@ -6706,8 +6697,8 @@ synonym: "synteny" RELATED [] xref: MeSH:Synteny xref: SO:0000860 xref: SO:0005858 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000010 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6720,8 +6711,8 @@ synonym: "paralogous to" EXACT [] xref: SO:0000854 xref: SO:0000859 xref: SO:paralogous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000011 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6734,8 +6725,8 @@ def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20 synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] synonym: "syntenic paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000012 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with @@ -6746,8 +6737,8 @@ id: RO:HOM0000013 name: in syntenic orthology relationship with def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] synonym: "syntenic orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000013 is_symmetric: true is_a: RO:HOM0000010 ! in syntenic homology relationship with @@ -6763,8 +6754,8 @@ synonym: "partial correspondence" RELATED [] synonym: "partial homologous to" EXACT [] synonym: "percent homology" RELATED [] synonym: "segmental homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000014 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6775,8 +6766,8 @@ name: in protein structural homology relationship with def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] synonym: "protein structural homologous to" EXACT [] xref: MeSH:Structural_Homology\,_Protein -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000015 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6788,8 +6779,8 @@ def: "Structural homology that involves a pseudogenic feature and its functional synonym: "non functional homologous to" EXACT [] synonym: "pseudogene" BROAD [] xref: SO:non_functional_homolog_of -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000016 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -6805,8 +6796,8 @@ xref: ECO:00000060 xref: SO:0000855 xref: SO:0000858 xref: SO:orthologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000017 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6817,8 +6808,8 @@ name: in xenology relationship with def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). synonym: "xenologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000018 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6830,8 +6821,8 @@ def: "Historical homology that involves two members sharing no other homologs in synonym: "1 to 1 homologous to" EXACT [] synonym: "1:1 homology" EXACT [] synonym: "one-to-one homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000019 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -6843,8 +6834,8 @@ def: "Orthology that involves two genes that did not experience any duplication synonym: "1 to 1 orthologous to" EXACT [] synonym: "1:1 orthology" EXACT [] synonym: "one-to-one orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000020 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -6856,8 +6847,8 @@ name: in ohnology relationship with def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] synonym: "homoeology" RELATED [] synonym: "ohnologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000022 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6869,8 +6860,8 @@ def: "Paralogy that results from a lineage-specific duplication subsequent to a synonym: "in-paralogous to" EXACT [] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000023 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6883,8 +6874,8 @@ def: "Paralogy that results from a duplication preceding a given speciation even synonym: "alloparalogy" EXACT [] synonym: "out-paralogous to" EXACT [] synonym: "outparalogy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000024 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -6894,8 +6885,8 @@ id: RO:HOM0000025 name: in pro-orthology relationship with def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] synonym: "pro-orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000025 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with @@ -6906,8 +6897,8 @@ name: in semi-orthology relationship with def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] comment: The converse of pro-orthologous. synonym: "semi-orthologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000026 is_symmetric: true is_a: RO:HOM0000034 ! in 1 to many orthology relationship with @@ -6918,8 +6909,8 @@ name: in serial homology relationship with def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] synonym: "homonomy" RELATED [] synonym: "serial homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000027 is_symmetric: true is_a: RO:HOM0000066 ! in iterative homology relationship with @@ -6930,8 +6921,8 @@ name: in heterochronous homology relationship with def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] synonym: "heterochronous homologous to" EXACT [] synonym: "heterochrony" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000028 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -6942,8 +6933,8 @@ name: in paedomorphorsis relationship with def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000029 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with @@ -6953,8 +6944,8 @@ disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with id: RO:HOM0000030 name: in peramorphosis relationship with def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000030 is_symmetric: true is_a: RO:HOM0000028 ! in heterochronous homology relationship with @@ -6963,8 +6954,8 @@ is_a: RO:HOM0000028 ! in heterochronous homology relationship with id: RO:HOM0000031 name: in progenesis relationship with def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000031 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -6975,8 +6966,8 @@ name: in neoteny relationship with def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] synonym: "juvenilization" EXACT [] synonym: "neotenous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000032 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -6986,8 +6977,8 @@ id: RO:HOM0000033 name: in mimicry relationship with def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] synonym: "mimicrous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000033 is_symmetric: true is_a: RO:HOM0000004 ! in convergence relationship with @@ -7001,8 +6992,8 @@ synonym: "1:many orthology" EXACT [] synonym: "co-orthology" RELATED [] synonym: "many to 1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000034 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -7015,8 +7006,8 @@ def: "Historical homology that involves two members of a larger set of homologs. synonym: "many to many homologous to" EXACT [] synonym: "many-to-many homology" EXACT [] synonym: "many:many homology " EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000036 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7028,8 +7019,8 @@ def: "Historical homology that involves a structure that has no other homologs i synonym: "1 to many homologous to" EXACT [] synonym: "1:many homology" RELATED [] synonym: "one-to-many homology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000037 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7040,8 +7031,8 @@ name: in apomorphy relationship with def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] synonym: "apomorphous to" EXACT [] synonym: "synapomorphy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000042 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7054,8 +7045,8 @@ def: "Historical homology that is based on distant shared ancestry." [http://pur comment: This term is usually contrasted to apomorphy. synonym: "plesiomorphous to" EXACT [] synonym: "symplesiomorphy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000043 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7069,8 +7060,8 @@ synonym: "deep genetic homology" EXACT [] synonym: "deep homologous to" EXACT [] synonym: "generative homology" RELATED [] synonym: "homoiology" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000044 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -7081,8 +7072,8 @@ id: RO:HOM0000045 name: in hemiplasy relationship with def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] synonym: "hemiplasous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000045 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7092,8 +7083,8 @@ id: RO:HOM0000046 name: in gametology relationship with def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] synonym: "gametologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000046 is_symmetric: true is_a: RO:HOM0000047 ! in chromosomal homology relationship with @@ -7104,8 +7095,8 @@ name: in chromosomal homology relationship with def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] synonym: "chromosomal homologous to" EXACT [] xref: MeSH:Chromosome_Pairing -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000047 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7120,8 +7111,8 @@ synonym: "many-to-many orthology" EXACT [] synonym: "many:many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000048 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -7132,8 +7123,8 @@ id: RO:HOM0000049 name: in within-species paralogy relationship with def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "within-species paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000049 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7145,8 +7136,8 @@ name: in between-species paralogy relationship with def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] comment: The genes have diverged before a speciation event. synonym: "between-species paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000050 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7156,8 +7147,8 @@ id: RO:HOM0000051 name: in postdisplacement relationship with def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] synonym: "post-displacement" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000051 is_symmetric: true is_a: RO:HOM0000029 ! in paedomorphorsis relationship with @@ -7166,8 +7157,8 @@ is_a: RO:HOM0000029 ! in paedomorphorsis relationship with id: RO:HOM0000052 name: in hypermorphosis relationship with def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000052 is_symmetric: true is_a: RO:HOM0000030 ! in peramorphosis relationship with @@ -7177,8 +7168,8 @@ id: RO:HOM0000053 name: in synology relationship with def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] synonym: "synologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000053 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -7189,8 +7180,8 @@ name: in isoorthology relationship with def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] synonym: "isoorthologous to" EXACT [] xref: ECO:0000080 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000054 is_symmetric: true is_a: RO:HOM0000017 ! in orthology relationship with @@ -7203,8 +7194,8 @@ def: "Paralogy that is characterized by duplication of adjacent sequences on a c synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] synonym: "tandem paralogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000055 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7221,8 +7212,8 @@ synonym: "homoplastic tendency" RELATED [] synonym: "latent homologous to" EXACT [] synonym: "re-awakening" RELATED [] synonym: "underlying synapomorphy" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000057 is_symmetric: true is_a: RO:HOM0000005 ! in parallelism relationship with @@ -7235,8 +7226,8 @@ def: "Homocracy that involves recognizably corresponding characters that occurs comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. synonym: "generative homology" EXACT [] synonym: "syngenous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000058 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -7250,8 +7241,8 @@ synonym: "1:1 paralogy" EXACT [] synonym: "apparent 1:1 orthology" EXACT [] synonym: "apparent orthologous to" EXACT [] synonym: "pseudoorthology" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000060 is_symmetric: true is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with @@ -7263,8 +7254,8 @@ name: in pseudoparalogy relationship with def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] comment: These genes may come out as paralogs in a single-genome analysis. synonym: "pseudoparalogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000061 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -7275,8 +7266,8 @@ name: in equivalogy relationship with def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] comment: This may include examples of orthology, paralogy and xenology. synonym: "equivalogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000062 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7287,8 +7278,8 @@ id: RO:HOM0000063 name: in interology relationship with def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] synonym: "interologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000063 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with @@ -7298,8 +7289,8 @@ id: RO:HOM0000065 name: in functional equivalence relationship with def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] synonym: "functional similarity" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000065 is_symmetric: true is_a: RO:HOM0000000 ! in similarity relationship with @@ -7309,8 +7300,8 @@ id: RO:HOM0000066 name: in iterative homology relationship with def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] synonym: "iterative homologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000066 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -7322,8 +7313,8 @@ def: "Xenology that is characterized by multiple horizontal transfer events, res synonym: "duplicate xenology" EXACT [] synonym: "multiple xenology" EXACT [] synonym: "paraxenologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000068 is_symmetric: true is_a: RO:HOM0000018 ! in xenology relationship with @@ -7334,8 +7325,8 @@ name: in plerology relationship with def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] comment: This phenomenon is usually due to gene conversion process. synonym: "plerologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000069 is_symmetric: true is_a: RO:HOM0000011 ! in paralogy relationship with @@ -7346,8 +7337,8 @@ name: in homotopy relationship with def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. synonym: "homotopous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000071 is_symmetric: true is_a: RO:HOM0000006 ! in structural homology relationship with @@ -7358,8 +7349,8 @@ id: RO:HOM0000072 name: in homeosis relationship with def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] synonym: "heterotopy" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000072 is_symmetric: true is_a: RO:HOM0000008 ! in biological homology relationship with @@ -7370,8 +7361,8 @@ name: in homoeology relationship with def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. synonym: "homoeologous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000073 is_symmetric: true is_a: RO:HOM0000022 ! in ohnology relationship with @@ -7382,8 +7373,8 @@ id: RO:HOM0000074 name: in paramorphism relationship with def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] synonym: "axis paramorphism" RELATED [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000074 is_symmetric: true is_a: RO:HOM0000003 ! in homocracy relationship with @@ -7394,8 +7385,8 @@ id: RO:HOM0000075 name: in regulogy relationship with def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] synonym: "regulogous to" EXACT [] -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000075 is_symmetric: true is_a: RO:HOM0000007 ! in historical homology relationship with diff --git a/ro.owl b/ro.owl index 26104ba3..c50e7d26 100644 --- a/ro.owl +++ b/ro.owl @@ -21,11 +21,11 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://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 - 2023-06-28 + 2023-08-18 https://github.com/oborel/obo-relations/ @@ -1164,12 +1164,6 @@ Where we have an annotation assertion - - - - - - @@ -1647,7 +1641,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1802,7 +1796,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1956,7 +1950,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. @@ -1972,7 +1965,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. @@ -1988,7 +1980,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. @@ -2053,24 +2044,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - contained_in - - - contained in + obsolete contained in + + true @@ -2079,9 +2059,9 @@ range: spatial region or site (immaterial continuant) contains - - - contains + obsolete contains + + true @@ -2172,7 +2152,7 @@ range: spatial region or site (immaterial continuant) Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in @@ -2259,7 +2239,7 @@ range: spatial region or site (immaterial continuant) - + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). @@ -10573,7 +10553,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10607,7 +10587,7 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10619,7 +10599,6 @@ For example, protein A (transcription factor) indirectly increases by expression - A relation between entities in which one increases or decreases as the other does the same. directly correlated with @@ -11044,8 +11023,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu TODO: Add homeomorphy axiom - - + + ECO:0000041 SO:similar_to sameness @@ -11079,8 +11058,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from common evolutionary origin. - - + + homologous to This broad definition encompasses all the working definitions proposed so far in the literature. in homology relationship with @@ -11104,8 +11083,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - - + + homoplasous to analogy in homoplasy relationship with @@ -11128,8 +11107,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - + + ECO:0000075 homocracous to Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. @@ -11154,8 +11133,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - - + + analogy Convergence usually implies a notion of adaptation. in convergence relationship with @@ -11177,8 +11156,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - - + + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. in parallelism relationship with @@ -11200,8 +11179,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - - + + ECO:0000071 MI:2163 structural homologous to @@ -11227,8 +11206,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - - + + homology ECO:0000080 RO_proposed_relation:homologous_to @@ -11262,8 +11241,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - + + ECO:0000067 biological homologous to transformational homology @@ -11288,8 +11267,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - + + atavism rudiment reversion @@ -11312,8 +11291,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - - + + MeSH:Synteny SO:0000860 SO:0005858 @@ -11339,8 +11318,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - - + + SO:0000854 SO:0000859 SO:paralogous_to @@ -11367,8 +11346,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - - + + syntenic paralogous to duplicon paralogon @@ -11392,8 +11371,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - - + + syntenic orthologous to in syntenic orthology relationship with @@ -11414,8 +11393,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - + + fractional homology partial homologous to segmental homology @@ -11443,8 +11422,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - + + MeSH:Structural_Homology,_Protein protein structural homologous to in protein structural homology relationship with @@ -11467,8 +11446,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - - + + pseudogene SO:non_functional_homolog_of non functional homologous to @@ -11491,8 +11470,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - - + + ECO:00000060 SO:0000855 SO:0000858 @@ -11521,8 +11500,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - + + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). in xenology relationship with @@ -11545,8 +11524,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - - + + 1 to 1 homologous to 1:1 homology one-to-one homology @@ -11570,8 +11549,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - + + 1 to 1 orthologous to 1:1 orthology one-to-one orthology @@ -11595,8 +11574,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - - + + ohnologous to homoeology in ohnology relationship with @@ -11619,8 +11598,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - + + in-paralogous to inparalogy symparalogy @@ -11643,8 +11622,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - - + + alloparalogy out-paralogous to outparalogy @@ -11667,8 +11646,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - + + pro-orthologous to in pro-orthology relationship with @@ -11690,8 +11669,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - + + semi-orthologous to The converse of pro-orthologous. in semi-orthology relationship with @@ -11714,8 +11693,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - - + + serial homologous to homonomy in serial homology relationship with @@ -11737,8 +11716,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - + + heterochronous homologous to heterochrony in heterochronous homology relationship with @@ -11761,8 +11740,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - + + juvenification pedomorphosis in paedomorphorsis relationship with @@ -11785,8 +11764,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - + + in peramorphosis relationship with @@ -11806,8 +11785,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - + + in progenesis relationship with @@ -11828,8 +11807,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - - + + juvenilization neotenous to in neoteny relationship with @@ -11852,8 +11831,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - - + + mimicrous to in mimicry relationship with @@ -11875,8 +11854,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - + + 1 to many orthologous to 1:many orthology one-to-many orthology @@ -11902,8 +11881,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - - + + many to many homologous to many-to-many homology many:many homology @@ -11926,8 +11905,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - + + 1 to many homologous to one-to-many homology 1:many homology @@ -11951,8 +11930,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - + + apomorphous to synapomorphy in apomorphy relationship with @@ -11974,8 +11953,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - - + + plesiomorphous to symplesiomorphy This term is usually contrasted to apomorphy. @@ -11999,8 +11978,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - + + deep genetic homology deep homologous to generative homology @@ -12026,8 +12005,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - + + hemiplasous to in hemiplasy relationship with @@ -12048,8 +12027,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - + + gametologous to in gametology relationship with @@ -12070,8 +12049,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - + + MeSH:Chromosome_Pairing chromosomal homologous to in chromosomal homology relationship with @@ -12094,8 +12073,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - + + many to many orthologous to many-to-many orthology many:many orthology @@ -12123,8 +12102,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - - + + within-species paralogous to in within-species paralogy relationship with @@ -12145,8 +12124,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - - + + between-species paralogous to The genes have diverged before a speciation event. in between-species paralogy relationship with @@ -12168,8 +12147,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - + + post-displacement in postdisplacement relationship with @@ -12190,8 +12169,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - - + + in hypermorphosis relationship with @@ -12212,8 +12191,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - + + synologous to in synology relationship with @@ -12236,8 +12215,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - - + + ECO:0000080 isoorthologous to in isoorthology relationship with @@ -12259,8 +12238,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - + + tandem paralogous to iterative paralogy serial paralogy @@ -12285,8 +12264,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - + + apomorphic tendency cryptic homology latent homologous to @@ -12317,8 +12296,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - + + generative homology syngenous to Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. @@ -12343,8 +12322,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - + + 1:1 paralogy apparent 1:1 orthology apparent orthologous to @@ -12370,8 +12349,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - + + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. in pseudoparalogy relationship with @@ -12394,8 +12373,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - - + + equivalogous to This may include examples of orthology, paralogy and xenology. in equivalogy relationship with @@ -12417,8 +12396,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - + + interologous to in interology relationship with @@ -12440,8 +12419,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - - + + functional similarity in functional equivalence relationship with @@ -12463,8 +12442,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - - + + iterative homologous to in iterative homology relationship with @@ -12485,8 +12464,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - + + duplicate xenology multiple xenology paraxenologous to @@ -12509,8 +12488,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - + + plerologous to This phenomenon is usually due to gene conversion process. in plerology relationship with @@ -12533,8 +12512,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - - + + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. in homotopy relationship with @@ -12558,8 +12537,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - - + + heterotopy in homeosis relationship with @@ -12582,8 +12561,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - - + + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. in homoeology relationship with @@ -12606,8 +12585,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - + + axis paramorphism in paramorphism relationship with @@ -12629,8 +12608,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - + + regulogous to in regulogy relationship with @@ -15455,6 +15434,18 @@ No imports misnomer + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + previous name + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + legal name + diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl index b1081d5f..745b699f 100644 --- a/src/ontology/imports/cl_import.owl +++ b/src/ontology/imports/cl_import.owl @@ -7,10 +7,10 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( "An ontology of cell types.") -Annotation( ) +Annotation( ) Annotation( "Cell Ontology") Annotation( ) Annotation( ) @@ -23,8 +23,8 @@ Annotation( ) Annotation( ) Annotation(rdfs:comment "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.") -Annotation(owl:versionInfo "2023-06-22") -Annotation(owl:versionInfo "2023-06-28") +Annotation(owl:versionInfo "2023-07-20") +Annotation(owl:versionInfo "2023-08-16") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl index 39a70d0b..9be9a9b3 100644 --- a/src/ontology/imports/cob_import.owl +++ b/src/ontology/imports/cob_import.owl @@ -11,4 +11,4 @@ - + \ No newline at end of file diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl index 4f7e66e9..3218a356 100644 --- a/src/ontology/imports/envo_import.owl +++ b/src/ontology/imports/envo_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( "http://orcid.org/0000-0002-6601-2165") @@ -26,7 +26,7 @@ Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6]") Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2]") Annotation(owl:versionInfo "2023-02-13") -Annotation(owl:versionInfo "2023-06-28") +Annotation(owl:versionInfo "2023-08-16") Annotation( "http://environmentontology.org/"^^xsd:anyURI) Declaration(Class()) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index ee1e5e75..3f9d9c71 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,15 +7,18 @@ Prefix(rdfs:=) Ontology( - + +Annotation( ) +Annotation( ) +Annotation( ) Annotation( "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.") -Annotation( ) +Annotation( ) Annotation( "Gene Ontology") Annotation( ) Annotation( "gene_ontology") Annotation( "1.2") -Annotation(owl:versionInfo "2023-06-11") -Annotation(owl:versionInfo "2023-06-28") +Annotation(owl:versionInfo "2023-07-27") +Annotation(owl:versionInfo "2023-08-16") Declaration(Class()) Declaration(Class()) @@ -26,6 +29,7 @@ Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 5e598187..c9dd3cfe 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-06-28") + +Annotation( ) +Annotation(owl:versionInfo "2023-08-16") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index 0e0caea9..2ecb7af4 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-06-28") + +Annotation(owl:versionInfo "2023-08-16") Declaration(Class()) Declaration(Class()) @@ -671,4 +671,12 @@ AnnotationAssertion(rdfs:label "mis AnnotationAssertion( "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "misnomer") +AnnotationAssertion( "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.") +AnnotationAssertion( "A synonym type for names that have been used as primary labels in the past.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "previous name") +AnnotationAssertion( "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College") +AnnotationAssertion( "A synonym type for the legal entity name") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "legal name") ) \ No newline at end of file diff --git a/src/ontology/imports/orcidio_import.owl b/src/ontology/imports/orcidio_import.owl index 9f9c776a..46124dcd 100644 --- a/src/ontology/imports/orcidio_import.owl +++ b/src/ontology/imports/orcidio_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-06-28") + +Annotation(owl:versionInfo "2023-08-16") Declaration(NamedIndividual()) Declaration(NamedIndividual()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 3ad1e5dd..64359663 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( "An ontology of phenotypic qualities (properties, attributes or characteristics).") Annotation( ) @@ -16,7 +16,7 @@ Annotation( "quality") Annotation( "1.2") Annotation(owl:versionInfo "2023-05-18") -Annotation(owl:versionInfo "2023-06-28") +Annotation(owl:versionInfo "2023-08-16") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index 57a32020..6cab6d88 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( ) @@ -36,7 +36,7 @@ Annotation( ) Annotation( ) Annotation( ) -Annotation( ) +Annotation( ) Annotation( ) Annotation( ) Annotation( ) @@ -68,7 +68,7 @@ Annotation( "PMID:16417468 Forgotten and Annotation( "aggregates AAO from 13:04:2012") Annotation( "aggregates TAO from 09:08:2012") Annotation( "aggregates VSAO from 16:07:2012") -Annotation(owl:versionInfo "2023-06-28") +Annotation(owl:versionInfo "2023-08-16") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index 2f828f3f..0fbdb4d5 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -36,7 +36,7 @@ Import() Import() Annotation(terms:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en) Annotation(terms:license ) -Annotation(terms:title "OBO Relations Ontologyyy"@en) +Annotation(terms:title "OBO Relations Ontology"@en) Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI) Declaration(Class(obo:BFO_0000019)) diff --git a/src/ontology/subsets/ro-causal.json b/src/ontology/subsets/ro-causal.json index 8b89b440..22c6414d 100644 --- a/src/ontology/subsets/ro-causal.json +++ b/src/ontology/subsets/ro-causal.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 942e3a70..aae8993f 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index 716fd015..40bb5909 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/src/ontology/subsets/ro-causal.tsv b/src/ontology/subsets/ro-causal.tsv index b039df98..f63b8b06 100644 --- a/src/ontology/subsets/ro-causal.tsv +++ b/src/ontology/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid1 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid18 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid22 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid26 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid33 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid37 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid40 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid5 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid52 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid58 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid61 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid64 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid67 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid9 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid1 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid18 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid22 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid26 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid33 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid37 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid40 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid5 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid52 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid58 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid61 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid64 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid67 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 diff --git a/src/ontology/subsets/ro-chado.json b/src/ontology/subsets/ro-chado.json index f86a1d5d..a473678c 100644 --- a/src/ontology/subsets/ro-chado.json +++ b/src/ontology/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-28" + "val" : "2023-08-18" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -205,7 +205,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -1753,6 +1753,36 @@ "val" : "https://orcid.org/0000-0003-4423-4370" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003008", + "lbl" : "previous name", + "meta" : { + "definition" : { + "val" : "A synonym type for names that have been used as primary labels in the past." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003009", + "lbl" : "legal name", + "meta" : { + "definition" : { + "val" : "A synonym type for the legal entity name" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", "lbl" : "characteristic of", @@ -1862,7 +1892,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -2201,10 +2231,9 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "lbl" : "contained in", + "lbl" : "obsolete contained in", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contained in" @@ -2214,30 +2243,28 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained_in" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "lbl" : "contains", + "lbl" : "obsolete contains", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contains" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001020", @@ -2314,7 +2341,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12180,7 +12207,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" @@ -12779,10 +12806,10 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12804,10 +12831,10 @@ "val" : "homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12831,10 +12858,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12859,10 +12886,10 @@ "val" : "ECO:0000075" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12884,10 +12911,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12909,10 +12936,10 @@ "val" : "parallel evolution" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12941,10 +12968,10 @@ "val" : "MI:2163" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12995,10 +13022,10 @@ "val" : "TAO:homologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13026,10 +13053,10 @@ "val" : "ECO:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13056,10 +13083,10 @@ "val" : "reversion" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13090,10 +13117,10 @@ "val" : "SO:0005858" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13121,10 +13148,10 @@ "val" : "SO:paralogous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13151,10 +13178,10 @@ "val" : "paralogon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13175,10 +13202,10 @@ "val" : "syntenic orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13217,10 +13244,10 @@ "val" : "percent homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13244,10 +13271,10 @@ "val" : "MeSH:Structural_Homology,_Protein" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13274,10 +13301,10 @@ "val" : "SO:non_functional_homolog_of" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13308,10 +13335,10 @@ "val" : "SO:orthologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13333,10 +13360,10 @@ "val" : "xenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13363,10 +13390,10 @@ "val" : "one-to-one homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13393,10 +13420,10 @@ "val" : "one-to-one orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13420,10 +13447,10 @@ "val" : "homoeology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13450,10 +13477,10 @@ "val" : "symparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13480,10 +13507,10 @@ "val" : "outparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13504,10 +13531,10 @@ "val" : "pro-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13529,10 +13556,10 @@ "val" : "semi-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13556,10 +13583,10 @@ "val" : "homonomy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13583,10 +13610,10 @@ "val" : "heterochrony" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13610,10 +13637,10 @@ "val" : "pedomorphosis" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13630,10 +13657,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000030" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13650,10 +13677,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13677,10 +13704,10 @@ "val" : "neotenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13701,10 +13728,10 @@ "val" : "mimicrous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13737,10 +13764,10 @@ "val" : "many to 1 orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13767,10 +13794,10 @@ "val" : "many:many homology " } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13797,10 +13824,10 @@ "val" : "1:many homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13824,10 +13851,10 @@ "val" : "synapomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13852,10 +13879,10 @@ "val" : "symplesiomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13886,10 +13913,10 @@ "val" : "homoiology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13910,10 +13937,10 @@ "val" : "hemiplasous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13934,10 +13961,10 @@ "val" : "gametologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13961,10 +13988,10 @@ "val" : "MeSH:Chromosome_Pairing" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14000,10 +14027,10 @@ "val" : "trans-homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14024,10 +14051,10 @@ "val" : "within-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14049,10 +14076,10 @@ "val" : "between-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14073,10 +14100,10 @@ "val" : "post-displacement" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14093,10 +14120,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000052", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14117,10 +14144,10 @@ "val" : "synologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14144,10 +14171,10 @@ "val" : "ECO:0000080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14174,10 +14201,10 @@ "val" : "serial paralogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14217,10 +14244,10 @@ "val" : "re-awakening" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14245,10 +14272,10 @@ "val" : "syngenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14279,10 +14306,10 @@ "val" : "pseudoorthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14304,10 +14331,10 @@ "val" : "pseudoparalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14329,10 +14356,10 @@ "val" : "equivalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14353,10 +14380,10 @@ "val" : "interologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14377,10 +14404,10 @@ "val" : "functional similarity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14401,10 +14428,10 @@ "val" : "iterative homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14431,10 +14458,10 @@ "val" : "paraxenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14456,10 +14483,10 @@ "val" : "plerologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14481,10 +14508,10 @@ "val" : "homotopous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14505,10 +14532,10 @@ "val" : "heterotopy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14530,10 +14557,10 @@ "val" : "homoeologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14554,10 +14581,10 @@ "val" : "axis paramorphism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14578,10 +14605,10 @@ "val" : "regulogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14976,7 +15003,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001018" + "obj" : "http://purl.obolibrary.org/obo/RO_0001025" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "subPropertyOf", @@ -17697,10 +17724,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0001015", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001018", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", @@ -18164,9 +18187,6 @@ }, { "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_0001018", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index f42318df..fe43ab79 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -13,7 +13,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-06-28" xsd:string +property_value: owl:versionInfo "2023-08-18" xsd:string [Typedef] id: BFO:0000050 @@ -176,21 +176,18 @@ is_a: RO:0000052 ! characteristic of id: RO:0000300 name: obsolete_in_neural_circuit_with def: "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." [] -is_transitive: true is_obsolete: true [Typedef] id: RO:0000301 name: obsolete_upstream_in_neural_circuit_with def: "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." [] -is_transitive: true is_obsolete: true [Typedef] id: RO:0000302 name: obsolete_downstream_in_neural_circuit_with def: "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." [] -is_transitive: true is_obsolete: true [Typedef] @@ -213,13 +210,13 @@ inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 -name: contained_in -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains +name: obsolete_contained_in +is_obsolete: true [Typedef] id: RO:0001019 -name: contains +name: obsolete_contains +is_obsolete: true [Typedef] id: RO:0001020 @@ -282,7 +279,7 @@ is_a: RO:0002170 ! connected to 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)." [] -is_a: RO:0001018 ! contained in +is_a: RO:0001025 ! located in [Typedef] id: RO:0002005 @@ -3674,7 +3671,6 @@ holds_over_chain: RO:0002215 RO:0002233 id: RO:0017003 name: positively_correlated_with def: "A relation between entities in which one increases or decreases as the other does the same." [] -is_reflexive: true is_symmetric: true is_a: RO:0002610 ! correlated with diff --git a/src/ontology/subsets/ro-chado.owl b/src/ontology/subsets/ro-chado.owl index f2a43fda..389234a4 100644 --- a/src/ontology/subsets/ro-chado.owl +++ b/src/ontology/subsets/ro-chado.owl @@ -21,8 +21,8 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2023-06-28 + + 2023-08-18 @@ -1160,12 +1160,6 @@ Where we have an annotation assertion - - - - - - @@ -1637,7 +1631,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1783,7 +1777,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1925,7 +1919,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. @@ -1941,7 +1934,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. @@ -1957,7 +1949,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. @@ -2022,22 +2013,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - contained_in - - - contained in + obsolete contained in + + true @@ -2046,9 +2028,9 @@ range: spatial region or site (immaterial continuant) contains - - - contains + obsolete contains + + true @@ -2113,7 +2095,7 @@ range: spatial region or site (immaterial continuant) Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in @@ -2186,7 +2168,7 @@ range: spatial region or site (immaterial continuant) - + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). tracheates @@ -10015,7 +9997,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10049,7 +10031,7 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10061,7 +10043,6 @@ For example, protein A (transcription factor) indirectly increases by expression - A relation between entities in which one increases or decreases as the other does the same. directly correlated with @@ -10484,8 +10465,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu TODO: Add homeomorphy axiom - - + + ECO:0000041 SO:similar_to sameness @@ -10519,8 +10500,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from common evolutionary origin. - - + + homologous to This broad definition encompasses all the working definitions proposed so far in the literature. in homology relationship with @@ -10544,8 +10525,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - - + + homoplasous to analogy in homoplasy relationship with @@ -10568,8 +10549,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - + + ECO:0000075 homocracous to Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. @@ -10594,8 +10575,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - - + + analogy Convergence usually implies a notion of adaptation. in convergence relationship with @@ -10617,8 +10598,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - - + + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. in parallelism relationship with @@ -10640,8 +10621,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - - + + ECO:0000071 MI:2163 structural homologous to @@ -10667,8 +10648,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - - + + homology ECO:0000080 RO_proposed_relation:homologous_to @@ -10702,8 +10683,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - + + ECO:0000067 biological homologous to transformational homology @@ -10728,8 +10709,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - + + atavism rudiment reversion @@ -10752,8 +10733,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - - + + MeSH:Synteny SO:0000860 SO:0005858 @@ -10779,8 +10760,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - - + + SO:0000854 SO:0000859 SO:paralogous_to @@ -10807,8 +10788,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - - + + syntenic paralogous to duplicon paralogon @@ -10832,8 +10813,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - - + + syntenic orthologous to in syntenic orthology relationship with @@ -10854,8 +10835,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - + + fractional homology partial homologous to segmental homology @@ -10883,8 +10864,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - + + MeSH:Structural_Homology,_Protein protein structural homologous to in protein structural homology relationship with @@ -10907,8 +10888,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - - + + pseudogene SO:non_functional_homolog_of non functional homologous to @@ -10931,8 +10912,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - - + + ECO:00000060 SO:0000855 SO:0000858 @@ -10961,8 +10942,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - + + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). in xenology relationship with @@ -10985,8 +10966,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - - + + 1 to 1 homologous to 1:1 homology one-to-one homology @@ -11010,8 +10991,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - + + 1 to 1 orthologous to 1:1 orthology one-to-one orthology @@ -11035,8 +11016,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - - + + ohnologous to homoeology in ohnology relationship with @@ -11059,8 +11040,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - + + in-paralogous to inparalogy symparalogy @@ -11083,8 +11064,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - - + + alloparalogy out-paralogous to outparalogy @@ -11107,8 +11088,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - + + pro-orthologous to in pro-orthology relationship with @@ -11130,8 +11111,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - + + semi-orthologous to The converse of pro-orthologous. in semi-orthology relationship with @@ -11154,8 +11135,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - - + + serial homologous to homonomy in serial homology relationship with @@ -11177,8 +11158,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - + + heterochronous homologous to heterochrony in heterochronous homology relationship with @@ -11201,8 +11182,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - + + juvenification pedomorphosis in paedomorphorsis relationship with @@ -11225,8 +11206,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - + + in peramorphosis relationship with @@ -11246,8 +11227,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - + + in progenesis relationship with @@ -11268,8 +11249,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - - + + juvenilization neotenous to in neoteny relationship with @@ -11292,8 +11273,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - - + + mimicrous to in mimicry relationship with @@ -11315,8 +11296,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - + + 1 to many orthologous to 1:many orthology one-to-many orthology @@ -11342,8 +11323,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - - + + many to many homologous to many-to-many homology many:many homology @@ -11366,8 +11347,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - + + 1 to many homologous to one-to-many homology 1:many homology @@ -11391,8 +11372,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - + + apomorphous to synapomorphy in apomorphy relationship with @@ -11414,8 +11395,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - - + + plesiomorphous to symplesiomorphy This term is usually contrasted to apomorphy. @@ -11439,8 +11420,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - + + deep genetic homology deep homologous to generative homology @@ -11466,8 +11447,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - + + hemiplasous to in hemiplasy relationship with @@ -11488,8 +11469,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - + + gametologous to in gametology relationship with @@ -11510,8 +11491,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - + + MeSH:Chromosome_Pairing chromosomal homologous to in chromosomal homology relationship with @@ -11534,8 +11515,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - + + many to many orthologous to many-to-many orthology many:many orthology @@ -11563,8 +11544,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - - + + within-species paralogous to in within-species paralogy relationship with @@ -11585,8 +11566,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - - + + between-species paralogous to The genes have diverged before a speciation event. in between-species paralogy relationship with @@ -11608,8 +11589,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - + + post-displacement in postdisplacement relationship with @@ -11630,8 +11611,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - - + + in hypermorphosis relationship with @@ -11652,8 +11633,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - + + synologous to in synology relationship with @@ -11676,8 +11657,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - - + + ECO:0000080 isoorthologous to in isoorthology relationship with @@ -11699,8 +11680,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - + + tandem paralogous to iterative paralogy serial paralogy @@ -11725,8 +11706,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - + + apomorphic tendency cryptic homology latent homologous to @@ -11757,8 +11738,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - + + generative homology syngenous to Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. @@ -11783,8 +11764,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - + + 1:1 paralogy apparent 1:1 orthology apparent orthologous to @@ -11810,8 +11791,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - + + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. in pseudoparalogy relationship with @@ -11834,8 +11815,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - - + + equivalogous to This may include examples of orthology, paralogy and xenology. in equivalogy relationship with @@ -11857,8 +11838,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - + + interologous to in interology relationship with @@ -11880,8 +11861,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - - + + functional similarity in functional equivalence relationship with @@ -11903,8 +11884,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - - + + iterative homologous to in iterative homology relationship with @@ -11925,8 +11906,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - + + duplicate xenology multiple xenology paraxenologous to @@ -11949,8 +11930,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - + + plerologous to This phenomenon is usually due to gene conversion process. in plerology relationship with @@ -11973,8 +11954,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - - + + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. in homotopy relationship with @@ -11998,8 +11979,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - - + + heterotopy in homeosis relationship with @@ -12022,8 +12003,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - - + + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. in homoeology relationship with @@ -12046,8 +12027,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - + + axis paramorphism in paramorphism relationship with @@ -12069,8 +12050,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - + + regulogous to in regulogy relationship with @@ -12975,6 +12956,18 @@ No imports misnomer + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + previous name + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + legal name + diff --git a/src/ontology/subsets/ro-developmental.json b/src/ontology/subsets/ro-developmental.json index 3962522d..f4109945 100644 --- a/src/ontology/subsets/ro-developmental.json +++ b/src/ontology/subsets/ro-developmental.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 9dcabaf6..1b9a7611 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index 4276963b..d5a7ed64 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/src/ontology/subsets/ro-developmental.tsv b/src/ontology/subsets/ro-developmental.tsv index 87b847f2..2409aaef 100644 --- a/src/ontology/subsets/ro-developmental.tsv +++ b/src/ontology/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid1 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid18 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid22 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid26 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid33 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid37 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid40 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid5 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid52 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid58 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid61 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid64 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid67 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid9 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid1 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid18 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid22 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid26 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid33 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid37 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid40 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid5 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid52 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid58 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid61 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid64 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid67 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 diff --git a/src/ontology/subsets/ro-hom.json b/src/ontology/subsets/ro-hom.json index b36f3b6d..4316ff3e 100644 --- a/src/ontology/subsets/ro-hom.json +++ b/src/ontology/subsets/ro-hom.json @@ -269,10 +269,10 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -300,10 +300,10 @@ "val" : "RO:HOM0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -333,10 +333,10 @@ "val" : "RO:HOM0000002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -366,10 +366,10 @@ "val" : "RO:HOM0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -397,10 +397,10 @@ "val" : "RO:HOM0000004" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -428,10 +428,10 @@ "val" : "RO:HOM0000005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -465,10 +465,10 @@ "val" : "RO:HOM0000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -524,10 +524,10 @@ "val" : "RO:HOM0000007" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -560,10 +560,10 @@ "val" : "RO:HOM0000008" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -596,10 +596,10 @@ "val" : "RO:HOM0000009" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -635,10 +635,10 @@ "val" : "RO:HOM0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -671,10 +671,10 @@ "val" : "RO:HOM0000011" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -707,10 +707,10 @@ "val" : "RO:HOM0000012" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -737,10 +737,10 @@ "val" : "RO:HOM0000013" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -785,10 +785,10 @@ "val" : "RO:HOM0000014" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -817,10 +817,10 @@ "val" : "RO:HOM0000015" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -852,10 +852,10 @@ "val" : "RO:HOM0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -891,10 +891,10 @@ "val" : "RO:HOM0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -922,10 +922,10 @@ "val" : "RO:HOM0000018" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -958,10 +958,10 @@ "val" : "RO:HOM0000019" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -994,10 +994,10 @@ "val" : "RO:HOM0000020" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1027,10 +1027,10 @@ "val" : "RO:HOM0000022" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1063,10 +1063,10 @@ "val" : "RO:HOM0000023" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1099,10 +1099,10 @@ "val" : "RO:HOM0000024" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1129,10 +1129,10 @@ "val" : "RO:HOM0000025" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1160,10 +1160,10 @@ "val" : "RO:HOM0000026" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1193,10 +1193,10 @@ "val" : "RO:HOM0000027" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1226,10 +1226,10 @@ "val" : "RO:HOM0000028" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1259,10 +1259,10 @@ "val" : "RO:HOM0000029" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1285,10 +1285,10 @@ "val" : "RO:HOM0000030" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1311,10 +1311,10 @@ "val" : "RO:HOM0000031" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1344,10 +1344,10 @@ "val" : "RO:HOM0000032" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1374,10 +1374,10 @@ "val" : "RO:HOM0000033" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1416,10 +1416,10 @@ "val" : "RO:HOM0000034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1452,10 +1452,10 @@ "val" : "RO:HOM0000036" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1488,10 +1488,10 @@ "val" : "RO:HOM0000037" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1521,10 +1521,10 @@ "val" : "RO:HOM0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1555,10 +1555,10 @@ "val" : "RO:HOM0000043" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1595,10 +1595,10 @@ "val" : "RO:HOM0000044" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1625,10 +1625,10 @@ "val" : "RO:HOM0000045" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1655,10 +1655,10 @@ "val" : "RO:HOM0000046" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1687,10 +1687,10 @@ "val" : "RO:HOM0000047" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1732,10 +1732,10 @@ "val" : "RO:HOM0000048" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1762,10 +1762,10 @@ "val" : "RO:HOM0000049" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1793,10 +1793,10 @@ "val" : "RO:HOM0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1823,10 +1823,10 @@ "val" : "RO:HOM0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1849,10 +1849,10 @@ "val" : "RO:HOM0000052" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1879,10 +1879,10 @@ "val" : "RO:HOM0000053" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1911,10 +1911,10 @@ "val" : "RO:HOM0000054" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1947,10 +1947,10 @@ "val" : "RO:HOM0000055" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1996,10 +1996,10 @@ "val" : "RO:HOM0000057" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2030,10 +2030,10 @@ "val" : "RO:HOM0000058" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2070,10 +2070,10 @@ "val" : "RO:HOM0000060" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2101,10 +2101,10 @@ "val" : "RO:HOM0000061" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2132,10 +2132,10 @@ "val" : "RO:HOM0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2162,10 +2162,10 @@ "val" : "RO:HOM0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2192,10 +2192,10 @@ "val" : "RO:HOM0000065" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2222,10 +2222,10 @@ "val" : "RO:HOM0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2258,10 +2258,10 @@ "val" : "RO:HOM0000068" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2289,10 +2289,10 @@ "val" : "RO:HOM0000069" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2320,10 +2320,10 @@ "val" : "RO:HOM0000071" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2350,10 +2350,10 @@ "val" : "RO:HOM0000072" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2381,10 +2381,10 @@ "val" : "RO:HOM0000073" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2411,10 +2411,10 @@ "val" : "RO:HOM0000074" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2441,10 +2441,10 @@ "val" : "RO:HOM0000075" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", diff --git a/src/ontology/subsets/ro-hom.obo b/src/ontology/subsets/ro-hom.obo index 1a6836f2..209bb6ef 100644 --- a/src/ontology/subsets/ro-hom.obo +++ b/src/ontology/subsets/ro-hom.obo @@ -59,8 +59,8 @@ synonym: "1 to 1 homologous to" EXACT [] synonym: "1:1 homology" EXACT [] synonym: "one-to-one homology" EXACT [] xref: RO:HOM0000019 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000019 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -73,8 +73,8 @@ synonym: "1 to 1 orthologous to" EXACT [] synonym: "1:1 orthology" EXACT [] synonym: "one-to-one orthology" EXACT [] xref: RO:HOM0000020 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000020 is_symmetric: true is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with @@ -88,8 +88,8 @@ synonym: "1 to many homologous to" EXACT [] synonym: "1:many homology" RELATED [] synonym: "one-to-many homology" EXACT [] xref: RO:HOM0000037 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000037 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -104,8 +104,8 @@ synonym: "co-orthology" RELATED [] synonym: "many to 1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] xref: RO:HOM0000034 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000034 is_symmetric: true is_a: in_1_to_many_homology_relationship_with ! in 1 to many homology relationship with @@ -118,8 +118,8 @@ def: "Historical homology that is based on recent shared ancestry, characterizin synonym: "apomorphous to" EXACT [] synonym: "synapomorphy" RELATED [] xref: RO:HOM0000042 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000042 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -135,8 +135,8 @@ synonym: "apparent 1:1 orthology" EXACT [] synonym: "apparent orthologous to" EXACT [] synonym: "pseudoorthology" EXACT [] xref: RO:HOM0000060 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000060 is_symmetric: true is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with @@ -149,8 +149,8 @@ def: "Paralogy that involves genes from different species." [http://purl.obolibr comment: The genes have diverged before a speciation event. synonym: "between-species paralogous to" EXACT [] xref: RO:HOM0000050 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000050 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -164,8 +164,8 @@ synonym: "biological homologous to" EXACT [] synonym: "transformational homology" RELATED [] xref: ECO:0000067 xref: RO:HOM0000008 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000008 is_symmetric: true is_a: in_homology_relationship_with ! in homology relationship with @@ -177,8 +177,8 @@ def: "Historical homology that involves the chromosomes able to pair (synapse) d synonym: "chromosomal homologous to" EXACT [] xref: MeSH:Chromosome_Pairing xref: RO:HOM0000047 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000047 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -190,8 +190,8 @@ def: "Homoplasy that involves different underlying mechanisms or structures." [h comment: Convergence usually implies a notion of adaptation. synonym: "analogy" RELATED [] xref: RO:HOM0000004 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000004 is_symmetric: true is_a: in_homoplasy_relationship_with ! in homoplasy relationship with @@ -206,8 +206,8 @@ synonym: "deep homologous to" EXACT [] synonym: "generative homology" RELATED [] synonym: "homoiology" RELATED [] xref: RO:HOM0000044 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000044 is_symmetric: true is_a: in_homocracy_relationship_with ! in homocracy relationship with @@ -220,8 +220,8 @@ def: "Historical homology that involves functional equivalent genes with retenti comment: This may include examples of orthology, paralogy and xenology. synonym: "equivalogous to" EXACT [] xref: RO:HOM0000062 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000062 is_symmetric: true is_a: in_functional_equivalence_relationship_with ! in functional equivalence relationship with @@ -233,8 +233,8 @@ name: in functional equivalence relationship with def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] synonym: "functional similarity" RELATED [] xref: RO:HOM0000065 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000065 is_symmetric: true is_a: in_similarity_relationship_with ! in similarity relationship with @@ -245,8 +245,8 @@ name: in gametology relationship with def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] synonym: "gametologous to" EXACT [] xref: RO:HOM0000046 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000046 is_symmetric: true is_a: in_chromosomal_homology_relationship_with ! in chromosomal homology relationship with @@ -257,8 +257,8 @@ name: in hemiplasy relationship with def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] synonym: "hemiplasous to" EXACT [] xref: RO:HOM0000045 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000045 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -270,8 +270,8 @@ def: "Biological homology that is characterized by changes, over evolutionary ti synonym: "heterochronous homologous to" EXACT [] synonym: "heterochrony" EXACT [] xref: RO:HOM0000028 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000028 is_symmetric: true is_a: in_biological_homology_relationship_with ! in biological homology relationship with @@ -294,8 +294,8 @@ xref: SO:0000853 xref: SO:0000857 xref: SO:homologous_to xref: TAO:homologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000007 is_symmetric: true is_a: in_homology_relationship_with ! in homology relationship with @@ -306,8 +306,8 @@ name: in homeosis relationship with def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] synonym: "heterotopy" RELATED [] xref: RO:HOM0000072 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000072 is_symmetric: true is_a: in_biological_homology_relationship_with ! in biological homology relationship with @@ -320,8 +320,8 @@ comment: Homology and homocracy are not mutually exclusive. The homology relatio synonym: "homocracous to" EXACT [] xref: ECO:0000075 xref: RO:HOM0000003 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000003 is_symmetric: true is_a: evolutionarily_related_to ! evolutionarily related to @@ -334,8 +334,8 @@ def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pna comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. synonym: "homoeologous to" EXACT [] xref: RO:HOM0000073 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000073 is_symmetric: true is_a: in_ohnology_relationship_with ! in ohnology relationship with @@ -348,8 +348,8 @@ def: "Similarity that results from common evolutionary origin." [http://dx.doi.o comment: This broad definition encompasses all the working definitions proposed so far in the literature. synonym: "homologous to" EXACT [] xref: RO:HOM0000001 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000001 is_symmetric: true is_a: in_similarity_relationship_with ! in similarity relationship with @@ -363,8 +363,8 @@ def: "Similarity that results from independent evolution." [http://dx.doi.org/10 synonym: "analogy" RELATED [] synonym: "homoplasous to" EXACT [] xref: RO:HOM0000002 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000002 is_symmetric: true is_a: in_similarity_relationship_with ! in similarity relationship with @@ -376,8 +376,8 @@ def: "Structural homology that involves structures with the same or similar rela comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. synonym: "homotopous to" EXACT [] xref: RO:HOM0000071 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000071 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -388,8 +388,8 @@ id: in_hypermorphosis_relationship_with name: in hypermorphosis relationship with def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] xref: RO:HOM0000052 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000052 is_symmetric: true is_a: in_peramorphosis_relationship_with ! in peramorphosis relationship with @@ -402,8 +402,8 @@ synonym: "in-paralogous to" EXACT [] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] xref: RO:HOM0000023 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000023 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -415,8 +415,8 @@ name: in interology relationship with def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] synonym: "interologous to" EXACT [] xref: RO:HOM0000063 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000063 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -428,8 +428,8 @@ def: "Orthology that involves functional equivalent genes with retention of the synonym: "isoorthologous to" EXACT [] xref: ECO:0000080 xref: RO:HOM0000054 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000054 is_symmetric: true is_a: in_equivalogy_relationship_with ! in equivalogy relationship with @@ -441,8 +441,8 @@ name: in iterative homology relationship with def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] synonym: "iterative homologous to" EXACT [] xref: RO:HOM0000066 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000066 is_symmetric: true is_a: in_biological_homology_relationship_with ! in biological homology relationship with @@ -460,8 +460,8 @@ synonym: "latent homologous to" EXACT [] synonym: "re-awakening" RELATED [] synonym: "underlying synapomorphy" EXACT [] xref: RO:HOM0000057 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000057 is_symmetric: true is_a: in_parallelism_relationship_with ! in parallelism relationship with @@ -475,8 +475,8 @@ synonym: "many to many homologous to" EXACT [] synonym: "many-to-many homology" EXACT [] synonym: "many:many homology " EXACT [] xref: RO:HOM0000036 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000036 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -492,8 +492,8 @@ synonym: "many:many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] xref: RO:HOM0000048 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000048 is_symmetric: true is_a: in_many_to_many_homology_relationship_with ! in many to many homology relationship with @@ -505,8 +505,8 @@ name: in mimicry relationship with def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] synonym: "mimicrous to" EXACT [] xref: RO:HOM0000033 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000033 is_symmetric: true is_a: in_convergence_relationship_with ! in convergence relationship with @@ -518,8 +518,8 @@ def: "Paedomorphosis that is produced by a retardation of somatic development." synonym: "juvenilization" EXACT [] synonym: "neotenous to" EXACT [] xref: RO:HOM0000032 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000032 is_symmetric: true is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with @@ -532,8 +532,8 @@ synonym: "non functional homologous to" EXACT [] synonym: "pseudogene" BROAD [] xref: RO:HOM0000016 xref: SO:non_functional_homolog_of -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000016 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -546,8 +546,8 @@ def: "Paralogy that results from a whole genome duplication event." [http://dx.d synonym: "homoeology" RELATED [] synonym: "ohnologous to" EXACT [] xref: RO:HOM0000022 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000022 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -563,8 +563,8 @@ xref: RO:HOM0000017 xref: SO:0000855 xref: SO:0000858 xref: SO:orthologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000017 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -577,8 +577,8 @@ synonym: "alloparalogy" EXACT [] synonym: "out-paralogous to" EXACT [] synonym: "outparalogy" EXACT [] xref: RO:HOM0000024 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000024 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -590,8 +590,8 @@ def: "Heterochronous homology that is produced by a retention in adults of a spe synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] xref: RO:HOM0000029 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000029 is_symmetric: true is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with @@ -604,8 +604,8 @@ def: "Homoplasy that involves homologous underlying mechanisms or structures." [ comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. synonym: "parallel evolution" EXACT [] xref: RO:HOM0000005 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000005 is_symmetric: true is_a: in_homoplasy_relationship_with ! in homoplasy relationship with @@ -619,8 +619,8 @@ xref: RO:HOM0000011 xref: SO:0000854 xref: SO:0000859 xref: SO:paralogous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000011 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -632,8 +632,8 @@ name: in paramorphism relationship with def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] synonym: "axis paramorphism" RELATED [] xref: RO:HOM0000074 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000074 is_symmetric: true is_a: in_homocracy_relationship_with ! in homocracy relationship with @@ -647,8 +647,8 @@ synonym: "duplicate xenology" EXACT [] synonym: "multiple xenology" EXACT [] synonym: "paraxenologous to" EXACT [] xref: RO:HOM0000068 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000068 is_symmetric: true is_a: in_xenology_relationship_with ! in xenology relationship with @@ -665,8 +665,8 @@ synonym: "partial homologous to" EXACT [] synonym: "percent homology" RELATED [] synonym: "segmental homology" EXACT [] xref: RO:HOM0000014 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000014 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -676,8 +676,8 @@ id: in_peramorphosis_relationship_with name: in peramorphosis relationship with def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] xref: RO:HOM0000030 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000030 is_symmetric: true is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with @@ -689,8 +689,8 @@ def: "Paralogy that is characterized by extra similarity between paralogous sequ comment: This phenomenon is usually due to gene conversion process. synonym: "plerologous to" EXACT [] xref: RO:HOM0000069 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000069 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -703,8 +703,8 @@ comment: This term is usually contrasted to apomorphy. synonym: "plesiomorphous to" EXACT [] synonym: "symplesiomorphy" RELATED [] xref: RO:HOM0000043 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000043 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -715,8 +715,8 @@ name: in postdisplacement relationship with def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] synonym: "post-displacement" EXACT [] xref: RO:HOM0000051 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000051 is_symmetric: true is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with @@ -727,8 +727,8 @@ name: in pro-orthology relationship with def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] synonym: "pro-orthologous to" EXACT [] xref: RO:HOM0000025 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000025 is_symmetric: true is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with @@ -738,8 +738,8 @@ id: in_progenesis_relationship_with name: in progenesis relationship with def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] xref: RO:HOM0000031 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000031 is_symmetric: true is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with @@ -751,8 +751,8 @@ def: "Structural homology that is detected at the level of the 3D protein struct synonym: "protein structural homologous to" EXACT [] xref: MeSH:Structural_Homology\,_Protein xref: RO:HOM0000015 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000015 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -764,8 +764,8 @@ def: "Xenology that involves genes that ended up in a given genome as a result o comment: These genes may come out as paralogs in a single-genome analysis. synonym: "pseudoparalogous to" EXACT [] xref: RO:HOM0000061 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000061 is_symmetric: true is_a: in_xenology_relationship_with ! in xenology relationship with @@ -776,8 +776,8 @@ name: in regulogy relationship with def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] synonym: "regulogous to" EXACT [] xref: RO:HOM0000075 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000075 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -790,8 +790,8 @@ synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] xref: RO:HOM0000009 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000009 is_symmetric: true is_a: in_homoplasy_relationship_with ! in homoplasy relationship with @@ -803,8 +803,8 @@ def: "1:many orthology that involves a gene in species A and its ortholog in spe comment: The converse of pro-orthologous. synonym: "semi-orthologous to" EXACT [] xref: RO:HOM0000026 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000026 is_symmetric: true is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with @@ -816,8 +816,8 @@ def: "Iterative homology that involves structures arranged along the main body a synonym: "homonomy" RELATED [] synonym: "serial homologous to" EXACT [] xref: RO:HOM0000027 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000027 is_symmetric: true is_a: in_iterative_homology_relationship_with ! in iterative homology relationship with @@ -833,8 +833,8 @@ synonym: "similar to" EXACT [] xref: ECO:0000041 xref: RO:HOM0000000 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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/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 @@ -850,8 +850,8 @@ synonym: "structural homologous to" EXACT [] xref: ECO:0000071 xref: MI:2163 xref: RO:HOM0000006 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000006 is_symmetric: true is_a: in_homology_relationship_with ! in homology relationship with @@ -864,8 +864,8 @@ comment: Cannot be used when orthologous patterning gene are organizing obviousl synonym: "generative homology" EXACT [] synonym: "syngenous to" EXACT [] xref: RO:HOM0000058 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000058 is_symmetric: true is_a: in_homocracy_relationship_with ! in homocracy relationship with @@ -876,8 +876,8 @@ name: in synology relationship with def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] synonym: "synologous to" EXACT [] xref: RO:HOM0000053 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000053 is_symmetric: true is_a: in_xenology_relationship_with ! in xenology relationship with @@ -892,8 +892,8 @@ xref: MeSH:Synteny xref: RO:HOM0000010 xref: SO:0000860 xref: SO:0005858 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000010 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -904,8 +904,8 @@ name: in syntenic orthology relationship with def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] synonym: "syntenic orthologous to" EXACT [] xref: RO:HOM0000013 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000013 is_symmetric: true is_a: in_syntenic_homology_relationship_with ! in syntenic homology relationship with @@ -918,8 +918,8 @@ synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] synonym: "syntenic paralogous to" EXACT [] xref: RO:HOM0000012 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000012 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -933,8 +933,8 @@ synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] synonym: "tandem paralogous to" EXACT [] xref: RO:HOM0000055 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000055 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -961,8 +961,8 @@ name: in within-species paralogy relationship with def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "within-species paralogous to" EXACT [] xref: RO:HOM0000049 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000049 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -975,8 +975,8 @@ def: "Historical homology that is characterized by an interspecies (horizontal) comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). synonym: "xenologous to" EXACT [] xref: RO:HOM0000018 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000018 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with diff --git a/src/ontology/subsets/ro-hom.owl b/src/ontology/subsets/ro-hom.owl index 48b144e7..62fa8f00 100644 --- a/src/ontology/subsets/ro-hom.owl +++ b/src/ontology/subsets/ro-hom.owl @@ -1,13 +1,13 @@ @@ -78,15 +78,15 @@ - + - + - + - + @@ -293,8 +293,8 @@ TODO: Add homeomorphy axiom - - + + ECO:0000041 RO:HOM0000000 SO:similar_to @@ -330,8 +330,8 @@ Similarity that results from common evolutionary origin. - - + + RO:HOM0000001 homologous to in_homology_relationship_with @@ -357,8 +357,8 @@ Similarity that results from independent evolution. - - + + RO:HOM0000002 homoplasous to analogy @@ -383,8 +383,8 @@ Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - + + ECO:0000075 RO:HOM0000003 homocracous to @@ -411,8 +411,8 @@ Homoplasy that involves different underlying mechanisms or structures. - - + + RO:HOM0000004 analogy in_convergence_relationship_with @@ -436,8 +436,8 @@ Homoplasy that involves homologous underlying mechanisms or structures. - - + + RO:HOM0000005 parallel evolution in_parallelism_relationship_with @@ -461,8 +461,8 @@ Homology that is defined by similarity with regard to selected structural parameters. - - + + ECO:0000071 MI:2163 RO:HOM0000006 @@ -490,8 +490,8 @@ Homology that is defined by common descent. - - + + homology ECO:0000080 RO:HOM0000007 @@ -527,8 +527,8 @@ Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - + + ECO:0000067 RO:HOM0000008 biological homologous to @@ -555,8 +555,8 @@ Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - + + RO:HOM0000009 atavism rudiment @@ -581,8 +581,8 @@ Structural homology that is detected by similarity in content and organization between chromosomes. - - + + MeSH:Synteny RO:HOM0000010 SO:0000860 @@ -610,8 +610,8 @@ Historical homology that involves genes that diverged after a duplication event. - - + + RO:HOM0000011 SO:0000854 SO:0000859 @@ -640,8 +640,8 @@ Paralogy that involves sets of syntenic blocks. - - + + RO:HOM0000012 syntenic paralogous to duplicon @@ -667,8 +667,8 @@ Syntenic homology that involves chromosomes of different species. - - + + RO:HOM0000013 syntenic orthologous to in_syntenic_orthology_relationship_with @@ -691,8 +691,8 @@ Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - + + RO:HOM0000014 fractional homology partial homologous to @@ -722,8 +722,8 @@ Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - + + MeSH:Structural_Homology,_Protein RO:HOM0000015 protein structural homologous to @@ -748,8 +748,8 @@ Structural homology that involves a pseudogenic feature and its functional ancestor. - - + + pseudogene RO:HOM0000016 SO:non_functional_homolog_of @@ -774,8 +774,8 @@ Historical homology that involves genes that diverged after a speciation event. - - + + ECO:00000060 RO:HOM0000017 SO:0000855 @@ -806,8 +806,8 @@ Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - + + RO:HOM0000018 xenologous to in_xenology_relationship_with @@ -832,8 +832,8 @@ Historical homology that involves two members sharing no other homologs in the lineages considered. - - + + RO:HOM0000019 1 to 1 homologous to 1:1 homology @@ -859,8 +859,8 @@ Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - + + RO:HOM0000020 1 to 1 orthologous to 1:1 orthology @@ -886,8 +886,8 @@ Paralogy that results from a whole genome duplication event. - - + + RO:HOM0000022 ohnologous to homoeology @@ -912,8 +912,8 @@ Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - + + RO:HOM0000023 in-paralogous to inparalogy @@ -938,8 +938,8 @@ Paralogy that results from a duplication preceding a given speciation event. - - + + RO:HOM0000024 alloparalogy out-paralogous to @@ -964,8 +964,8 @@ 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - + + RO:HOM0000025 pro-orthologous to in_pro-orthology_relationship_with @@ -989,8 +989,8 @@ 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - + + RO:HOM0000026 semi-orthologous to in_semi-orthology_relationship_with @@ -1015,8 +1015,8 @@ Iterative homology that involves structures arranged along the main body axis. - - + + RO:HOM0000027 serial homologous to homonomy @@ -1040,8 +1040,8 @@ Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - + + RO:HOM0000028 heterochronous homologous to heterochrony @@ -1066,8 +1066,8 @@ Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - + + RO:HOM0000029 juvenification pedomorphosis @@ -1092,8 +1092,8 @@ Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - + + RO:HOM0000030 in_peramorphosis_relationship_with in peramorphosis relationship with @@ -1115,8 +1115,8 @@ Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - + + RO:HOM0000031 in_progenesis_relationship_with in progenesis relationship with @@ -1139,8 +1139,8 @@ Paedomorphosis that is produced by a retardation of somatic development. - - + + RO:HOM0000032 juvenilization neotenous to @@ -1165,8 +1165,8 @@ Convergence that results from co-evolution usually involving an evolutionary arms race. - - + + RO:HOM0000033 mimicrous to in_mimicry_relationship_with @@ -1190,8 +1190,8 @@ Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - + + RO:HOM0000034 1 to many orthologous to 1:many orthology @@ -1219,8 +1219,8 @@ Historical homology that involves two members of a larger set of homologs. - - + + RO:HOM0000036 many to many homologous to many-to-many homology @@ -1245,8 +1245,8 @@ Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - + + RO:HOM0000037 1 to many homologous to one-to-many homology @@ -1272,8 +1272,8 @@ Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - + + RO:HOM0000042 apomorphous to synapomorphy @@ -1297,8 +1297,8 @@ Historical homology that is based on distant shared ancestry. - - + + RO:HOM0000043 plesiomorphous to symplesiomorphy @@ -1324,8 +1324,8 @@ Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - + + RO:HOM0000044 deep genetic homology deep homologous to @@ -1353,8 +1353,8 @@ Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - + + RO:HOM0000045 hemiplasous to in_hemiplasy_relationship_with @@ -1377,8 +1377,8 @@ Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - + + RO:HOM0000046 gametologous to in_gametology_relationship_with @@ -1401,8 +1401,8 @@ Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - + + MeSH:Chromosome_Pairing RO:HOM0000047 chromosomal homologous to @@ -1427,8 +1427,8 @@ Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - + + RO:HOM0000048 many to many orthologous to many-to-many orthology @@ -1458,8 +1458,8 @@ Paralogy that involves genes from the same species. - - + + RO:HOM0000049 within-species paralogous to in_within-species_paralogy_relationship_with @@ -1482,8 +1482,8 @@ Paralogy that involves genes from different species. - - + + RO:HOM0000050 between-species paralogous to in_between-species_paralogy_relationship_with @@ -1507,8 +1507,8 @@ Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - + + RO:HOM0000051 post-displacement in_postdisplacement_relationship_with @@ -1531,8 +1531,8 @@ Peramorphosis that is produced by a delay in the offset of development. - - + + RO:HOM0000052 in_hypermorphosis_relationship_with in hypermorphosis relationship with @@ -1555,8 +1555,8 @@ Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - + + RO:HOM0000053 synologous to in_synology_relationship_with @@ -1581,8 +1581,8 @@ Orthology that involves functional equivalent genes with retention of the ancestral function. - - + + ECO:0000080 RO:HOM0000054 isoorthologous to @@ -1606,8 +1606,8 @@ Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - + + RO:HOM0000055 tandem paralogous to iterative paralogy @@ -1634,8 +1634,8 @@ Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - + + RO:HOM0000057 apomorphic tendency cryptic homology @@ -1668,8 +1668,8 @@ Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - + + RO:HOM0000058 generative homology syngenous to @@ -1696,8 +1696,8 @@ Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - + + RO:HOM0000060 1:1 paralogy apparent 1:1 orthology @@ -1725,8 +1725,8 @@ Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - + + RO:HOM0000061 pseudoparalogous to in_pseudoparalogy_relationship_with @@ -1751,8 +1751,8 @@ Historical homology that involves functional equivalent genes with retention of the ancestral function. - - + + RO:HOM0000062 equivalogous to in_equivalogy_relationship_with @@ -1776,8 +1776,8 @@ Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - + + RO:HOM0000063 interologous to in_interology_relationship_with @@ -1801,8 +1801,8 @@ Similarity that is characterized by interchangeability in function. - - + + RO:HOM0000065 functional similarity in_functional_equivalence_relationship_with @@ -1826,8 +1826,8 @@ Biological homology that involves parts of the same organism. - - + + RO:HOM0000066 iterative homologous to in_iterative_homology_relationship_with @@ -1850,8 +1850,8 @@ Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - + + RO:HOM0000068 duplicate xenology multiple xenology @@ -1876,8 +1876,8 @@ Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - + + RO:HOM0000069 plerologous to in_plerology_relationship_with @@ -1902,8 +1902,8 @@ Structural homology that involves structures with the same or similar relative positions. - - + + RO:HOM0000071 homotopous to in_homotopy_relationship_with @@ -1929,8 +1929,8 @@ Biological homology that involves an ectopic structure and the normally positioned structure. - - + + RO:HOM0000072 heterotopy in_homeosis_relationship_with @@ -1955,8 +1955,8 @@ Synology that results from allopolyploidy. - - + + RO:HOM0000073 homoeologous to in_homoeology_relationship_with @@ -1981,8 +1981,8 @@ Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - + + RO:HOM0000074 axis paramorphism in_paramorphism_relationship_with @@ -2006,8 +2006,8 @@ Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - + + RO:HOM0000075 regulogous to in_regulogy_relationship_with diff --git a/src/ontology/subsets/ro-interaction.json b/src/ontology/subsets/ro-interaction.json index 4a01601a..f20717da 100644 --- a/src/ontology/subsets/ro-interaction.json +++ b/src/ontology/subsets/ro-interaction.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index d0b641be..4ef159e2 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index b9a16f07..cd814966 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/src/ontology/subsets/ro-interaction.tsv b/src/ontology/subsets/ro-interaction.tsv index a67d022a..9b1bc3ad 100644 --- a/src/ontology/subsets/ro-interaction.tsv +++ b/src/ontology/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid1 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid18 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid22 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid26 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid33 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid37 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid40 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid5 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid52 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid58 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid61 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid64 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid67 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid9 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid1 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid18 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid22 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid26 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid33 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid37 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid40 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid5 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid52 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid58 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid61 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid64 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid67 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 diff --git a/src/ontology/subsets/ro-mereotopology.json b/src/ontology/subsets/ro-mereotopology.json index 080ee607..b4fa7b87 100644 --- a/src/ontology/subsets/ro-mereotopology.json +++ b/src/ontology/subsets/ro-mereotopology.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index f034bad4..b3bbb2c2 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 14422f3a..0fd2522d 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/src/ontology/subsets/ro-mereotopology.tsv b/src/ontology/subsets/ro-mereotopology.tsv index 54a82ec4..58250b17 100644 --- a/src/ontology/subsets/ro-mereotopology.tsv +++ b/src/ontology/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid1 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid18 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid22 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid26 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid33 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid37 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid40 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid5 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid52 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid58 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid61 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid64 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid67 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid9 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid1 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid18 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid22 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid26 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid33 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid37 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid40 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid5 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid52 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid58 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid61 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid64 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid67 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 diff --git a/src/ontology/subsets/ro-sequence.json b/src/ontology/subsets/ro-sequence.json index 668e1a01..10e06877 100644 --- a/src/ontology/subsets/ro-sequence.json +++ b/src/ontology/subsets/ro-sequence.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 6f5694a7..37ac9123 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index e8536f0f..985fe0d8 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/src/ontology/subsets/ro-sequence.tsv b/src/ontology/subsets/ro-sequence.tsv index c1f7657a..80c67530 100644 --- a/src/ontology/subsets/ro-sequence.tsv +++ b/src/ontology/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid1 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid18 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid22 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid26 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid33 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid37 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid40 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid5 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid52 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid58 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid61 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid64 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid67 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid9 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid1 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid18 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid22 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid26 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid33 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid37 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid40 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid5 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid52 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid58 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid61 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid64 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid67 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 diff --git a/src/ontology/subsets/ro-time-interval.json b/src/ontology/subsets/ro-time-interval.json index a5d73b5b..ca09a23e 100644 --- a/src/ontology/subsets/ro-time-interval.json +++ b/src/ontology/subsets/ro-time-interval.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 3517257d..394d300d 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index d131f24e..1d0ac69e 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/src/ontology/subsets/ro-time-interval.tsv b/src/ontology/subsets/ro-time-interval.tsv index 406af670..58e569a4 100644 --- a/src/ontology/subsets/ro-time-interval.tsv +++ b/src/ontology/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid1 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid18 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid22 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid26 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid33 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid37 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid40 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid5 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid52 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid58 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid61 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid64 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid67 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid9 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid1 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid18 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid22 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid26 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid33 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid37 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid40 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid5 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid52 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid58 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid61 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid64 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid67 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9 diff --git a/subsets/ro-causal.json b/subsets/ro-causal.json index 8b89b440..22c6414d 100644 --- a/subsets/ro-causal.json +++ b/subsets/ro-causal.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 942e3a70..aae8993f 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index 716fd015..40bb5909 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/subsets/ro-causal.tsv b/subsets/ro-causal.tsv index b039df98..f63b8b06 100644 --- a/subsets/ro-causal.tsv +++ b/subsets/ro-causal.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid1 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid18 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid22 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid26 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid33 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid37 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid40 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid5 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid52 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid58 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid61 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid64 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid67 -_:B402fda13X2Db6e1X2D4032X2Da12dX2Da4a8865dde4bgenid9 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid1 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid18 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid22 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid26 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid33 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid37 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid40 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid5 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid52 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid58 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid61 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid64 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid67 +_:B455354aeX2Dc78cX2D4a8eX2Db495X2D1a8830eba41agenid9 diff --git a/subsets/ro-chado.json b/subsets/ro-chado.json index f86a1d5d..a473678c 100644 --- a/subsets/ro-chado.json +++ b/subsets/ro-chado.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-06-28" + "val" : "2023-08-18" } ], - "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-06-28/subsets/ro-chado.owl" + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/subsets/ro-chado.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -205,7 +205,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -1753,6 +1753,36 @@ "val" : "https://orcid.org/0000-0003-4423-4370" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003008", + "lbl" : "previous name", + "meta" : { + "definition" : { + "val" : "A synonym type for names that have been used as primary labels in the past." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003009", + "lbl" : "legal name", + "meta" : { + "definition" : { + "val" : "A synonym type for the legal entity name" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", "lbl" : "characteristic of", @@ -1862,7 +1892,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } @@ -2201,10 +2231,9 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "lbl" : "contained in", + "lbl" : "obsolete contained in", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contained in" @@ -2214,30 +2243,28 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contained_in" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "lbl" : "contains", + "lbl" : "obsolete contains", "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contains" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/693" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001020", @@ -2314,7 +2341,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12180,7 +12207,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" @@ -12779,10 +12806,10 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12804,10 +12831,10 @@ "val" : "homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12831,10 +12858,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12859,10 +12886,10 @@ "val" : "ECO:0000075" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12884,10 +12911,10 @@ "val" : "analogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12909,10 +12936,10 @@ "val" : "parallel evolution" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12941,10 +12968,10 @@ "val" : "MI:2163" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -12995,10 +13022,10 @@ "val" : "TAO:homologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13026,10 +13053,10 @@ "val" : "ECO:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13056,10 +13083,10 @@ "val" : "reversion" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13090,10 +13117,10 @@ "val" : "SO:0005858" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13121,10 +13148,10 @@ "val" : "SO:paralogous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13151,10 +13178,10 @@ "val" : "paralogon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13175,10 +13202,10 @@ "val" : "syntenic orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13217,10 +13244,10 @@ "val" : "percent homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13244,10 +13271,10 @@ "val" : "MeSH:Structural_Homology,_Protein" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13274,10 +13301,10 @@ "val" : "SO:non_functional_homolog_of" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13308,10 +13335,10 @@ "val" : "SO:orthologous_to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13333,10 +13360,10 @@ "val" : "xenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13363,10 +13390,10 @@ "val" : "one-to-one homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13393,10 +13420,10 @@ "val" : "one-to-one orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13420,10 +13447,10 @@ "val" : "homoeology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13450,10 +13477,10 @@ "val" : "symparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13480,10 +13507,10 @@ "val" : "outparalogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13504,10 +13531,10 @@ "val" : "pro-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13529,10 +13556,10 @@ "val" : "semi-orthologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13556,10 +13583,10 @@ "val" : "homonomy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13583,10 +13610,10 @@ "val" : "heterochrony" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13610,10 +13637,10 @@ "val" : "pedomorphosis" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13630,10 +13657,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000030" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13650,10 +13677,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13677,10 +13704,10 @@ "val" : "neotenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13701,10 +13728,10 @@ "val" : "mimicrous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13737,10 +13764,10 @@ "val" : "many to 1 orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13767,10 +13794,10 @@ "val" : "many:many homology " } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13797,10 +13824,10 @@ "val" : "1:many homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13824,10 +13851,10 @@ "val" : "synapomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13852,10 +13879,10 @@ "val" : "symplesiomorphy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13886,10 +13913,10 @@ "val" : "homoiology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13910,10 +13937,10 @@ "val" : "hemiplasous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13934,10 +13961,10 @@ "val" : "gametologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -13961,10 +13988,10 @@ "val" : "MeSH:Chromosome_Pairing" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14000,10 +14027,10 @@ "val" : "trans-homology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14024,10 +14051,10 @@ "val" : "within-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14049,10 +14076,10 @@ "val" : "between-species paralogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14073,10 +14100,10 @@ "val" : "post-displacement" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14093,10 +14120,10 @@ "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000052", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14117,10 +14144,10 @@ "val" : "synologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14144,10 +14171,10 @@ "val" : "ECO:0000080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14174,10 +14201,10 @@ "val" : "serial paralogy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14217,10 +14244,10 @@ "val" : "re-awakening" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14245,10 +14272,10 @@ "val" : "syngenous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14279,10 +14306,10 @@ "val" : "pseudoorthology" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14304,10 +14331,10 @@ "val" : "pseudoparalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14329,10 +14356,10 @@ "val" : "equivalogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14353,10 +14380,10 @@ "val" : "interologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14377,10 +14404,10 @@ "val" : "functional similarity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14401,10 +14428,10 @@ "val" : "iterative homologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14431,10 +14458,10 @@ "val" : "paraxenologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14456,10 +14483,10 @@ "val" : "plerologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14481,10 +14508,10 @@ "val" : "homotopous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14505,10 +14532,10 @@ "val" : "heterotopy" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14530,10 +14557,10 @@ "val" : "homoeologous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14554,10 +14581,10 @@ "val" : "axis paramorphism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14578,10 +14605,10 @@ "val" : "regulogous to" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", @@ -14976,7 +15003,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002004", "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001018" + "obj" : "http://purl.obolibrary.org/obo/RO_0001025" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002006", "pred" : "subPropertyOf", @@ -17697,10 +17724,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0001015", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0001018", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0001019" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0001020", "pred" : "inverseOf", @@ -18164,9 +18187,6 @@ }, { "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_0001018", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index f42318df..fe43ab79 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -13,7 +13,7 @@ property_value: http://purl.org/dc/terms/description "The OBO Relations Ontology property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://purl.org/dc/terms/title "OBO Relations Ontology" xsd:string property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-06-28" xsd:string +property_value: owl:versionInfo "2023-08-18" xsd:string [Typedef] id: BFO:0000050 @@ -176,21 +176,18 @@ is_a: RO:0000052 ! characteristic of id: RO:0000300 name: obsolete_in_neural_circuit_with def: "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." [] -is_transitive: true is_obsolete: true [Typedef] id: RO:0000301 name: obsolete_upstream_in_neural_circuit_with def: "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." [] -is_transitive: true is_obsolete: true [Typedef] id: RO:0000302 name: obsolete_downstream_in_neural_circuit_with def: "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." [] -is_transitive: true is_obsolete: true [Typedef] @@ -213,13 +210,13 @@ inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 -name: contained_in -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains +name: obsolete_contained_in +is_obsolete: true [Typedef] id: RO:0001019 -name: contains +name: obsolete_contains +is_obsolete: true [Typedef] id: RO:0001020 @@ -282,7 +279,7 @@ is_a: RO:0002170 ! connected to 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)." [] -is_a: RO:0001018 ! contained in +is_a: RO:0001025 ! located in [Typedef] id: RO:0002005 @@ -3674,7 +3671,6 @@ holds_over_chain: RO:0002215 RO:0002233 id: RO:0017003 name: positively_correlated_with def: "A relation between entities in which one increases or decreases as the other does the same." [] -is_reflexive: true is_symmetric: true is_a: RO:0002610 ! correlated with diff --git a/subsets/ro-chado.owl b/subsets/ro-chado.owl index f2a43fda..389234a4 100644 --- a/subsets/ro-chado.owl +++ b/subsets/ro-chado.owl @@ -21,8 +21,8 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2023-06-28 + + 2023-08-18 @@ -1160,12 +1160,6 @@ Where we have an annotation assertion - - - - - - @@ -1637,7 +1631,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1783,7 +1777,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1925,7 +1919,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. @@ -1941,7 +1934,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. @@ -1957,7 +1949,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. @@ -2022,22 +2013,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - contained_in - - - contained in + obsolete contained in + + true @@ -2046,9 +2028,9 @@ range: spatial region or site (immaterial continuant) contains - - - contains + obsolete contains + + true @@ -2113,7 +2095,7 @@ range: spatial region or site (immaterial continuant) Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in https://wiki.geneontology.org/Located_in @@ -2186,7 +2168,7 @@ range: spatial region or site (immaterial continuant) - + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). tracheates @@ -10015,7 +9997,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z has disease https://github.com/oborel/obo-relations/issues/478 @@ -10049,7 +10031,7 @@ For example, protein A (transcription factor) indirectly increases by expression A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -10061,7 +10043,6 @@ For example, protein A (transcription factor) indirectly increases by expression - A relation between entities in which one increases or decreases as the other does the same. directly correlated with @@ -10484,8 +10465,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu TODO: Add homeomorphy axiom - - + + ECO:0000041 SO:similar_to sameness @@ -10519,8 +10500,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from common evolutionary origin. - - + + homologous to This broad definition encompasses all the working definitions proposed so far in the literature. in homology relationship with @@ -10544,8 +10525,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - - + + homoplasous to analogy in homoplasy relationship with @@ -10568,8 +10549,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - + + ECO:0000075 homocracous to Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. @@ -10594,8 +10575,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - - + + analogy Convergence usually implies a notion of adaptation. in convergence relationship with @@ -10617,8 +10598,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - - + + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. in parallelism relationship with @@ -10640,8 +10621,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - - + + ECO:0000071 MI:2163 structural homologous to @@ -10667,8 +10648,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - - + + homology ECO:0000080 RO_proposed_relation:homologous_to @@ -10702,8 +10683,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - + + ECO:0000067 biological homologous to transformational homology @@ -10728,8 +10709,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - + + atavism rudiment reversion @@ -10752,8 +10733,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - - + + MeSH:Synteny SO:0000860 SO:0005858 @@ -10779,8 +10760,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - - + + SO:0000854 SO:0000859 SO:paralogous_to @@ -10807,8 +10788,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - - + + syntenic paralogous to duplicon paralogon @@ -10832,8 +10813,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - - + + syntenic orthologous to in syntenic orthology relationship with @@ -10854,8 +10835,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - + + fractional homology partial homologous to segmental homology @@ -10883,8 +10864,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - + + MeSH:Structural_Homology,_Protein protein structural homologous to in protein structural homology relationship with @@ -10907,8 +10888,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - - + + pseudogene SO:non_functional_homolog_of non functional homologous to @@ -10931,8 +10912,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - - + + ECO:00000060 SO:0000855 SO:0000858 @@ -10961,8 +10942,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - + + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). in xenology relationship with @@ -10985,8 +10966,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - - + + 1 to 1 homologous to 1:1 homology one-to-one homology @@ -11010,8 +10991,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - + + 1 to 1 orthologous to 1:1 orthology one-to-one orthology @@ -11035,8 +11016,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - - + + ohnologous to homoeology in ohnology relationship with @@ -11059,8 +11040,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - + + in-paralogous to inparalogy symparalogy @@ -11083,8 +11064,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - - + + alloparalogy out-paralogous to outparalogy @@ -11107,8 +11088,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - + + pro-orthologous to in pro-orthology relationship with @@ -11130,8 +11111,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - + + semi-orthologous to The converse of pro-orthologous. in semi-orthology relationship with @@ -11154,8 +11135,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - - + + serial homologous to homonomy in serial homology relationship with @@ -11177,8 +11158,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - + + heterochronous homologous to heterochrony in heterochronous homology relationship with @@ -11201,8 +11182,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - + + juvenification pedomorphosis in paedomorphorsis relationship with @@ -11225,8 +11206,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - + + in peramorphosis relationship with @@ -11246,8 +11227,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - + + in progenesis relationship with @@ -11268,8 +11249,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - - + + juvenilization neotenous to in neoteny relationship with @@ -11292,8 +11273,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - - + + mimicrous to in mimicry relationship with @@ -11315,8 +11296,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - + + 1 to many orthologous to 1:many orthology one-to-many orthology @@ -11342,8 +11323,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - - + + many to many homologous to many-to-many homology many:many homology @@ -11366,8 +11347,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - + + 1 to many homologous to one-to-many homology 1:many homology @@ -11391,8 +11372,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - + + apomorphous to synapomorphy in apomorphy relationship with @@ -11414,8 +11395,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - - + + plesiomorphous to symplesiomorphy This term is usually contrasted to apomorphy. @@ -11439,8 +11420,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - + + deep genetic homology deep homologous to generative homology @@ -11466,8 +11447,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - + + hemiplasous to in hemiplasy relationship with @@ -11488,8 +11469,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - + + gametologous to in gametology relationship with @@ -11510,8 +11491,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - + + MeSH:Chromosome_Pairing chromosomal homologous to in chromosomal homology relationship with @@ -11534,8 +11515,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - + + many to many orthologous to many-to-many orthology many:many orthology @@ -11563,8 +11544,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - - + + within-species paralogous to in within-species paralogy relationship with @@ -11585,8 +11566,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - - + + between-species paralogous to The genes have diverged before a speciation event. in between-species paralogy relationship with @@ -11608,8 +11589,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - + + post-displacement in postdisplacement relationship with @@ -11630,8 +11611,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - - + + in hypermorphosis relationship with @@ -11652,8 +11633,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - + + synologous to in synology relationship with @@ -11676,8 +11657,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - - + + ECO:0000080 isoorthologous to in isoorthology relationship with @@ -11699,8 +11680,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - + + tandem paralogous to iterative paralogy serial paralogy @@ -11725,8 +11706,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - + + apomorphic tendency cryptic homology latent homologous to @@ -11757,8 +11738,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - + + generative homology syngenous to Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. @@ -11783,8 +11764,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - + + 1:1 paralogy apparent 1:1 orthology apparent orthologous to @@ -11810,8 +11791,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - + + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. in pseudoparalogy relationship with @@ -11834,8 +11815,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - - + + equivalogous to This may include examples of orthology, paralogy and xenology. in equivalogy relationship with @@ -11857,8 +11838,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - + + interologous to in interology relationship with @@ -11880,8 +11861,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - - + + functional similarity in functional equivalence relationship with @@ -11903,8 +11884,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - - + + iterative homologous to in iterative homology relationship with @@ -11925,8 +11906,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - + + duplicate xenology multiple xenology paraxenologous to @@ -11949,8 +11930,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - + + plerologous to This phenomenon is usually due to gene conversion process. in plerology relationship with @@ -11973,8 +11954,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - - + + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. in homotopy relationship with @@ -11998,8 +11979,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - - + + heterotopy in homeosis relationship with @@ -12022,8 +12003,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - - + + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. in homoeology relationship with @@ -12046,8 +12027,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - + + axis paramorphism in paramorphism relationship with @@ -12069,8 +12050,8 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - + + regulogous to in regulogy relationship with @@ -12975,6 +12956,18 @@ No imports misnomer + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + previous name + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + legal name + diff --git a/subsets/ro-developmental.json b/subsets/ro-developmental.json index 3962522d..f4109945 100644 --- a/subsets/ro-developmental.json +++ b/subsets/ro-developmental.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 9dcabaf6..1b9a7611 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 4276963b..d5a7ed64 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/subsets/ro-developmental.tsv b/subsets/ro-developmental.tsv index 87b847f2..2409aaef 100644 --- a/subsets/ro-developmental.tsv +++ b/subsets/ro-developmental.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid1 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid18 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid22 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid26 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid33 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid37 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid40 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid5 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid52 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid58 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid61 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid64 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid67 -_:B13d9cb22X2Db01bX2D4e6eX2Da499X2D60f9ccb8fca7genid9 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid1 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid18 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid22 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid26 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid33 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid37 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid40 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid5 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid52 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid58 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid61 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid64 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid67 +_:Bd880c650X2Dd120X2D48e4X2D9686X2D1ec297b490f0genid9 diff --git a/subsets/ro-hom.json b/subsets/ro-hom.json index b36f3b6d..4316ff3e 100644 --- a/subsets/ro-hom.json +++ b/subsets/ro-hom.json @@ -269,10 +269,10 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -300,10 +300,10 @@ "val" : "RO:HOM0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -333,10 +333,10 @@ "val" : "RO:HOM0000002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -366,10 +366,10 @@ "val" : "RO:HOM0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -397,10 +397,10 @@ "val" : "RO:HOM0000004" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -428,10 +428,10 @@ "val" : "RO:HOM0000005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -465,10 +465,10 @@ "val" : "RO:HOM0000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -524,10 +524,10 @@ "val" : "RO:HOM0000007" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -560,10 +560,10 @@ "val" : "RO:HOM0000008" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -596,10 +596,10 @@ "val" : "RO:HOM0000009" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -635,10 +635,10 @@ "val" : "RO:HOM0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -671,10 +671,10 @@ "val" : "RO:HOM0000011" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -707,10 +707,10 @@ "val" : "RO:HOM0000012" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -737,10 +737,10 @@ "val" : "RO:HOM0000013" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -785,10 +785,10 @@ "val" : "RO:HOM0000014" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -817,10 +817,10 @@ "val" : "RO:HOM0000015" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -852,10 +852,10 @@ "val" : "RO:HOM0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -891,10 +891,10 @@ "val" : "RO:HOM0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -922,10 +922,10 @@ "val" : "RO:HOM0000018" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -958,10 +958,10 @@ "val" : "RO:HOM0000019" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -994,10 +994,10 @@ "val" : "RO:HOM0000020" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1027,10 +1027,10 @@ "val" : "RO:HOM0000022" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1063,10 +1063,10 @@ "val" : "RO:HOM0000023" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1099,10 +1099,10 @@ "val" : "RO:HOM0000024" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1129,10 +1129,10 @@ "val" : "RO:HOM0000025" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1160,10 +1160,10 @@ "val" : "RO:HOM0000026" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1193,10 +1193,10 @@ "val" : "RO:HOM0000027" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1226,10 +1226,10 @@ "val" : "RO:HOM0000028" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1259,10 +1259,10 @@ "val" : "RO:HOM0000029" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1285,10 +1285,10 @@ "val" : "RO:HOM0000030" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1311,10 +1311,10 @@ "val" : "RO:HOM0000031" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1344,10 +1344,10 @@ "val" : "RO:HOM0000032" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1374,10 +1374,10 @@ "val" : "RO:HOM0000033" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1416,10 +1416,10 @@ "val" : "RO:HOM0000034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1452,10 +1452,10 @@ "val" : "RO:HOM0000036" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1488,10 +1488,10 @@ "val" : "RO:HOM0000037" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1521,10 +1521,10 @@ "val" : "RO:HOM0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1555,10 +1555,10 @@ "val" : "RO:HOM0000043" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1595,10 +1595,10 @@ "val" : "RO:HOM0000044" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1625,10 +1625,10 @@ "val" : "RO:HOM0000045" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1655,10 +1655,10 @@ "val" : "RO:HOM0000046" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1687,10 +1687,10 @@ "val" : "RO:HOM0000047" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1732,10 +1732,10 @@ "val" : "RO:HOM0000048" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1762,10 +1762,10 @@ "val" : "RO:HOM0000049" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1793,10 +1793,10 @@ "val" : "RO:HOM0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1823,10 +1823,10 @@ "val" : "RO:HOM0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1849,10 +1849,10 @@ "val" : "RO:HOM0000052" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1879,10 +1879,10 @@ "val" : "RO:HOM0000053" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1911,10 +1911,10 @@ "val" : "RO:HOM0000054" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1947,10 +1947,10 @@ "val" : "RO:HOM0000055" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -1996,10 +1996,10 @@ "val" : "RO:HOM0000057" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2030,10 +2030,10 @@ "val" : "RO:HOM0000058" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2070,10 +2070,10 @@ "val" : "RO:HOM0000060" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2101,10 +2101,10 @@ "val" : "RO:HOM0000061" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2132,10 +2132,10 @@ "val" : "RO:HOM0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2162,10 +2162,10 @@ "val" : "RO:HOM0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2192,10 +2192,10 @@ "val" : "RO:HOM0000065" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2222,10 +2222,10 @@ "val" : "RO:HOM0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2258,10 +2258,10 @@ "val" : "RO:HOM0000068" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2289,10 +2289,10 @@ "val" : "RO:HOM0000069" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2320,10 +2320,10 @@ "val" : "RO:HOM0000071" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2350,10 +2350,10 @@ "val" : "RO:HOM0000072" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2381,10 +2381,10 @@ "val" : "RO:HOM0000073" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2411,10 +2411,10 @@ "val" : "RO:HOM0000074" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -2441,10 +2441,10 @@ "val" : "RO:HOM0000075" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.org/dc/terms/creator", "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", diff --git a/subsets/ro-hom.obo b/subsets/ro-hom.obo index 1a6836f2..209bb6ef 100644 --- a/subsets/ro-hom.obo +++ b/subsets/ro-hom.obo @@ -59,8 +59,8 @@ synonym: "1 to 1 homologous to" EXACT [] synonym: "1:1 homology" EXACT [] synonym: "one-to-one homology" EXACT [] xref: RO:HOM0000019 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000019 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -73,8 +73,8 @@ synonym: "1 to 1 orthologous to" EXACT [] synonym: "1:1 orthology" EXACT [] synonym: "one-to-one orthology" EXACT [] xref: RO:HOM0000020 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000020 is_symmetric: true is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with @@ -88,8 +88,8 @@ synonym: "1 to many homologous to" EXACT [] synonym: "1:many homology" RELATED [] synonym: "one-to-many homology" EXACT [] xref: RO:HOM0000037 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000037 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -104,8 +104,8 @@ synonym: "co-orthology" RELATED [] synonym: "many to 1 orthology" RELATED [] synonym: "one-to-many orthology" EXACT [] xref: RO:HOM0000034 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000034 is_symmetric: true is_a: in_1_to_many_homology_relationship_with ! in 1 to many homology relationship with @@ -118,8 +118,8 @@ def: "Historical homology that is based on recent shared ancestry, characterizin synonym: "apomorphous to" EXACT [] synonym: "synapomorphy" RELATED [] xref: RO:HOM0000042 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000042 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -135,8 +135,8 @@ synonym: "apparent 1:1 orthology" EXACT [] synonym: "apparent orthologous to" EXACT [] synonym: "pseudoorthology" EXACT [] xref: RO:HOM0000060 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000060 is_symmetric: true is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with @@ -149,8 +149,8 @@ def: "Paralogy that involves genes from different species." [http://purl.obolibr comment: The genes have diverged before a speciation event. synonym: "between-species paralogous to" EXACT [] xref: RO:HOM0000050 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000050 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -164,8 +164,8 @@ synonym: "biological homologous to" EXACT [] synonym: "transformational homology" RELATED [] xref: ECO:0000067 xref: RO:HOM0000008 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000008 is_symmetric: true is_a: in_homology_relationship_with ! in homology relationship with @@ -177,8 +177,8 @@ def: "Historical homology that involves the chromosomes able to pair (synapse) d synonym: "chromosomal homologous to" EXACT [] xref: MeSH:Chromosome_Pairing xref: RO:HOM0000047 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000047 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -190,8 +190,8 @@ def: "Homoplasy that involves different underlying mechanisms or structures." [h comment: Convergence usually implies a notion of adaptation. synonym: "analogy" RELATED [] xref: RO:HOM0000004 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000004 is_symmetric: true is_a: in_homoplasy_relationship_with ! in homoplasy relationship with @@ -206,8 +206,8 @@ synonym: "deep homologous to" EXACT [] synonym: "generative homology" RELATED [] synonym: "homoiology" RELATED [] xref: RO:HOM0000044 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000044 is_symmetric: true is_a: in_homocracy_relationship_with ! in homocracy relationship with @@ -220,8 +220,8 @@ def: "Historical homology that involves functional equivalent genes with retenti comment: This may include examples of orthology, paralogy and xenology. synonym: "equivalogous to" EXACT [] xref: RO:HOM0000062 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000062 is_symmetric: true is_a: in_functional_equivalence_relationship_with ! in functional equivalence relationship with @@ -233,8 +233,8 @@ name: in functional equivalence relationship with def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] synonym: "functional similarity" RELATED [] xref: RO:HOM0000065 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000065 is_symmetric: true is_a: in_similarity_relationship_with ! in similarity relationship with @@ -245,8 +245,8 @@ name: in gametology relationship with def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] synonym: "gametologous to" EXACT [] xref: RO:HOM0000046 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000046 is_symmetric: true is_a: in_chromosomal_homology_relationship_with ! in chromosomal homology relationship with @@ -257,8 +257,8 @@ name: in hemiplasy relationship with def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] synonym: "hemiplasous to" EXACT [] xref: RO:HOM0000045 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000045 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -270,8 +270,8 @@ def: "Biological homology that is characterized by changes, over evolutionary ti synonym: "heterochronous homologous to" EXACT [] synonym: "heterochrony" EXACT [] xref: RO:HOM0000028 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000028 is_symmetric: true is_a: in_biological_homology_relationship_with ! in biological homology relationship with @@ -294,8 +294,8 @@ xref: SO:0000853 xref: SO:0000857 xref: SO:homologous_to xref: TAO:homologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000007 is_symmetric: true is_a: in_homology_relationship_with ! in homology relationship with @@ -306,8 +306,8 @@ name: in homeosis relationship with def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] synonym: "heterotopy" RELATED [] xref: RO:HOM0000072 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000072 is_symmetric: true is_a: in_biological_homology_relationship_with ! in biological homology relationship with @@ -320,8 +320,8 @@ comment: Homology and homocracy are not mutually exclusive. The homology relatio synonym: "homocracous to" EXACT [] xref: ECO:0000075 xref: RO:HOM0000003 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000003 is_symmetric: true is_a: evolutionarily_related_to ! evolutionarily related to @@ -334,8 +334,8 @@ def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pna comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. synonym: "homoeologous to" EXACT [] xref: RO:HOM0000073 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000073 is_symmetric: true is_a: in_ohnology_relationship_with ! in ohnology relationship with @@ -348,8 +348,8 @@ def: "Similarity that results from common evolutionary origin." [http://dx.doi.o comment: This broad definition encompasses all the working definitions proposed so far in the literature. synonym: "homologous to" EXACT [] xref: RO:HOM0000001 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000001 is_symmetric: true is_a: in_similarity_relationship_with ! in similarity relationship with @@ -363,8 +363,8 @@ def: "Similarity that results from independent evolution." [http://dx.doi.org/10 synonym: "analogy" RELATED [] synonym: "homoplasous to" EXACT [] xref: RO:HOM0000002 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000002 is_symmetric: true is_a: in_similarity_relationship_with ! in similarity relationship with @@ -376,8 +376,8 @@ def: "Structural homology that involves structures with the same or similar rela comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. synonym: "homotopous to" EXACT [] xref: RO:HOM0000071 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000071 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -388,8 +388,8 @@ id: in_hypermorphosis_relationship_with name: in hypermorphosis relationship with def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] xref: RO:HOM0000052 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000052 is_symmetric: true is_a: in_peramorphosis_relationship_with ! in peramorphosis relationship with @@ -402,8 +402,8 @@ synonym: "in-paralogous to" EXACT [] synonym: "inparalogy" EXACT [] synonym: "symparalogy" EXACT [] xref: RO:HOM0000023 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000023 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -415,8 +415,8 @@ name: in interology relationship with def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] synonym: "interologous to" EXACT [] xref: RO:HOM0000063 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000063 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -428,8 +428,8 @@ def: "Orthology that involves functional equivalent genes with retention of the synonym: "isoorthologous to" EXACT [] xref: ECO:0000080 xref: RO:HOM0000054 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000054 is_symmetric: true is_a: in_equivalogy_relationship_with ! in equivalogy relationship with @@ -441,8 +441,8 @@ name: in iterative homology relationship with def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] synonym: "iterative homologous to" EXACT [] xref: RO:HOM0000066 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000066 is_symmetric: true is_a: in_biological_homology_relationship_with ! in biological homology relationship with @@ -460,8 +460,8 @@ synonym: "latent homologous to" EXACT [] synonym: "re-awakening" RELATED [] synonym: "underlying synapomorphy" EXACT [] xref: RO:HOM0000057 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000057 is_symmetric: true is_a: in_parallelism_relationship_with ! in parallelism relationship with @@ -475,8 +475,8 @@ synonym: "many to many homologous to" EXACT [] synonym: "many-to-many homology" EXACT [] synonym: "many:many homology " EXACT [] xref: RO:HOM0000036 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000036 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -492,8 +492,8 @@ synonym: "many:many orthology" EXACT [] synonym: "trans-homology" RELATED [] synonym: "trans-orthology" EXACT [] xref: RO:HOM0000048 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000048 is_symmetric: true is_a: in_many_to_many_homology_relationship_with ! in many to many homology relationship with @@ -505,8 +505,8 @@ name: in mimicry relationship with def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] synonym: "mimicrous to" EXACT [] xref: RO:HOM0000033 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000033 is_symmetric: true is_a: in_convergence_relationship_with ! in convergence relationship with @@ -518,8 +518,8 @@ def: "Paedomorphosis that is produced by a retardation of somatic development." synonym: "juvenilization" EXACT [] synonym: "neotenous to" EXACT [] xref: RO:HOM0000032 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000032 is_symmetric: true is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with @@ -532,8 +532,8 @@ synonym: "non functional homologous to" EXACT [] synonym: "pseudogene" BROAD [] xref: RO:HOM0000016 xref: SO:non_functional_homolog_of -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000016 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -546,8 +546,8 @@ def: "Paralogy that results from a whole genome duplication event." [http://dx.d synonym: "homoeology" RELATED [] synonym: "ohnologous to" EXACT [] xref: RO:HOM0000022 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000022 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -563,8 +563,8 @@ xref: RO:HOM0000017 xref: SO:0000855 xref: SO:0000858 xref: SO:orthologous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000017 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -577,8 +577,8 @@ synonym: "alloparalogy" EXACT [] synonym: "out-paralogous to" EXACT [] synonym: "outparalogy" EXACT [] xref: RO:HOM0000024 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000024 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -590,8 +590,8 @@ def: "Heterochronous homology that is produced by a retention in adults of a spe synonym: "juvenification" EXACT [] synonym: "pedomorphosis" EXACT [] xref: RO:HOM0000029 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000029 is_symmetric: true is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with @@ -604,8 +604,8 @@ def: "Homoplasy that involves homologous underlying mechanisms or structures." [ comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. synonym: "parallel evolution" EXACT [] xref: RO:HOM0000005 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000005 is_symmetric: true is_a: in_homoplasy_relationship_with ! in homoplasy relationship with @@ -619,8 +619,8 @@ xref: RO:HOM0000011 xref: SO:0000854 xref: SO:0000859 xref: SO:paralogous_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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000011 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -632,8 +632,8 @@ name: in paramorphism relationship with def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] synonym: "axis paramorphism" RELATED [] xref: RO:HOM0000074 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000074 is_symmetric: true is_a: in_homocracy_relationship_with ! in homocracy relationship with @@ -647,8 +647,8 @@ synonym: "duplicate xenology" EXACT [] synonym: "multiple xenology" EXACT [] synonym: "paraxenologous to" EXACT [] xref: RO:HOM0000068 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000068 is_symmetric: true is_a: in_xenology_relationship_with ! in xenology relationship with @@ -665,8 +665,8 @@ synonym: "partial homologous to" EXACT [] synonym: "percent homology" RELATED [] synonym: "segmental homology" EXACT [] xref: RO:HOM0000014 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000014 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -676,8 +676,8 @@ id: in_peramorphosis_relationship_with name: in peramorphosis relationship with def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] xref: RO:HOM0000030 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000030 is_symmetric: true is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with @@ -689,8 +689,8 @@ def: "Paralogy that is characterized by extra similarity between paralogous sequ comment: This phenomenon is usually due to gene conversion process. synonym: "plerologous to" EXACT [] xref: RO:HOM0000069 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000069 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -703,8 +703,8 @@ comment: This term is usually contrasted to apomorphy. synonym: "plesiomorphous to" EXACT [] synonym: "symplesiomorphy" RELATED [] xref: RO:HOM0000043 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000043 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -715,8 +715,8 @@ name: in postdisplacement relationship with def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] synonym: "post-displacement" EXACT [] xref: RO:HOM0000051 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000051 is_symmetric: true is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with @@ -727,8 +727,8 @@ name: in pro-orthology relationship with def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] synonym: "pro-orthologous to" EXACT [] xref: RO:HOM0000025 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000025 is_symmetric: true is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with @@ -738,8 +738,8 @@ id: in_progenesis_relationship_with name: in progenesis relationship with def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] xref: RO:HOM0000031 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000031 is_symmetric: true is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with @@ -751,8 +751,8 @@ def: "Structural homology that is detected at the level of the 3D protein struct synonym: "protein structural homologous to" EXACT [] xref: MeSH:Structural_Homology\,_Protein xref: RO:HOM0000015 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000015 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -764,8 +764,8 @@ def: "Xenology that involves genes that ended up in a given genome as a result o comment: These genes may come out as paralogs in a single-genome analysis. synonym: "pseudoparalogous to" EXACT [] xref: RO:HOM0000061 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000061 is_symmetric: true is_a: in_xenology_relationship_with ! in xenology relationship with @@ -776,8 +776,8 @@ name: in regulogy relationship with def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] synonym: "regulogous to" EXACT [] xref: RO:HOM0000075 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000075 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with @@ -790,8 +790,8 @@ synonym: "atavism" EXACT [] synonym: "reversion" RELATED [] synonym: "rudiment" EXACT [] xref: RO:HOM0000009 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000009 is_symmetric: true is_a: in_homoplasy_relationship_with ! in homoplasy relationship with @@ -803,8 +803,8 @@ def: "1:many orthology that involves a gene in species A and its ortholog in spe comment: The converse of pro-orthologous. synonym: "semi-orthologous to" EXACT [] xref: RO:HOM0000026 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000026 is_symmetric: true is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with @@ -816,8 +816,8 @@ def: "Iterative homology that involves structures arranged along the main body a synonym: "homonomy" RELATED [] synonym: "serial homologous to" EXACT [] xref: RO:HOM0000027 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000027 is_symmetric: true is_a: in_iterative_homology_relationship_with ! in iterative homology relationship with @@ -833,8 +833,8 @@ synonym: "similar to" EXACT [] xref: ECO:0000041 xref: RO:HOM0000000 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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/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 @@ -850,8 +850,8 @@ synonym: "structural homologous to" EXACT [] xref: ECO:0000071 xref: MI:2163 xref: RO:HOM0000006 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000006 is_symmetric: true is_a: in_homology_relationship_with ! in homology relationship with @@ -864,8 +864,8 @@ comment: Cannot be used when orthologous patterning gene are organizing obviousl synonym: "generative homology" EXACT [] synonym: "syngenous to" EXACT [] xref: RO:HOM0000058 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000058 is_symmetric: true is_a: in_homocracy_relationship_with ! in homocracy relationship with @@ -876,8 +876,8 @@ name: in synology relationship with def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] synonym: "synologous to" EXACT [] xref: RO:HOM0000053 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000053 is_symmetric: true is_a: in_xenology_relationship_with ! in xenology relationship with @@ -892,8 +892,8 @@ xref: MeSH:Synteny xref: RO:HOM0000010 xref: SO:0000860 xref: SO:0005858 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000010 is_symmetric: true is_a: in_structural_homology_relationship_with ! in structural homology relationship with @@ -904,8 +904,8 @@ name: in syntenic orthology relationship with def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] synonym: "syntenic orthologous to" EXACT [] xref: RO:HOM0000013 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000013 is_symmetric: true is_a: in_syntenic_homology_relationship_with ! in syntenic homology relationship with @@ -918,8 +918,8 @@ synonym: "duplicon" RELATED [] synonym: "paralogon" RELATED [] synonym: "syntenic paralogous to" EXACT [] xref: RO:HOM0000012 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000012 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -933,8 +933,8 @@ synonym: "iterative paralogy" RELATED [] synonym: "serial paralogy" RELATED [] synonym: "tandem paralogous to" EXACT [] xref: RO:HOM0000055 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000055 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -961,8 +961,8 @@ name: in within-species paralogy relationship with def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] synonym: "within-species paralogous to" EXACT [] xref: RO:HOM0000049 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000049 is_symmetric: true is_a: in_paralogy_relationship_with ! in paralogy relationship with @@ -975,8 +975,8 @@ def: "Historical homology that is characterized by an interspecies (horizontal) comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). synonym: "xenologous to" EXACT [] xref: RO:HOM0000018 -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: http://purl.org/dc/terms/creator http://bgee.unil.ch +property_value: http://purl.org/dc/terms/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: seeAlso HOM:0000018 is_symmetric: true is_a: in_historical_homology_relationship_with ! in historical homology relationship with diff --git a/subsets/ro-hom.owl b/subsets/ro-hom.owl index 48b144e7..62fa8f00 100644 --- a/subsets/ro-hom.owl +++ b/subsets/ro-hom.owl @@ -1,13 +1,13 @@ @@ -78,15 +78,15 @@ - + - + - + - + @@ -293,8 +293,8 @@ TODO: Add homeomorphy axiom - - + + ECO:0000041 RO:HOM0000000 SO:similar_to @@ -330,8 +330,8 @@ Similarity that results from common evolutionary origin. - - + + RO:HOM0000001 homologous to in_homology_relationship_with @@ -357,8 +357,8 @@ Similarity that results from independent evolution. - - + + RO:HOM0000002 homoplasous to analogy @@ -383,8 +383,8 @@ Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - + + ECO:0000075 RO:HOM0000003 homocracous to @@ -411,8 +411,8 @@ Homoplasy that involves different underlying mechanisms or structures. - - + + RO:HOM0000004 analogy in_convergence_relationship_with @@ -436,8 +436,8 @@ Homoplasy that involves homologous underlying mechanisms or structures. - - + + RO:HOM0000005 parallel evolution in_parallelism_relationship_with @@ -461,8 +461,8 @@ Homology that is defined by similarity with regard to selected structural parameters. - - + + ECO:0000071 MI:2163 RO:HOM0000006 @@ -490,8 +490,8 @@ Homology that is defined by common descent. - - + + homology ECO:0000080 RO:HOM0000007 @@ -527,8 +527,8 @@ Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - + + ECO:0000067 RO:HOM0000008 biological homologous to @@ -555,8 +555,8 @@ Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - + + RO:HOM0000009 atavism rudiment @@ -581,8 +581,8 @@ Structural homology that is detected by similarity in content and organization between chromosomes. - - + + MeSH:Synteny RO:HOM0000010 SO:0000860 @@ -610,8 +610,8 @@ Historical homology that involves genes that diverged after a duplication event. - - + + RO:HOM0000011 SO:0000854 SO:0000859 @@ -640,8 +640,8 @@ Paralogy that involves sets of syntenic blocks. - - + + RO:HOM0000012 syntenic paralogous to duplicon @@ -667,8 +667,8 @@ Syntenic homology that involves chromosomes of different species. - - + + RO:HOM0000013 syntenic orthologous to in_syntenic_orthology_relationship_with @@ -691,8 +691,8 @@ Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - + + RO:HOM0000014 fractional homology partial homologous to @@ -722,8 +722,8 @@ Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - + + MeSH:Structural_Homology,_Protein RO:HOM0000015 protein structural homologous to @@ -748,8 +748,8 @@ Structural homology that involves a pseudogenic feature and its functional ancestor. - - + + pseudogene RO:HOM0000016 SO:non_functional_homolog_of @@ -774,8 +774,8 @@ Historical homology that involves genes that diverged after a speciation event. - - + + ECO:00000060 RO:HOM0000017 SO:0000855 @@ -806,8 +806,8 @@ Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - + + RO:HOM0000018 xenologous to in_xenology_relationship_with @@ -832,8 +832,8 @@ Historical homology that involves two members sharing no other homologs in the lineages considered. - - + + RO:HOM0000019 1 to 1 homologous to 1:1 homology @@ -859,8 +859,8 @@ Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - + + RO:HOM0000020 1 to 1 orthologous to 1:1 orthology @@ -886,8 +886,8 @@ Paralogy that results from a whole genome duplication event. - - + + RO:HOM0000022 ohnologous to homoeology @@ -912,8 +912,8 @@ Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - + + RO:HOM0000023 in-paralogous to inparalogy @@ -938,8 +938,8 @@ Paralogy that results from a duplication preceding a given speciation event. - - + + RO:HOM0000024 alloparalogy out-paralogous to @@ -964,8 +964,8 @@ 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - + + RO:HOM0000025 pro-orthologous to in_pro-orthology_relationship_with @@ -989,8 +989,8 @@ 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - + + RO:HOM0000026 semi-orthologous to in_semi-orthology_relationship_with @@ -1015,8 +1015,8 @@ Iterative homology that involves structures arranged along the main body axis. - - + + RO:HOM0000027 serial homologous to homonomy @@ -1040,8 +1040,8 @@ Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - + + RO:HOM0000028 heterochronous homologous to heterochrony @@ -1066,8 +1066,8 @@ Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - + + RO:HOM0000029 juvenification pedomorphosis @@ -1092,8 +1092,8 @@ Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - + + RO:HOM0000030 in_peramorphosis_relationship_with in peramorphosis relationship with @@ -1115,8 +1115,8 @@ Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - + + RO:HOM0000031 in_progenesis_relationship_with in progenesis relationship with @@ -1139,8 +1139,8 @@ Paedomorphosis that is produced by a retardation of somatic development. - - + + RO:HOM0000032 juvenilization neotenous to @@ -1165,8 +1165,8 @@ Convergence that results from co-evolution usually involving an evolutionary arms race. - - + + RO:HOM0000033 mimicrous to in_mimicry_relationship_with @@ -1190,8 +1190,8 @@ Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - + + RO:HOM0000034 1 to many orthologous to 1:many orthology @@ -1219,8 +1219,8 @@ Historical homology that involves two members of a larger set of homologs. - - + + RO:HOM0000036 many to many homologous to many-to-many homology @@ -1245,8 +1245,8 @@ Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - + + RO:HOM0000037 1 to many homologous to one-to-many homology @@ -1272,8 +1272,8 @@ Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - + + RO:HOM0000042 apomorphous to synapomorphy @@ -1297,8 +1297,8 @@ Historical homology that is based on distant shared ancestry. - - + + RO:HOM0000043 plesiomorphous to symplesiomorphy @@ -1324,8 +1324,8 @@ Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - + + RO:HOM0000044 deep genetic homology deep homologous to @@ -1353,8 +1353,8 @@ Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - + + RO:HOM0000045 hemiplasous to in_hemiplasy_relationship_with @@ -1377,8 +1377,8 @@ Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - + + RO:HOM0000046 gametologous to in_gametology_relationship_with @@ -1401,8 +1401,8 @@ Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - + + MeSH:Chromosome_Pairing RO:HOM0000047 chromosomal homologous to @@ -1427,8 +1427,8 @@ Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - + + RO:HOM0000048 many to many orthologous to many-to-many orthology @@ -1458,8 +1458,8 @@ Paralogy that involves genes from the same species. - - + + RO:HOM0000049 within-species paralogous to in_within-species_paralogy_relationship_with @@ -1482,8 +1482,8 @@ Paralogy that involves genes from different species. - - + + RO:HOM0000050 between-species paralogous to in_between-species_paralogy_relationship_with @@ -1507,8 +1507,8 @@ Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - + + RO:HOM0000051 post-displacement in_postdisplacement_relationship_with @@ -1531,8 +1531,8 @@ Peramorphosis that is produced by a delay in the offset of development. - - + + RO:HOM0000052 in_hypermorphosis_relationship_with in hypermorphosis relationship with @@ -1555,8 +1555,8 @@ Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - + + RO:HOM0000053 synologous to in_synology_relationship_with @@ -1581,8 +1581,8 @@ Orthology that involves functional equivalent genes with retention of the ancestral function. - - + + ECO:0000080 RO:HOM0000054 isoorthologous to @@ -1606,8 +1606,8 @@ Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - + + RO:HOM0000055 tandem paralogous to iterative paralogy @@ -1634,8 +1634,8 @@ Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - + + RO:HOM0000057 apomorphic tendency cryptic homology @@ -1668,8 +1668,8 @@ Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - + + RO:HOM0000058 generative homology syngenous to @@ -1696,8 +1696,8 @@ Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - + + RO:HOM0000060 1:1 paralogy apparent 1:1 orthology @@ -1725,8 +1725,8 @@ Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - + + RO:HOM0000061 pseudoparalogous to in_pseudoparalogy_relationship_with @@ -1751,8 +1751,8 @@ Historical homology that involves functional equivalent genes with retention of the ancestral function. - - + + RO:HOM0000062 equivalogous to in_equivalogy_relationship_with @@ -1776,8 +1776,8 @@ Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - + + RO:HOM0000063 interologous to in_interology_relationship_with @@ -1801,8 +1801,8 @@ Similarity that is characterized by interchangeability in function. - - + + RO:HOM0000065 functional similarity in_functional_equivalence_relationship_with @@ -1826,8 +1826,8 @@ Biological homology that involves parts of the same organism. - - + + RO:HOM0000066 iterative homologous to in_iterative_homology_relationship_with @@ -1850,8 +1850,8 @@ Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - + + RO:HOM0000068 duplicate xenology multiple xenology @@ -1876,8 +1876,8 @@ Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - + + RO:HOM0000069 plerologous to in_plerology_relationship_with @@ -1902,8 +1902,8 @@ Structural homology that involves structures with the same or similar relative positions. - - + + RO:HOM0000071 homotopous to in_homotopy_relationship_with @@ -1929,8 +1929,8 @@ Biological homology that involves an ectopic structure and the normally positioned structure. - - + + RO:HOM0000072 heterotopy in_homeosis_relationship_with @@ -1955,8 +1955,8 @@ Synology that results from allopolyploidy. - - + + RO:HOM0000073 homoeologous to in_homoeology_relationship_with @@ -1981,8 +1981,8 @@ Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - + + RO:HOM0000074 axis paramorphism in_paramorphism_relationship_with @@ -2006,8 +2006,8 @@ Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - + + RO:HOM0000075 regulogous to in_regulogy_relationship_with diff --git a/subsets/ro-interaction.json b/subsets/ro-interaction.json index 4a01601a..f20717da 100644 --- a/subsets/ro-interaction.json +++ b/subsets/ro-interaction.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index d0b641be..4ef159e2 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index b9a16f07..cd814966 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/subsets/ro-interaction.tsv b/subsets/ro-interaction.tsv index a67d022a..9b1bc3ad 100644 --- a/subsets/ro-interaction.tsv +++ b/subsets/ro-interaction.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid1 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid18 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid22 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid26 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid33 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid37 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid40 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid5 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid52 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid58 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid61 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid64 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid67 -_:B8b03a081X2D0694X2D4236X2Db685X2D8240a1793646genid9 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid1 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid18 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid22 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid26 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid33 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid37 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid40 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid5 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid52 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid58 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid61 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid64 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid67 +_:Be82b1b36X2De8a5X2D4ef8X2D844eX2Dafbd4d83af90genid9 diff --git a/subsets/ro-mereotopology.json b/subsets/ro-mereotopology.json index 080ee607..b4fa7b87 100644 --- a/subsets/ro-mereotopology.json +++ b/subsets/ro-mereotopology.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index f034bad4..b3bbb2c2 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 14422f3a..0fd2522d 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/subsets/ro-mereotopology.tsv b/subsets/ro-mereotopology.tsv index 54a82ec4..58250b17 100644 --- a/subsets/ro-mereotopology.tsv +++ b/subsets/ro-mereotopology.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid1 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid18 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid22 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid26 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid33 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid37 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid40 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid5 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid52 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid58 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid61 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid64 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid67 -_:B48f8f610X2De836X2D4c2aX2D9e89X2Dea4f01c111d6genid9 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid1 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid18 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid22 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid26 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid33 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid37 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid40 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid5 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid52 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid58 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid61 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid64 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid67 +_:Bc7a875caX2D029eX2D4742X2D9623X2De0edd49f6352genid9 diff --git a/subsets/ro-sequence.json b/subsets/ro-sequence.json index 668e1a01..10e06877 100644 --- a/subsets/ro-sequence.json +++ b/subsets/ro-sequence.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 6f5694a7..37ac9123 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index e8536f0f..985fe0d8 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/subsets/ro-sequence.tsv b/subsets/ro-sequence.tsv index c1f7657a..80c67530 100644 --- a/subsets/ro-sequence.tsv +++ b/subsets/ro-sequence.tsv @@ -1,18 +1,18 @@ ?x ?label -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid1 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid18 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid22 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid26 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid33 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid37 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid40 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid5 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid52 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid58 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid61 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid64 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid67 -_:B7715b03eX2D5d5cX2D4353X2Da1c0X2Db0252d4eac0fgenid9 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid1 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid18 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid22 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid26 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid33 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid37 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid40 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid5 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid52 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid58 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid61 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid64 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid67 +_:Bcb241ff9X2D80e8X2D4b81X2Dad97X2Dc32ee58abb6bgenid9 diff --git a/subsets/ro-time-interval.json b/subsets/ro-time-interval.json index a5d73b5b..ca09a23e 100644 --- a/subsets/ro-time-interval.json +++ b/subsets/ro-time-interval.json @@ -147,7 +147,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -304,7 +304,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", @@ -10889,7 +10889,7 @@ } ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "https://orcid.org/0000-0002-7463-6306" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2021-11-05T17:30:44Z" diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 3517257d..394d300d 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -1887,7 +1887,7 @@ id: has_disease name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7463-6306 property_value: http://purl.org/dc/terms/date "2021-11-05T17:30:44Z" xsd:dateTime property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease @@ -2360,7 +2360,7 @@ id: has_participant name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3940,7 +3940,7 @@ name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index d131f24e..1d0ac69e 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -1,7 +1,6 @@ - - - - - @@ -334,7 +327,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by @@ -431,7 +424,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant has participant @@ -7931,7 +7924,7 @@ For example, protein A (transcription factor) indirectly increases by expression A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - + 2021-11-05T17:30:44Z RO:0016002 has_disease diff --git a/subsets/ro-time-interval.tsv b/subsets/ro-time-interval.tsv index 406af670..58e569a4 100644 --- a/subsets/ro-time-interval.tsv +++ b/subsets/ro-time-interval.tsv @@ -1,18 +1,18 @@ ?x ?label -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid1 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid18 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid22 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid26 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid33 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid37 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid40 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid5 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid52 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid58 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid61 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid64 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid67 -_:Bf49f508dX2D0157X2D442aX2D902eX2D79dfefd18afegenid9 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid1 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid18 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid22 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid26 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid33 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid37 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid40 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid5 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid52 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid58 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid61 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid64 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid67 +_:Bd54e11b3X2Dea1fX2D474fX2Da448X2D635cd025f674genid9