diff --git a/apollo_sv-base.json b/apollo_sv-base.json index ef50d17..504ba22 100644 --- a/apollo_sv-base.json +++ b/apollo_sv-base.json @@ -26,18 +26,21 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "Apollo Structured Vocabulary (Apollo-SV)" }, { "pred" : "http://purl.org/dc/elements/1.1/type", "val" : "http://purl.obolibrary.org/obo/IAO_8000001" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/terms/description", "val" : "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/licenses/by/4.0/" + }, { + "pred" : "http://purl.org/dc/terms/title", + "val" : "Apollo Structured Vocabulary (Apollo-SV)" }, { "pred" : "http://www.referent-tracking.com/RTS_00000001", "val" : "C87985BA-6A8A-483A-A6B6-63975101F672" @@ -49,12 +52,9 @@ "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)." }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-01-10" - }, { - "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-15" + "val" : "2024-12-24" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-08-15/apollo_sv-base.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000000", @@ -12310,11 +12310,11 @@ "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.org/dc/elements/1.1/title", + "id" : "http://purl.org/dc/elements/1.1/type", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.org/dc/elements/1.1/type", + "id" : "http://purl.org/dc/terms/contributor", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -12325,6 +12325,10 @@ "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.referent-tracking.com/RTS_00000001", "type" : "PROPERTY", diff --git a/apollo_sv-base.obo b/apollo_sv-base.obo index db03b9d..3582af5 100644 --- a/apollo_sv-base.obo +++ b/apollo_sv-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2024-08-15/apollo_sv-base.owl +data-version: apollo_sv/releases/2024-12-24/apollo_sv-base.owl idspace: ace_lexicon http://attempto.ifi.uzh.ch/ace_lexicon# idspace: dc http://purl.org/dc/elements/1.1/ idspace: doap http://usefulinc.com/ns/doap# @@ -20,12 +20,12 @@ property_value: dc:contributor "Mike Wagner" xsd:string property_value: dc:contributor "Shawn T. Brown" xsd:string property_value: dc:contributor "William R. Hogan" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: dc:title "Apollo Structured Vocabulary (Apollo-SV)" xsd:string property_value: dc:type IAO:8000001 -property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2024-08-15" xsd:string +property_value: owl:versionInfo "2024-12-24" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string +property_value: terms:title "Apollo Structured Vocabulary (Apollo-SV)" xsd:string property_value: www:RTS_00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: www:RTS_00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string diff --git a/apollo_sv-base.owl b/apollo_sv-base.owl index 9945ad1..b27f6d3 100644 --- a/apollo_sv-base.owl +++ b/apollo_sv-base.owl @@ -25,7 +25,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -34,15 +34,15 @@ Shawn T. Brown William R. Hogan Mathias Brochhausen - Apollo Structured Vocabulary (Apollo-SV) + https://orcid.org/0000-0002-9881-1017 An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. https://creativecommons.org/licenses/by/4.0/ + Apollo Structured Vocabulary (Apollo-SV) C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). - 2023-01-10 - 2024-08-15 + 2024-12-24 @@ -234,15 +234,15 @@ For the 1982-10-17 date, we suggest the dc:created annotation. - + - + - + - + @@ -258,6 +258,12 @@ For the 1982-10-17 date, we suggest the dc:created annotation. + + + + + + diff --git a/apollo_sv-full.json b/apollo_sv-full.json index f47b660..e2ca93e 100644 --- a/apollo_sv-full.json +++ b/apollo_sv-full.json @@ -27,14 +27,17 @@ "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "Apollo Structured Vocabulary (Apollo-SV)" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/terms/description", "val" : "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/licenses/by/4.0/" + }, { + "pred" : "http://purl.org/dc/terms/title", + "val" : "Apollo Structured Vocabulary (Apollo-SV)" }, { "pred" : "http://www.referent-tracking.com/RTS_00000001", "val" : "C87985BA-6A8A-483A-A6B6-63975101F672" @@ -46,12 +49,9 @@ "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)." }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-01-10" - }, { - "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-15" + "val" : "2024-12-24" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-08-15/apollo_sv-full.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160", @@ -13587,30 +13587,6 @@ "val" : "pub_type" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_49443", - "lbl" : "Anatomical cluster", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_55457", - "lbl" : "vocal fold", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_64854", - "lbl" : "Subdivision of larynx", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_64989", - "lbl" : "Heterogeneous cluster", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_67135", - "lbl" : "Anatomical structure", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_67165", - "lbl" : "Material anatomical entity", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000001", "lbl" : "geopolitical entity", @@ -14292,9 +14268,6 @@ "val" : "Wikipedia:Viral_life_cycle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0022415" }, { @@ -14508,18 +14481,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" @@ -14763,9 +14724,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20191" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4895" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -14939,9 +14897,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "unitId" } ] } }, { @@ -14950,7 +14905,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." + "val" : "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -14958,18 +14913,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "purpose of a study; support of hypothesis, discovery of new information" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: original definition when imported from OBI read: \"objective is an\nnon realizable information entity which can serve as that proper part\nof a plan towards which the realization of the plan is directed.\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\"" @@ -15042,7 +14988,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a directive information entity that describes an action the bearer will take" + "val" : "A directive information entity that describes an action the bearer will take." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -15050,9 +14996,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -15086,9 +15029,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "datum label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -15110,9 +15050,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "label" } ] } }, { @@ -15368,14 +15305,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." + "val" : "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Data items include counts of things, analyte concentrations, and statistical summaries." @@ -15388,12 +15322,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." @@ -15406,21 +15334,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Jonathan Rees" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data" @@ -15432,7 +15351,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a smallish, word-like datum..." + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -15491,7 +15410,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" + "val" : "A generically dependent continuant that is about some thing." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -15502,9 +15421,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." @@ -15514,12 +15430,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000142" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000142" @@ -15589,12 +15499,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be\nconcretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." @@ -15792,9 +15696,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000124" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MSI" @@ -16244,9 +16145,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -16265,15 +16163,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000042" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000042" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "dataSets" } ] } }, { @@ -16332,18 +16224,15 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications." + "val" : "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." }, - "comments" : [ "2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them", "2/3/2009 Comment from OBI review.\n \n Action specification not well enough specified.\n Conditional specification not well enough specified.\n Question whether all plan specifications have objective specifications.\n \n Request that IAO either clarify these or change definitions not to use them" ], + "comments" : [ "2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -16419,9 +16308,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -16473,9 +16359,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000124" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" @@ -16612,9 +16495,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a hard drive" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -20075,9 +19955,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "name" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" @@ -20109,122 +19986,13 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020002", - "lbl" : "utterance", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An utterance is an information content entity that is a complete unit of speech in spoken language. " - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia: http://en.wikipedia.org/wiki/Utterance" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020003", - "lbl" : "mechanical wave quality", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attributive collection of qualities inhering in energy when transported through a medium in a wave." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020004", - "lbl" : "writing quality", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "is a quality that is the concretization of graphemes and inheres in a material object." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020005", - "lbl" : "writing bearer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "is a material information bearer that bears the concretization of graphemes." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting," - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020006", - "lbl" : "portion of energy", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020007", - "lbl" : "sound energy", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Energy that is transported in a sound wave." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020008", - "lbl" : "utterance energy", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Sound energy bearing the concretization of an utterance and being the output of an uttering process. " - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020009", - "lbl" : "oscillating", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Oscillation" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020010", "lbl" : "identifier creating process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." + "val" : "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -20249,25 +20017,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020011", - "lbl" : "utterance process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "is a planned process of making speech sounds which may or may not have an actual language involved. " - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wiktionary.org/wiki/utter" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020015", "lbl" : "personal name", @@ -20308,9 +20057,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "first name" @@ -20336,9 +20082,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "last name" @@ -20361,7 +20104,7 @@ "definition" : { "val" : "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." }, - "comments" : [ "Code sets might include non-entities/things (e.g. missing thumbs).", "Does not imply absence vs. presence of any taxonomy.", "Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.", "Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories).", "Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).", "Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).", "For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).", "For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.", "Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain.", "Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.", "The identifiers do not denote each other.", "The information content entities do not denote each other." ], + "comments" : [ "Code sets might include non-entities/things (e.g. missing thumbs).", "Does not imply absence vs. presence of any taxonomy.", "Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.", "Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).", "For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).", "For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.", "Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.", "The information content entities do not denote each other." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -20409,6 +20152,36 @@ "val" : "William R. Hogan" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0021003", + "lbl" : "social act", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." + }, + "comments" : [ "The phrase \"in need of being perceived\" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: \"The command is according to its essence in need of being heard (vernehmungsbedürtig\". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target.\" (A. Reinach: The Apriori Foundations of the Civil Law.\" Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0021009", + "lbl" : "deontic declaration", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A social act that creates or revokes a deontic role." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000000", "lbl" : "ontology module", @@ -31604,6 +31377,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "branch derived" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" @@ -32543,6 +32322,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -33246,6 +33028,9 @@ "lbl" : "inpatient encounter", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Albert Goldfain" @@ -33333,93 +33118,29 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen\n" + "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000007", - "lbl" : "gender role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Gender_role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "sex" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000008", - "lbl" : "male gender role", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000010", + "lbl" : "human health care role", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question." + "val" : "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "male gender" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000009", - "lbl" : "female gender role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "female gender" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000010", - "lbl" : "human health care role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. " - }, - "comments" : [ "Mathias Brochhausen" ], - "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "health care role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33428,8 +33149,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A role borne by an organism being as the recipient of a health care service." + "val" : "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." }, + "comments" : [ "In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" @@ -33441,10 +33163,7 @@ "val" : "patient" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Patient" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "val" : "CAFE domain expert working group." } ] } }, { @@ -33452,36 +33171,35 @@ "lbl" : "health care provider organization role", "type" : "CLASS", "meta" : { - "comments" : [ "Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division)." ], + "definition" : { + "val" : "A role that inheres in an organization and that is realized by the providing of services in a health care encounter." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "lbl" : "collection of organisms", + "lbl" : "aggregate of objectual organisms", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An object aggregate of organisms." + "val" : "An object aggregate of objectual organisms." }, - "comments" : [ "Any arbitrary collection of organisms. They need not be of the same taxonomic class. " ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species." - } ] + "comments" : [ "Any arbitrary collection of organisms. They need not be of the same taxonomic class. " ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000023", "lbl" : "collection of humans", "type" : "CLASS", "meta" : { - "comments" : [ "An object aggregate all of whose components are human beings." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] + "definition" : { + "val" : "An object aggregate all of whose components are human beings." + } } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000025", @@ -33495,9 +33213,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33512,9 +33227,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan\nMathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33523,58 +33235,60 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organization social role that is realized by a health care process." + "val" : "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process" }, - "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] + "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000033", - "lbl" : "aggregate of organizations", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "lbl" : "human patient role", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An aggregate of organizations that have some feature in common, but is not itself an organization." - }, - "comments" : [ "It is often convenient to group organizations together that otherwise might not even interact with one another. " ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] + "val" : "A patient role that inheres in a human being." + } } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000052", - "lbl" : "hospital function", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000033", + "lbl" : "aggregate of organizations", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population." + "val" : "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" }, + "comments" : [ "It is often convenient to group organizations together that otherwise might not even interact with one another. " ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "val" : "William R. Hogan\nAmanda Hicks" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "lbl" : "material entity role", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "lbl" : "organism role", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "lbl" : "Homo sapiens role", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "lbl" : "organization role", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000053", "lbl" : "school function", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A function inhering in a facility that manifests by the facility participating in providing formal education to a student population." + "val" : "A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33583,14 +33297,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care." + "val" : "A healthcare provider role that inheres in an organization and is realized by providing inpatient care." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33604,9 +33315,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33620,9 +33328,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33636,9 +33341,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33647,14 +33349,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A human social role that is realized by the process of formal education that the bearer undergoes." + "val" : "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33662,16 +33361,9 @@ "lbl" : "nursery school role", "type" : "CLASS", "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data.\n" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "preschool" } ] } }, { @@ -33679,16 +33371,9 @@ "lbl" : "primary school role", "type" : "CLASS", "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "primarySchool" } ] } }, { @@ -33706,9 +33391,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://de.wikipedia.org/wiki/Bauwerk" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33722,28 +33404,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000063", - "lbl" : "hospital facility", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A facility that is run by a hospital organization and is the bearer of a hospital function." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "HealthcareFacility" } ] } }, { @@ -33757,12 +33417,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "SchoolFacility" } ] } }, { @@ -33770,152 +33424,62 @@ "lbl" : "secondary school role", "type" : "CLASS", "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "secondarySchool" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000074", - "lbl" : "housing unit", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function." - }, - "comments" : [ "Housing units are individuated by their residence functions." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "houses" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000076", - "lbl" : "household", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000086", + "lbl" : "human role within an organization", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function." + "val" : "A human social role that is created by a deontic declaration performed by an organization." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "Household" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000078", - "lbl" : "workplace facility", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "workplace" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000079", - "lbl" : "workplace function", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "human organizational role" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000098", - "lbl" : "racial identity datum", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "lbl" : "human traveling information", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method." + "val" : "An information content entity that is about human travel." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "race" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000102", - "lbl" : "health care facility", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/ufbmi/OMRSE/issues/79" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "lbl" : "identity datum", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Jie Zheng" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method." } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000172", + "lbl" : "health care function", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002072", "lbl" : "role in human social processes", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A role inhering in an entity realized by social interactions in human society." + "val" : "A role that inheres in some entity that is realized in a social act." }, "comments" : [ "Previous definition: A role played by an entity in human social processes." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" @@ -34157,20 +33721,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001025", - "lbl" : "pressure", - "type" : "CLASS", - "meta" : { - "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147487103" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001241", "lbl" : "physical object quality", @@ -35618,7 +35168,7 @@ "val" : "http://www.geneontology.org/formats/oboInOwl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147487102" + "val" : "_:genid2147487128" } ] } }, { @@ -37349,74 +36899,38 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020012", - "lbl" : "obsolete_designates", + "id" : "http://purl.obolibrary.org/obo/IDO_0000660", + "lbl" : "results_in", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000228" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/IAO_0000219" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020013", - "lbl" : "is_borrowed_reference_to", + "id" : "http://purl.obolibrary.org/obo/OBIB_0000732", + "lbl" : "owns", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020014", - "lbl" : "is_fixing_reference_to", + "id" : "http://purl.obolibrary.org/obo/OBIB_0000735", + "lbl" : "is owned by", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the." + "val" : "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020018", - "lbl" : "is designated by", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IDO_0000660", - "lbl" : "results_in", - "type" : "PROPERTY", - "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000293", "lbl" : "has_specified_input", @@ -37626,6 +37140,9 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." }, { @@ -37634,11 +37151,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. " - } ] + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000732" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", - "lbl" : "is owned by", + "lbl" : "obsolete is owned by", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -37648,33 +37169,32 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/omrse.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000735" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000068", + "lbl" : "is administered by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000070", "lbl" : "is enrolled in school", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000071", "lbl" : "is admitted to hospital", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", "lbl" : "inheres in", @@ -41697,6 +41217,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " @@ -42369,18 +41892,6 @@ "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020019", - "lbl" : "IUI", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "instance unique identifier" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0100001", "lbl" : "term replaced by", @@ -42472,10 +41983,6 @@ "val" : "https://github.com/oborel/obo-relations/wiki/ROAndTime" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", "type" : "PROPERTY", @@ -46137,30 +45644,6 @@ "sub" : "http://purl.obolibrary.org/obo/FBcv_0000787", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_49443", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_67135" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_55457", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_64854" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_64854", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_64989" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_64989", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_49443" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_67135", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_67165" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_67165", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000001", "pred" : "is_a", @@ -47437,42 +46920,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020004", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020005", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000178" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020006" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020007", - "pred" : "http://purl.obolibrary.org/obo/RO_0000053", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020003" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020007" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020009", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "is_a", @@ -47481,14 +46928,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020011", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020011", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020008" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020015", "pred" : "is_a", @@ -47500,7 +46939,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020017", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020015" + "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020020", "pred" : "is_a", @@ -47509,6 +46948,14 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0021003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0021009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0021003" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", "pred" : "is_a", @@ -47836,7 +47283,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IDO_0000629", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/IDO_0000654", "pred" : "is_a", @@ -50084,7 +49531,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000245", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000425", "pred" : "is_a", @@ -50293,6 +49740,10 @@ "sub" : "http://purl.obolibrary.org/obo/OGMS_0000096", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/OGMS_0000097", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/OGMS_0000097", "pred" : "is_a", @@ -50327,48 +49778,44 @@ "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000026" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000001", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000007", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000009", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000007" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000010", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000010", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000010" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000027" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000022" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000025", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000051" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000025", "pred" : "is_a", @@ -50376,27 +49823,63 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000026", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000026", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000027", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000052", + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000053", "pred" : "is_a", @@ -50408,7 +49891,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000055", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000025" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000056", "pred" : "is_a", @@ -50425,10 +49908,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000057", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000055" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000058", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000001" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000059", "pred" : "is_a", @@ -50446,49 +49925,51 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000061" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000063", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000102" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000062", + "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000068", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "09/09/2017" + } ] + } + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000062", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000053" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000065", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000055" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000074", + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000142", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000076", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000078", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000079", + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000172", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000098", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000132" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000102", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000172", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002072", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000001", "pred" : "is_a", @@ -50537,10 +50018,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001018", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001025", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001241", "pred" : "is_a", @@ -50577,10 +50054,6 @@ "sub" : "http://purl.obolibrary.org/obo/PCO_0000001", "pred" : "http://purl.obolibrary.org/obo/BFO_0000177", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000104" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000018", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000022" }, { "sub" : "http://purl.obolibrary.org/obo/PCO_0000018", "pred" : "is_a", @@ -51046,17 +50519,9 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020012", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020013", + "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020018", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", "pred" : "subPropertyOf", @@ -51092,13 +50557,13 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { - "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", + "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000070", + "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { @@ -51813,6 +51278,14 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000418", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/IAO_0000419" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000735" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000299", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000312" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000052", "pred" : "inverseOf", @@ -51938,10 +51411,6 @@ "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0010002" } ], - "equivalentNodesSets" : [ { - "representativeNodeId" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "nodeIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000022", "http://purl.obolibrary.org/obo/PCO_0000000" ] - } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000006", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] @@ -52464,16 +51933,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000312", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020010" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020005", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000178" ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020007", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020006" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020003" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020010", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], @@ -52540,6 +51999,41 @@ }, { "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0001530", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0001173" ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000011" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/BFO_0000040" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000048" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0100026" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000049" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000245" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000056", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000245" ], @@ -52554,6 +52048,27 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", "fillerId" : "http://purl.obolibrary.org/obo/OMRSE_00000055" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000062", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000061" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/BFO_0000034" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", + "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000172", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000054", + "fillerId" : "http://purl.obolibrary.org/obo/OGMS_0000097" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/VO_0000001", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000047" ], @@ -52601,6 +52116,36 @@ "pred" : "http://purl.obolibrary.org/obo/OBI_0000312", "obj" : "http://purl.obolibrary.org/obo/IAO_0000444" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000052", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002072", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000057", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] @@ -52694,10 +52239,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000583", "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000582" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/IAO_0020013", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000293", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] @@ -52853,6 +52394,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000039", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OMRSE_00000070", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000057" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OMRSE_00000071", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000056" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/apollo_sv-full.obo b/apollo_sv-full.obo index 16439b1..abcf89b 100644 --- a/apollo_sv-full.obo +++ b/apollo_sv-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: apollo_sv/releases/2024-08-15/apollo_sv-full.owl +data-version: apollo_sv/releases/2024-12-24/apollo_sv-full.owl subsetdef: attribute_slim "" subsetdef: common_anatomy "" subsetdef: gocheck_do_not_annotate "" @@ -48,11 +48,11 @@ property_value: dc:contributor "Mike Wagner" xsd:string property_value: dc:contributor "Shawn T. Brown" xsd:string property_value: dc:contributor "William R. Hogan" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: dc:title "Apollo Structured Vocabulary (Apollo-SV)" xsd:string -property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2024-08-15" xsd:string +property_value: owl:versionInfo "2024-12-24" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string +property_value: terms:title "Apollo Structured Vocabulary (Apollo-SV)" xsd:string property_value: www:RTS_00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: www:RTS_00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -6876,36 +6876,6 @@ subset: camcur is_a: IAO:0000310 ! document property_value: IAO:0000412 "http://purl.org/obo/owl/flybase_vocab" xsd:string -[Term] -id: FMA:49443 -name: Anatomical cluster -is_a: FMA:67135 ! Anatomical structure - -[Term] -id: FMA:55457 -name: vocal fold -is_a: FMA:64854 ! Subdivision of larynx - -[Term] -id: FMA:64854 -name: Subdivision of larynx -is_a: FMA:64989 ! Heterogeneous cluster - -[Term] -id: FMA:64989 -name: Heterogeneous cluster -is_a: FMA:49443 ! Anatomical cluster - -[Term] -id: FMA:67135 -name: Anatomical structure -is_a: FMA:67165 ! Material anatomical entity - -[Term] -id: FMA:67165 -name: Material anatomical entity -is_a: BFO:0000040 ! material entity - [Term] id: GEO:000000001 name: geopolitical entity @@ -7321,7 +7291,6 @@ synonym: "virulence" RELATED [] synonym: "virus process" EXACT [GOC:bf, GOC:jl] xref: Wikipedia:Viral_life_cycle is_a: GO:0008150 ! biological process -property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0016301 @@ -7426,10 +7395,6 @@ synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -property_value: RO:0002161 NCBITaxon:2 -property_value: RO:0002161 NCBITaxon:2157 -property_value: RO:0002161 NCBITaxon:4896 -property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -7523,7 +7488,6 @@ synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI -property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0048609 @@ -7589,7 +7553,6 @@ name: measurement unit label def: "A data item label that denotes a unit of measure." [] def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] is_a: IAO:0000009 ! datum label -property_value: APOLLO_SV:0000040 "unitId" xsd:string property_value: IAO:0000111 "measurement unit label" xsd:string property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -7604,14 +7567,10 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: IAO:0000005 name: objective specification def: "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] -def: "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000111 "objective specification" xsd:string property_value: IAO:0000112 "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." xsd:string -property_value: IAO:0000112 "purpose of a study; support of hypothesis, discovery of new information" xsd:string property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an\nnon realizable information entity which can serve as that proper part\nof a plan towards which the realization of the plan is directed.\"" xsd:string property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\"" xsd:string property_value: IAO:0000116 "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that." xsd:string property_value: IAO:0000116 "Answers the question, why did you do this experiment?" xsd:string @@ -7640,12 +7599,10 @@ property_value: IAO:0000119 "OBI_0000013" xsd:string [Term] id: IAO:0000007 name: action specification -def: "a directive information entity that describes an action the bearer will take" [] def: "A directive information entity that describes an action the bearer will take." [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000112 "Pour the contents of flask 1 into flask 2" xsd:string property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string @@ -7663,10 +7620,8 @@ name: datum label def: "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" [] def: "An information content entity that is part of some data item and is used to partially define the denotation of that data item." [] is_a: IAO:0000030 ! information content entity -property_value: APOLLO_SV:0000040 "label" xsd:string property_value: IAO:0000111 "data item label" xsd:string property_value: IAO:0000111 "datum label" xsd:string -property_value: IAO:0000111 "label" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" xsd:string @@ -7793,32 +7748,24 @@ property_value: IAO:0000119 "OBI_0000058" xsd:string [Term] id: IAO:0000027 name: data item -def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "data item" xsd:string -property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string -property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string -property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000118 "data" xsd:string [Term] id: IAO:0000028 name: symbol -def: "a smallish, word-like datum..." [] def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "symbol" xsd:string @@ -7845,18 +7792,14 @@ property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string id: IAO:0000030 name: information content entity def: "A generically dependent continuant that is about some thing." [] -def: "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" [] is_a: BFO:0000031 ! generically dependent continuant relationship: IAO:0000136 BFO:0000001 ! is about entity property_value: IAO:0000111 "information content entity" xsd:string property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000119 "OBI_0000142" xsd:string property_value: IAO:0000119 "OBI_0000142" xsd:string [Term] @@ -7890,8 +7833,6 @@ def: "An information content entity whose concretizations indicate to their bear is_a: IAO:0000030 ! information content entity relationship: IAO:0000136 BFO:0000017 ! is about realizable entity property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be\nconcretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it." xsd:string property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string @@ -7975,7 +7916,6 @@ is_a: IAO:0000001 ! conditional specification property_value: IAO:0000111 "rule" xsd:string property_value: IAO:0000112 "example to be added" xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000114 IAO:0000124 property_value: IAO:0000116 "MSI" xsd:string property_value: IAO:0000117 "PRS" xsd:string property_value: IAO:0000119 "OBI_0500021" xsd:string @@ -8013,7 +7953,6 @@ is_obsolete: true [Term] id: IAO:0000064 name: algorithm -def: "A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "algorithm" xsd:string @@ -8162,10 +8101,8 @@ id: IAO:0000100 name: data set def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] is_a: IAO:0000027 ! data item -property_value: APOLLO_SV:0000040 "dataSets" xsd:string property_value: IAO:0000111 "data set" xsd:string property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string @@ -8173,7 +8110,6 @@ property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 "group:OBI" xsd:string property_value: IAO:0000119 "OBI_0000042" xsd:string -property_value: IAO:0000119 "OBI_0000042" xsd:string [Term] id: IAO:0000101 @@ -8201,16 +8137,13 @@ property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000104 name: plan specification -def: "a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications." [] def: "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them -comment: 2/3/2009 Comment from OBI review.\n \n Action specification not well enough specified.\n Conditional specification not well enough specified.\n Question whether all plan specifications have objective specifications.\n \n Request that IAO either clarify these or change definitions not to use them is_a: IAO:0000033 ! directive information entity relationship: has_part IAO:0000005 ! objective specification relationship: has_part IAO:0000007 ! action specification property_value: IAO:0000111 "plan specification" xsd:string property_value: IAO:0000112 "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2014-03-31: A plan specification can have other parts, such as conditional specifications." xsd:string @@ -8242,7 +8175,6 @@ def: "A measurement datum is an information content entity that is a recording o is_a: IAO:0000027 ! data item property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string @@ -8266,7 +8198,6 @@ def: "A version number is an information content entity which is a sequence of c is_a: IAO:0000028 ! symbol property_value: IAO:0000111 "version number" xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000114 IAO:0000124 property_value: IAO:0000116 "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string @@ -8329,7 +8260,6 @@ property_value: IAO:0000111 "material information bearer" xsd:string property_value: IAO:0000112 "a brain" xsd:string property_value: IAO:0000112 "a hard drive" xsd:string property_value: IAO:0000112 "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: IAO" xsd:string @@ -9886,7 +9816,6 @@ intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output intersection_of: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process relationship: IAO:0000219 BFO:0000001 ! denotes entity relationship: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process -property_value: APOLLO_SV:0000040 "name" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string property_value: IAO:0000111 "identifier" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string @@ -9898,7 +9827,6 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020001 name: grapheme -def: "A grapheme is an information content entity that is a fundamental unit in a written language. " [] def: "An information content entity that is a fundamental unit in a written language." [] comment: Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there. is_a: IAO:0000030 ! information content entity @@ -9908,71 +9836,11 @@ property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Grapheme" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string -[Term] -id: IAO:0020002 -name: utterance -def: "An utterance is an information content entity that is a complete unit of speech in spoken language. " [] -is_a: IAO:0000030 ! information content entity -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Wikipedia: http://en.wikipedia.org/wiki/Utterance" xsd:string - -[Term] -id: IAO:0020003 -name: mechanical wave quality -def: "An attributive collection of qualities inhering in energy when transported through a medium in a wave." [] -is_a: BFO:0000019 ! quality -property_value: dc:creator "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020004 -name: writing quality -def: "is a quality that is the concretization of graphemes and inheres in a material object." [] -is_a: BFO:0000019 ! quality -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020005 -name: writing bearer -def: "is a material information bearer that bears the concretization of graphemes." [] -is_a: IAO:0000178 ! material information bearer -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000112 "pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting," xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020006 -name: portion of energy -is_a: BFO:0000004 ! independent continuant - -[Term] -id: IAO:0020007 -name: sound energy -def: "Energy that is transported in a sound wave." [] -is_a: IAO:0020006 ! portion of energy -relationship: RO:0000053 IAO:0020003 ! is bearer of mechanical wave quality -property_value: dc:creator "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020008 -name: utterance energy -def: "Sound energy bearing the concretization of an utterance and being the output of an uttering process. " [] -is_a: IAO:0020007 ! sound energy - -[Term] -id: IAO:0020009 -name: oscillating -def: "Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states." [] -is_a: BFO:0000015 ! process -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Oscillation" xsd:string - [Term] id: IAO:0020010 name: identifier creating process -def: "A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] def: "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] +def: "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000299 IAO:0020000 ! has_specified_output identifier @@ -9985,16 +9853,6 @@ property_value: IAO:0000118 "dubbing process" xsd:string property_value: IAO:0000118 "naming" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string -[Term] -id: IAO:0020011 -name: utterance process -def: "is a planned process of making speech sounds which may or may not have an actual language involved. " [] -is_a: OBI:0000011 ! planned process -relationship: OBI:0000299 IAO:0020008 ! has_specified_output utterance energy -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://en.wiktionary.org/wiki/utter" xsd:string - [Term] id: IAO:0020015 name: personal name @@ -10015,12 +9873,10 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020016 name: given name -def: "A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name" [] def: "A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name" [] is_a: IAO:0020015 ! personal name property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "first name" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Given_name" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string @@ -10028,12 +9884,10 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020017 name: family name -def: "A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children." [] def: "An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children." [] -is_a: IAO:0020015 ! personal name +is_a: IAO:0020000 ! identifier property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "last name" xsd:string property_value: IAO:0000118 "surname" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Family_name" xsd:string @@ -10042,19 +9896,15 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020020 name: code set -def: "An information content entity that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate." [] +def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate." [] def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." [] comment: Code sets might include non-entities/things (e.g. missing thumbs). comment: Does not imply absence vs. presence of any taxonomy. comment: Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. -comment: Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories). comment: Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). -comment: Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). -comment: Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain. comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. -comment: The identifiers do not denote each other. comment: The information content entities do not denote each other. is_a: IAO:0000030 ! information content entity relationship: has_part IAO:0020000 ! identifier @@ -10074,6 +9924,22 @@ property_value: IAO:0000118 "coding system" xsd:string property_value: IAO:0000118 "controlled vocabulary" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +[Term] +id: IAO:0021003 +name: social act +def: "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." [] +comment: The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote. +is_a: OBI:0000011 ! planned process +property_value: IAO:0000112 "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" xsd:string +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string + +[Term] +id: IAO:0021009 +name: deontic declaration +def: "A social act that creates or revokes a deontic role." [] +is_a: IAO:0021003 ! social act +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string + [Term] id: IAO:8000000 name: ontology module @@ -10632,7 +10498,7 @@ property_value: IAO:0000117 "Lindsay Cowell" xsd:string id: IDO:0000629 name: host role def: "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." [] -is_a: BFO:0000023 ! role +is_a: OMRSE:00000049 ! organism role property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000117 "Alexander Diehl" xsd:string property_value: IAO:0000117 "Lindsay Cowell" xsd:string @@ -15421,6 +15287,8 @@ property_value: IAO:0000116 "We are only considering successfully completed plan property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "branch derived" xsd:string +property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string +property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] @@ -15469,8 +15337,9 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: OBI:0000245 name: organization +def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] def: "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] -is_a: BFO:0000004 ! independent continuant +is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "organization" xsd:string property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -15829,6 +15698,7 @@ is_a: OBI:0000011 ! planned process relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective property_value: IAO:0000111 "data transformation" xsd:string property_value: IAO:0000112 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string +property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "Helen Parkinson" xsd:string @@ -16111,6 +15981,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string id: OGMS:0000097 name: health care encounter def: "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter" [] +is_a: OBI:0000011 ! planned process is_a: OGMS:0000096 ! health care process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string @@ -16139,6 +16010,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string [Term] id: OGMS:0000100 name: inpatient encounter +def: "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night." [] is_a: OGMS:0000097 ! health care encounter property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string @@ -16179,100 +16051,63 @@ id: OMRSE:00000001 name: human social role def: "A social role inhering in a human being." [] is_a: OMRSE:00000026 ! organism social role -relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens -property_value: IAO:0000117 "Mathias Brochhausen\n" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000007 -name: gender role -def: "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." [] -is_a: BFO:0000023 ! role -property_value: APOLLO_SV:0000040 "sex" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Gender_role" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000008 -name: male gender role -def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question." [] -is_a: OMRSE:00000007 ! gender role +is_a: OMRSE:00000050 ! Homo sapiens role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "male gender" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000009 -name: female gender role -def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question." [] -is_a: OMRSE:00000007 ! gender role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "female gender" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] id: OMRSE:00000010 name: human health care role -def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. " [] -comment: Mathias Brochhausen +def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis." [] is_a: OMRSE:00002072 ! role in human social processes +relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "health care role" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000011 name: patient role -def: "A human health care role that inheres in an organism [human?] as the recipient of a health care service." [] -def: "A role borne by an organism being as the recipient of a health care service." [] +def: "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." [] +comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. is_a: OMRSE:00000010 ! human health care role +is_a: OMRSE:00000049 ! organism role property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "patient" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Patient" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +property_value: IAO:0000119 "CAFE domain expert working group." xsd:string [Term] id: OMRSE:00000015 name: health care provider organization role -comment: Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). +def: "A role that inheres in an organization and that is realized by the providing of services in a health care encounter." [] is_a: OMRSE:00000027 ! organization health care role -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter +property_value: dc:contributor "Mathias Brochhausen" xsd:string +property_value: dc:creator "Amanda Hicks" xsd:string [Term] id: OMRSE:00000022 -name: collection of organisms -def: "An object aggregate of organisms." [] +name: aggregate of objectual organisms +def: "An object aggregate of objectual organisms." [] comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class. is_a: BFO:0000027 ! object aggregate -intersection_of: BFO:0000027 ! object aggregate -intersection_of: RO:0002351 OBI:0100026 ! has member organism -intersection_of: RO:0002351 OBI:0100026 {all_only="true"} ! has member organism -equivalent_to: PCO:0000000 ! PCO:collection of organisms -relationship: RO:0002351 OBI:0100026 ! has member organism -property_value: IAO:0000600 "This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species." xsd:string [Term] id: OMRSE:00000023 name: collection of humans -comment: An object aggregate all of whose components are human beings. -is_a: PCO:0000018 ! collection of organisms of the same species -intersection_of: OMRSE:00000022 ! collection of organisms -intersection_of: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens -intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens -relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +def: "An object aggregate all of whose components are human beings." [] +is_a: OMRSE:00000022 ! aggregate of objectual organisms +relationship: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens [Term] id: OMRSE:00000025 name: organization social role def: "A role in human social processes that inheres in an organization." [] comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. +is_a: OMRSE:00000051 ! organization role is_a: OMRSE:00002072 ! role in human social processes property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000026 @@ -16281,62 +16116,91 @@ def: "A role in human social processes that inheres in an organism." [] comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. comment: Previous definition: A role in human social processes played by an organism. -is_a: BFO:0000023 ! role -relationship: RO:0000052 OBI:0100026 ! inheres in organism +is_a: OMRSE:00000049 ! organism role +is_a: OMRSE:00002072 ! role in human social processes property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000027 name: organization health care role -def: "An organization social role that is realized by a health care process." [] +def: "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process" [] comment: Previous definition: An organization social role played by an organization in health care processes. is_a: OMRSE:00000025 ! organization social role -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string + +[Term] +id: OMRSE:00000030 +name: human patient role +def: "A patient role that inheres in a human being." [] +is_a: OMRSE:00000011 ! patient role +is_a: OMRSE:00000050 ! Homo sapiens role +intersection_of: OMRSE:00000011 ! patient role +intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens [Term] id: OMRSE:00000033 name: aggregate of organizations -def: "An aggregate of organizations that have some feature in common, but is not itself an organization." [] +def: "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" [] comment: It is often convenient to group organizations together that otherwise might not even interact with one another. -is_a: BFO:0000027 ! object aggregate -intersection_of: BFO:0000027 ! object aggregate -intersection_of: RO:0002351 OBI:0000245 ! has member organization -intersection_of: RO:0002351 OBI:0000245 {all_only="true"} ! has member organization +is_a: BFO:0000040 ! material entity relationship: RO:0002351 OBI:0000245 ! has member organization -property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string [Term] -id: OMRSE:00000052 -name: hospital function -def: "A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population." [] -is_a: BFO:0000034 ! function -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +id: OMRSE:00000048 +name: material entity role +is_a: BFO:0000023 ! role +intersection_of: BFO:0000023 ! role +intersection_of: RO:0000052 BFO:0000040 ! inheres in material entity +relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity +relationship: RO:0000052 BFO:0000040 ! inheres in material entity + +[Term] +id: OMRSE:00000049 +name: organism role +is_a: OMRSE:00000048 ! material entity role +intersection_of: OMRSE:00000048 ! material entity role +intersection_of: RO:0000052 OBI:0100026 ! inheres in organism +relationship: RO:0000052 OBI:0100026 {all_only="true"} ! inheres in organism +relationship: RO:0000052 OBI:0100026 ! inheres in organism + +[Term] +id: OMRSE:00000050 +name: Homo sapiens role +is_a: OMRSE:00000049 ! organism role +intersection_of: OMRSE:00000049 ! organism role +intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 {all_only="true"} ! inheres in Homo sapiens + +[Term] +id: OMRSE:00000051 +name: organization role +is_a: OMRSE:00000048 ! material entity role +intersection_of: BFO:0000023 ! role +intersection_of: RO:0000052 OBI:0000245 ! inheres in organization +relationship: RO:0000052 OBI:0000245 ! inheres in organization +relationship: RO:0000052 OBI:0000245 {all_only="true"} ! inheres in organization [Term] id: OMRSE:00000053 name: school function -def: "A function inhering in a facility that manifests by the facility participating in providing formal education to a student population." [] +def: "A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population." [] is_a: BFO:0000034 ! function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000054 name: hospital role -def: "A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care." [] +def: "A healthcare provider role that inheres in an organization and is realized by providing inpatient care." [] is_a: OMRSE:00000015 ! health care provider organization role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000055 name: school role -is_a: BFO:0000023 ! role +is_a: OMRSE:00000025 ! organization social role property_value: IAO:0000117 "An organization social role that inheres in an organization and is realized by providing formal education to students." xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000056 @@ -16347,7 +16211,6 @@ intersection_of: OBI:0000245 ! organization intersection_of: RO:0000053 OMRSE:00000054 ! is bearer of hospital role relationship: RO:0000053 OMRSE:00000054 ! is bearer of hospital role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000057 @@ -16358,33 +16221,24 @@ intersection_of: OBI:0000245 ! organization intersection_of: RO:0000053 OMRSE:00000055 ! is bearer of school role relationship: RO:0000053 OMRSE:00000055 ! is bearer of school role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000058 name: student role -def: "A human social role that is realized by the process of formal education that the bearer undergoes." [] -is_a: OMRSE:00000001 ! human social role +def: "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes." [] property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000059 name: nursery school role -comment: Key motivating use case was Synthia synthetic population data.\n is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "preschool" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000060 name: primary school role -comment: Key motivating use case was Synthia synthetic population data. is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "primarySchool" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000061 @@ -16395,111 +16249,68 @@ comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "http://de.wikipedia.org/wiki/Bauwerk" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000062 name: facility def: "An architectural structure that bears some function." [] is_a: OMRSE:00000061 ! architectural structure +intersection_of: OMRSE:00000061 ! architectural structure +intersection_of: RO:0000053 BFO:0000034 ! is bearer of function +relationship: OMRSE:00000068 OBI:0000245 {owl:versionInfo="09/09/2017"} ! is administered by organization +relationship: RO:0000053 BFO:0000034 ! is bearer of function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000063 -name: hospital facility -def: "A facility that is run by a hospital organization and is the bearer of a hospital function." [] -is_a: OMRSE:00000102 ! health care facility -property_value: APOLLO_SV:0000040 "HealthcareFacility" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000064 name: school facility def: "A facility that is run by a school organization and is the bearer of a school function." [] is_a: OMRSE:00000062 ! facility -property_value: APOLLO_SV:0000040 "SchoolFacility" xsd:string +relationship: RO:0000053 OMRSE:00000053 ! is bearer of school function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000065 name: secondary school role -comment: Key motivating use case was Synthia synthetic population data. is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "secondarySchool" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] -id: OMRSE:00000074 -name: housing unit -def: "A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function." [] -comment: Housing units are individuated by their residence functions. -is_a: BFO:0000040 ! material entity -property_value: APOLLO_SV:0000040 "houses" xsd:string +id: OMRSE:00000086 +name: human role within an organization +def: "A human social role that is created by a deontic declaration performed by an organization." [] property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +property_value: IAO:0000118 "human organizational role" xsd:string [Term] -id: OMRSE:00000076 -name: household -def: "A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function." [] -is_a: BFO:0000040 ! material entity -property_value: APOLLO_SV:0000040 "Household" xsd:string -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000078 -name: workplace facility -is_a: OMRSE:00000062 ! facility -property_value: APOLLO_SV:0000040 "workplace" xsd:string -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +id: OMRSE:00000142 +name: human traveling information +def: "An information content entity that is about human travel." [] +is_a: IAO:0000030 ! information content entity +intersection_of: IAO:0000030 ! information content entity +intersection_of: IAO:0000136 APOLLO_SV:00000532 ! is about human travel +relationship: IAO:0000136 APOLLO_SV:00000532 ! is about human travel +property_value: dc:contributor "Jie Zheng" xsd:string +property_value: dc:creator "Amanda Hicks" xsd:string +property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/issues/79" xsd:anyURI [Term] -id: OMRSE:00000079 -name: workplace function -def: "a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out" [] +id: OMRSE:00000172 +name: health care function is_a: BFO:0000034 ! function -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000098 -name: racial identity datum -def: "A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method." [] -is_a: OMRSE:00000132 ! identity datum -property_value: APOLLO_SV:0000040 "race" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000102 -name: health care facility -is_a: OMRSE:00000062 ! facility -property_value: IAO:0000117 "A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000132 -name: identity datum -is_a: IAO:0000030 ! information content entity -property_value: dc:creator "Amanda Hicks" xsd:string -property_value: dc:creator "An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +intersection_of: BFO:0000034 ! function +intersection_of: BFO:0000054 OGMS:0000097 ! is realized by health care encounter +relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter [Term] id: OMRSE:00002072 name: role in human social processes -def: "A role inhering in an entity realized by social interactions in human society." [] +def: "A role that inheres in some entity that is realized in a social act." [] comment: Previous definition: A role played by an entity in human social processes. -is_a: BFO:0000023 ! role +is_a: OMRSE:00000048 ! material entity role +relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity property_value: dc:contributor "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl" xsd:string [Term] id: PATO:0000001 @@ -16619,13 +16430,6 @@ property_value: IAO:0000111 "physical quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string -[Term] -id: PATO:0001025 -name: pressure -namespace: quality -subset: attribute_slim -is_a: BFO:0000019 ! quality - [Term] id: PATO:0001241 name: physical object quality @@ -16729,7 +16533,6 @@ property_value: IAO:0000119 "ISBN:0878932739" xsd:string id: PCO:0000018 name: collection of organisms of the same species def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] -is_a: OMRSE:00000022 ! collection of organisms is_a: PCO:0000000 ! PCO:collection of organisms [Term] @@ -17993,41 +17796,6 @@ property_value: IAO:0000117 "Alan Ruttenberg" xsd:string domain: IAO:0000582 ! time stamped measurement datum is_a: has_part ! has part -[Typedef] -id: IAO:0020012 -name: obsolete_designates -def: "x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.." [] -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000228 -is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty -is_obsolete: true -replaced_by: IAO:0000219 - -[Typedef] -id: IAO:0020013 -name: is_borrowed_reference_to -def: "x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place." [] -property_value: dc:creator "Mathias Brochhausen" xsd:string -domain: IAO:0020000 ! identifier -range: BFO:0000001 ! entity -is_asymmetric: true - -[Typedef] -id: IAO:0020014 -name: is_fixing_reference_to -def: "x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the." [] -property_value: dc:creator "Mathias Brochhausen" xsd:string -is_asymmetric: true - -[Typedef] -id: IAO:0020018 -name: is designated by -def: "p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context." [] -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty -is_obsolete: true -is_asymmetric: true - [Typedef] id: IDO:0000660 name: results_in @@ -18076,6 +17844,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has_participant +inverse_of: OBI:0000312 ! is_specified_output_of [Typedef] id: OBI:0000308 @@ -18117,29 +17886,58 @@ property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string +[Typedef] +id: OBIB:0000732 +name: owns +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal." xsd:string +inverse_of: OBIB:0000735 ! is owned by +is_asymmetric: true + +[Typedef] +id: OBIB:0000735 +name: is owned by +def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." [] +property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string +is_asymmetric: true + [Typedef] id: OMIABIS:0000008 +name: obsolete owns name: owns +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. " xsd:string +is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty +is_obsolete: true +replaced_by: OBIB:0000732 [Typedef] id: OMIABIS:0000048 name: is owned by +name: obsolete is owned by def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." [] property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string +property_value: IAO:0000119 "Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +replaced_by: OBIB:0000735 + +[Typedef] +id: OMRSE:00000068 +name: is administered by +is_asymmetric: true [Typedef] id: OMRSE:00000070 name: is enrolled in school -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +range: OMRSE:00000057 ! school organization +is_asymmetric: true [Typedef] id: OMRSE:00000071 name: is admitted to hospital -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +range: OMRSE:00000056 ! hospital organization [Typedef] id: RO:0000052 diff --git a/apollo_sv-full.owl b/apollo_sv-full.owl index dfa44c4..68ce4e4 100644 --- a/apollo_sv-full.owl +++ b/apollo_sv-full.owl @@ -27,7 +27,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -36,14 +36,14 @@ Shawn T. Brown William R. Hogan Mathias Brochhausen - Apollo Structured Vocabulary (Apollo-SV) + https://orcid.org/0000-0002-9881-1017 An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. https://creativecommons.org/licenses/by/4.0/ + Apollo Structured Vocabulary (Apollo-SV) C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). - 2023-01-10 - 2024-08-15 + 2024-12-24 @@ -331,7 +331,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred label editor preferred label editor preferred term editor preferred term @@ -376,7 +375,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 - has curation status has curation status @@ -408,6 +406,26 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -429,7 +447,6 @@ We also have the outstanding issue of how to aim different definitions to differ GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note editor note @@ -447,7 +464,6 @@ We also have the outstanding issue of how to aim different definitions to differ definition editor definition editor - term editor term editor @@ -467,7 +483,6 @@ We also have the outstanding issue of how to aim different definitions to differ Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label - alternative term alternative term @@ -485,7 +500,6 @@ We also have the outstanding issue of how to aim different definitions to differ Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source definition source @@ -511,7 +525,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note curator note @@ -827,16 +840,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - instance unique identifier - An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system. - IUI - - - - @@ -922,12 +925,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - @@ -2665,7 +2662,6 @@ Some currently missing phenomena that should be considered "about" are person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy http://purl.obolibrary.org/obo/iao.owl - is about is about @@ -2922,65 +2918,34 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + - - - x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.. - - - Mathias Brochhausen - obsolete_designates - true + + results_in - + - + + - - - - x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place. - Mathias Brochhausen - is_borrowed_reference_to - - - - - - - - - - x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the. - Mathias Brochhausen - is_fixing_reference_to - - - - - - - - - - - p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context. Mathias Brochhausen - is designated by - true + This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. + owns - + - - results_in + + + a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. + Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. + is owned by @@ -3037,6 +3002,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has_specified_output has_specified_output @@ -3115,11 +3081,16 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + + Mathias Brochhausen Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. http://purl.obolibrary.org/obo/omrse.owl This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. + + obsolete owns owns + true @@ -3130,8 +3101,20 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. + Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204. http://purl.obolibrary.org/obo/omrse.owl + is owned by + obsolete is owned by + + + + + + + + + is administered by @@ -3139,8 +3122,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - http://purl.obolibrary.org/obo/omrse.owl + + + + + + + + is enrolled in school @@ -3150,7 +3139,13 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - http://purl.obolibrary.org/obo/omrse.owl + + + + + + + is admitted to hospital @@ -21307,60 +21302,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - - - - Anatomical cluster - - - - - - - - - vocal fold - - - - - - - - - Subdivision of larynx - - - - - - - - - Heterogeneous cluster - - - - - - - - - Anatomical structure - - - - - - - - - Material anatomical entity - - - - @@ -22239,7 +22180,6 @@ Date accessed: 2015-04-13 A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle. - GO:0022415 Wikipedia:Viral_life_cycle virus process @@ -22488,10 +22428,6 @@ Date accessed: 2015-04-13 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. https://github.com/geneontology/go-ontology/issues/27189 - - - - jl 2012-09-19T16:07:47Z GO:0044707 @@ -22670,7 +22606,6 @@ Date accessed: 2015-04-13 Any process evolved to enable an interaction with an organism of a different species. https://github.com/geneontology/go-ontology/issues/20191 - interaction with another species interspecies interaction interspecies interaction between organisms @@ -22804,7 +22739,6 @@ of this, different, term. PERSON: Alan Ruttenberg PERSON: Melanie Courtot http://purl.obolibrary.org/obo/obi.owl - unitId measurement unit label @@ -22816,14 +22750,8 @@ of this, different, term. objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - purpose of a study; support of hypothesis, discovery of new information - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an -non realizable information entity which can serve as that proper part -of a plan towards which the realization of the plan is directed." 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? @@ -22863,9 +22791,7 @@ of a plan towards which the realization of the plan is directed." Pour the contents of flask 1 into flask 2 - A directive information entity that describes an action the bearer will take. - a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification @@ -22890,7 +22816,6 @@ of a plan towards which the realization of the plan is directed." data item label datum label - label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label @@ -22901,7 +22826,6 @@ of a plan towards which the realization of the plan is directed."9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. http://purl.obolibrary.org/obo/obi.owl - label data item label datum label @@ -23091,16 +23015,12 @@ Superclass was 'digital entity' - data item data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some @@ -23110,11 +23030,8 @@ process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert PERSON: Chris Stoeckert - PERSON: Jonathan Rees PERSON: Jonathan Rees data data item @@ -23132,7 +23049,6 @@ JAR: A data item is an approximately justified approximately true approximate be a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - a smallish, word-like datum... 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton @@ -23169,16 +23085,12 @@ JAR: A data item is an approximately justified approximately true approximate be information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. - A generically dependent continuant that is about some thing. - an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert PERSON: Chris Stoeckert - OBI_0000142 OBI_0000142 information content entity @@ -23241,10 +23153,7 @@ this case we explicitly refer to the singular form - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be -concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO @@ -23352,7 +23261,6 @@ superclass was 'digital document' rule example to be added - A rule is an executable which guides, defines, restricts actions. MSI PRS @@ -23407,7 +23315,6 @@ superclass was 'digital document' algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch @@ -23617,17 +23524,14 @@ XML document; The instructions in a XSD file" data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert - OBI_0000042 OBI_0000042 group:OBI - dataSets data set @@ -23682,10 +23586,8 @@ XML document; The instructions in a XSD file" plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. @@ -23701,13 +23603,6 @@ Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them - 2/3/2009 Comment from OBI review. - - Action specification not well enough specified. - Conditional specification not well enough specified. - Question whether all plan specifications have objective specifications. - - Request that IAO either clarify these or change definitions not to use them plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 @@ -23738,7 +23633,6 @@ superclass was 'digial entity' measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? @@ -23772,7 +23666,6 @@ Note: everybody agreed that identifier is probably a too general term. We howeve version number - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO @@ -23891,7 +23784,6 @@ Cons sometimes specifies a quality which is not a realizable. A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive - A material entity in which a concretization of an information content entity inheres. GROUP: IAO @@ -26528,7 +26420,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 - name Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier @@ -26541,7 +26432,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems - A grapheme is an information content entity that is a fundamental unit in a written language. An information content entity that is a fundamental unit in a written language. Justin Whorton http://en.wikipedia.org/wiki/Grapheme @@ -26553,222 +26443,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - - - - - An utterance is an information content entity that is a complete unit of speech in spoken language. - Mathias Brochhausen - Wikipedia: http://en.wikipedia.org/wiki/Utterance - Mathias Brochhausen - utterance - - - - - - - - - An attributive collection of qualities inhering in energy when transported through a medium in a wave. - Mathias Brochhausen - mechanical wave quality - - - - - - - - - is a quality that is the concretization of graphemes and inheres in a material object. - Mathias Brochhausen - Mathias Brochhausen - writing quality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting, - is a material information bearer that bears the concretization of graphemes. - Mathias Brochhausen - Mathias Brochhausen - writing bearer - - - - - - - - - portion of energy - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Energy that is transported in a sound wave. - Mathias Brochhausen - sound energy - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Sound energy bearing the concretization of an utterance and being the output of an uttering process. - utterance energy - - - - - - - - - Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states. - http://en.wikipedia.org/wiki/Oscillation - Mathias Brochhausen - oscillating - - - - @@ -26796,8 +26470,8 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. + An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen Mathias Brochhausen @@ -26810,31 +26484,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - - - - - - - - - - - - - - - - - is a planned process of making speech sounds which may or may not have an actual language involved. - Mathias Brochhausen - http://en.wiktionary.org/wiki/utter - Mathias Brochhausen - utterance process - - - - @@ -26869,10 +26518,8 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name Justin Whorton - Mathias Brochhausen Mathias Brochhausen first name http://en.wikipedia.org/wiki/Given_name @@ -26885,11 +26532,9 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - - A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. + An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. Justin Whorton - Mathias Brochhausen Mathias Brochhausen last name surname @@ -26910,7 +26555,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - An information content entity that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate. + An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate. An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. Alan Ruttenberg Justin Whorton @@ -26930,24 +26575,44 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta Code sets might include non-entities/things (e.g. missing thumbs). Does not imply absence vs. presence of any taxonomy. Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. - Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories). Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). - Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. - -When there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. - Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain. Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. - The identifiers do not denote each other. The information content entities do not denote each other. code set + + + + + Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom + A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. + Mathias Brochhausen + The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). +Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. +Thanks to W.R. Hogan for finding the Reinach quote. + social act + + + + + + + + + A social act that creates or revokes a deontic role. + Mathias Brochhausen + deontic declaration + + + + @@ -28111,7 +27776,7 @@ No imports - + @@ -38139,6 +37804,8 @@ No imports objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process @@ -38207,10 +37874,11 @@ objectives is a planned process. - + organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: @@ -38795,6 +38463,7 @@ This issue is outside the scope of OBI. data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + A data transformation is a process which produces output data from input data A planned process that produces output data from input data. @@ -39197,6 +38866,7 @@ See vaccination and antiviral treatment. + A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain @@ -39239,6 +38909,7 @@ See vaccination and antiviral treatment. + A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z @@ -39293,71 +38964,29 @@ See vaccination and antiviral treatment. - - - - - - + A social role inhering in a human being. - Mathias Brochhausen - + Mathias Brochhausen William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl human social role - - - - - A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Gender_role - http://purl.obolibrary.org/obo/omrse.owl - sex - gender role - - - - - - - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question. - Mathias Brochhausen - male gender - http://purl.obolibrary.org/obo/omrse.owl - male gender role - - - - - - - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question. - Mathias Brochhausen - female gender - http://purl.obolibrary.org/obo/omrse.owl - female gender role - - - - - A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. + + + + + + + A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. + Mathias Brochhausen William R. Hogan health care role - http://purl.obolibrary.org/obo/omrse.owl - Mathias Brochhausen human health care role @@ -39367,13 +38996,13 @@ See vaccination and antiviral treatment. - A human health care role that inheres in an organism [human?] as the recipient of a health care service. - A role borne by an organism being as the recipient of a health care service. + + A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter. Amanda Hicks Mathias Brochhausen patient - http://en.wikipedia.org/wiki/Patient - http://purl.obolibrary.org/obo/omrse.owl + CAFE domain expert working group. + In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. patient role @@ -39383,8 +39012,15 @@ See vaccination and antiviral treatment. - http://purl.obolibrary.org/obo/omrse.owl - Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). + + + + + + + A role that inheres in an organization and that is realized by the providing of services in a health care encounter. + Mathias Brochhausen + Amanda Hicks health care provider organization role @@ -39393,33 +39029,23 @@ See vaccination and antiviral treatment. - - - - - - - - - - - - - - - - - + + + + + + + + - An object aggregate of organisms. - This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species. + An object aggregate of objectual organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. - collection of organisms + aggregate of objectual organisms @@ -39427,30 +39053,14 @@ See vaccination and antiviral treatment. - - - - - - - - - - - - - - - - + - + - http://purl.obolibrary.org/obo/omrse.owl - An object aggregate all of whose components are human beings. + An object aggregate all of whose components are human beings. collection of humans @@ -39459,10 +39069,10 @@ See vaccination and antiviral treatment. + A role in human social processes that inheres in an organization. William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. @@ -39474,17 +39084,11 @@ Ditto for its current descendants. - - - - - - - + + A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. @@ -39499,55 +39103,196 @@ Ditto for its current descendants. - An organization social role that is realized by a health care process. - http://purl.obolibrary.org/obo/omrse.owl + An organization social role that, if realized, is realized by either a health care process or an ancillary health care process Previous definition: An organization social role played by an organization in health care processes. organization health care role + + + + + + + + + + + + + + + + + A patient role that inheres in a human being. + human patient role + + + + - + + + - + - + 2 + - + - An aggregate of organizations that have some feature in common, but is not itself an organization. - William R. Hogan + An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common + William R. Hogan +Amanda Hicks It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations - + - - - A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital function + + + + + + + + + + + + + + + + + + + + + + + + + + material entity role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Homo sapiens role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organization role @@ -39556,9 +39301,8 @@ Ditto for its current descendants. - A function inhering in a facility that manifests by the facility participating in providing formal education to a student population. + A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl school function @@ -39568,9 +39312,8 @@ Ditto for its current descendants. - A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care. + A healthcare provider role that inheres in an organization and is realized by providing inpatient care. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl hospital role @@ -39579,10 +39322,9 @@ Ditto for its current descendants. - + An organization social role that inheres in an organization and is realized by providing formal education to students. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl school role @@ -39611,7 +39353,6 @@ Ditto for its current descendants. An organization that is the bearer of a hospital role. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl hospital organization @@ -39640,7 +39381,6 @@ Ditto for its current descendants. An organization that is the bearer of a school role. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl school organization @@ -39649,10 +39389,29 @@ Ditto for its current descendants. - - A human social role that is realized by the process of formal education that the bearer undergoes. + + + + + + + + + + + + + + + + + + + + + + A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl student role @@ -39663,10 +39422,6 @@ Ditto for its current descendants. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - preschool - Key motivating use case was Synthia synthetic population data. - nursery school role @@ -39677,9 +39432,6 @@ Ditto for its current descendants. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - primarySchool - Key motivating use case was Synthia synthetic population data. primary school role @@ -39692,7 +39444,6 @@ Ditto for its current descendants. A material entity that is a human made strcuture with firm connection between its foundation and the ground. Mathias Brochhausen http://de.wikipedia.org/wiki/Bauwerk - http://purl.obolibrary.org/obo/omrse.owl "Building" is a subclass of this. This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". architectural structure @@ -39703,36 +39454,77 @@ Ditto for its current descendants. + + + + + + + + + + + + + + + + + + An architectural structure that bears some function. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl facility - - - - - - - - A facility that is run by a hospital organization and is the bearer of a hospital function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - HealthcareFacility - hospital facility - + + + + + + + + + 09/09/2017 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - SchoolFacility school facility @@ -39743,97 +39535,102 @@ Ditto for its current descendants. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - secondarySchool - Key motivating use case was Synthia synthetic population data. secondary school role - + - - - A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A human social role that is created by a deontic declaration performed by an organization. Amanda Hicks - https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household - http://purl.obolibrary.org/obo/omrse.owl - houses - Housing units are individuated by their residence functions. - housing unit + human organizational role + human role within an organization - - - - - A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function. - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Household - household - - - + - - - - - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace - workplace facility + + + + + + + + + + + + + + + + + + + + An information content entity that is about human travel. + https://github.com/ufbmi/OMRSE/issues/79 + Jie Zheng + Amanda Hicks + human traveling information - + - + + + + + + + + + + + + - a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace function - - - - - - - - - A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. - http://purl.obolibrary.org/obo/omrse.owl - race - racial identity datum - - - - - - - - - A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population. - http://purl.obolibrary.org/obo/omrse.owl - health care facility - - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - Amanda Hicks - An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method. - identity datum + + + + + + + health care function @@ -39841,10 +39638,15 @@ Ditto for its current descendants. - - A role inhering in an entity realized by social interactions in human society. + + + + + + + + A role that inheres in some entity that is realized in a social act. Matthew Diller - http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes @@ -40031,20 +39833,6 @@ Ditto for its current descendants. - - - - - - - - quality - - pressure - - - - @@ -40190,7 +39978,6 @@ Ditto for its current descendants. - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -41678,15 +41465,15 @@ This interpretation is *not* the same as an at-all-times relation - - - + + + @@ -42365,9 +42152,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42376,9 +42163,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42410,9 +42197,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42421,9 +42208,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42455,9 +42242,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42466,9 +42253,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42500,9 +42287,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42511,9 +42298,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42545,9 +42332,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42556,9 +42343,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42590,7 +42377,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42601,7 +42388,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42618,7 +42405,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42628,7 +42415,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42646,7 +42433,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42657,7 +42444,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42674,7 +42461,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42684,7 +42471,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42701,7 +42488,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42712,7 +42499,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42745,9 +42532,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42756,9 +42543,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42789,9 +42576,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42800,9 +42587,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42833,9 +42620,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42844,9 +42631,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42877,9 +42664,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42888,9 +42675,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42922,8 +42709,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -42933,8 +42720,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/apollo_sv.json b/apollo_sv.json index 5613ecb..97c710d 100644 --- a/apollo_sv.json +++ b/apollo_sv.json @@ -27,14 +27,17 @@ "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" }, { - "pred" : "http://purl.org/dc/elements/1.1/title", - "val" : "Apollo Structured Vocabulary (Apollo-SV)" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/terms/description", "val" : "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/licenses/by/4.0/" + }, { + "pred" : "http://purl.org/dc/terms/title", + "val" : "Apollo Structured Vocabulary (Apollo-SV)" }, { "pred" : "http://www.referent-tracking.com/RTS_00000001", "val" : "C87985BA-6A8A-483A-A6B6-63975101F672" @@ -46,12 +49,9 @@ "val" : "When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI)." }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-01-10" - }, { - "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-15" + "val" : "2024-12-24" } ], - "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-08-15/apollo_sv.json" + "version" : "http://purl.obolibrary.org/obo/apollo_sv/releases/2024-12-24/apollo_sv.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.obo/obo/NCBITaxon_7160", @@ -13587,30 +13587,6 @@ "val" : "pub_type" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_49443", - "lbl" : "Anatomical cluster", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_55457", - "lbl" : "vocal fold", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_64854", - "lbl" : "Subdivision of larynx", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_64989", - "lbl" : "Heterogeneous cluster", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_67135", - "lbl" : "Anatomical structure", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/FMA_67165", - "lbl" : "Material anatomical entity", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000001", "lbl" : "geopolitical entity", @@ -14292,9 +14268,6 @@ "val" : "Wikipedia:Viral_life_cycle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0022415" }, { @@ -14508,18 +14481,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/27189" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4896" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4932" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" @@ -14763,9 +14724,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/20191" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4895" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -14939,9 +14897,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "unitId" } ] } }, { @@ -14950,7 +14905,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." + "val" : "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -14958,18 +14913,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "purpose of a study; support of hypothesis, discovery of new information" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: original definition when imported from OBI read: \"objective is an\nnon realizable information entity which can serve as that proper part\nof a plan towards which the realization of the plan is directed.\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\"" @@ -15042,7 +14988,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a directive information entity that describes an action the bearer will take" + "val" : "A directive information entity that describes an action the bearer will take." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -15050,9 +14996,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -15086,9 +15029,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "datum label" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -15110,9 +15050,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "label" } ] } }, { @@ -15368,14 +15305,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." + "val" : "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Data items include counts of things, analyte concentrations, and statistical summaries." @@ -15388,12 +15322,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." @@ -15406,21 +15334,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Jonathan Rees" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data" @@ -15432,7 +15351,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a smallish, word-like datum..." + "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -15491,7 +15410,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" + "val" : "A generically dependent continuant that is about some thing." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -15502,9 +15421,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." @@ -15514,12 +15430,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON: Chris Stoeckert" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000142" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000142" @@ -15589,12 +15499,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be\nconcretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." @@ -15792,9 +15696,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000124" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MSI" @@ -16244,9 +16145,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -16265,15 +16163,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000042" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBI_0000042" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "dataSets" } ] } }, { @@ -16332,18 +16224,15 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications." + "val" : "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." }, - "comments" : [ "2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them", "2/3/2009 Comment from OBI review.\n \n Action specification not well enough specified.\n Conditional specification not well enough specified.\n Question whether all plan specifications have objective specifications.\n \n Request that IAO either clarify these or change definitions not to use them" ], + "comments" : [ "2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -16419,9 +16308,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -16473,9 +16359,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000124" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" @@ -16612,9 +16495,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a hard drive" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" @@ -20075,9 +19955,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "name" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" @@ -20109,122 +19986,13 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020002", - "lbl" : "utterance", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An utterance is an information content entity that is a complete unit of speech in spoken language. " - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia: http://en.wikipedia.org/wiki/Utterance" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020003", - "lbl" : "mechanical wave quality", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An attributive collection of qualities inhering in energy when transported through a medium in a wave." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020004", - "lbl" : "writing quality", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "is a quality that is the concretization of graphemes and inheres in a material object." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020005", - "lbl" : "writing bearer", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "is a material information bearer that bears the concretization of graphemes." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting," - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020006", - "lbl" : "portion of energy", - "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020007", - "lbl" : "sound energy", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Energy that is transported in a sound wave." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020008", - "lbl" : "utterance energy", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Sound energy bearing the concretization of an utterance and being the output of an uttering process. " - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020009", - "lbl" : "oscillating", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Oscillation" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020010", "lbl" : "identifier creating process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." + "val" : "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", @@ -20249,25 +20017,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020011", - "lbl" : "utterance process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "is a planned process of making speech sounds which may or may not have an actual language involved. " - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wiktionary.org/wiki/utter" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020015", "lbl" : "personal name", @@ -20308,9 +20057,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "first name" @@ -20336,9 +20082,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "last name" @@ -20361,7 +20104,7 @@ "definition" : { "val" : "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." }, - "comments" : [ "Code sets might include non-entities/things (e.g. missing thumbs).", "Does not imply absence vs. presence of any taxonomy.", "Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.", "Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories).", "Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).", "Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).", "For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).", "For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.", "Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain.", "Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.", "The identifiers do not denote each other.", "The information content entities do not denote each other." ], + "comments" : [ "Code sets might include non-entities/things (e.g. missing thumbs).", "Does not imply absence vs. presence of any taxonomy.", "Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.", "Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).", "For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).", "For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.", "Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.", "The information content entities do not denote each other." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -20409,6 +20152,36 @@ "val" : "William R. Hogan" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0021003", + "lbl" : "social act", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." + }, + "comments" : [ "The phrase \"in need of being perceived\" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: \"The command is according to its essence in need of being heard (vernehmungsbedürtig\". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target.\" (A. Reinach: The Apriori Foundations of the Civil Law.\" Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0021009", + "lbl" : "deontic declaration", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A social act that creates or revokes a deontic role." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000000", "lbl" : "ontology module", @@ -31604,6 +31377,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "branch derived" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" @@ -32543,6 +32322,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -33246,6 +33028,9 @@ "lbl" : "inpatient encounter", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Albert Goldfain" @@ -33333,93 +33118,29 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen\n" + "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000007", - "lbl" : "gender role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Gender_role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "sex" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000008", - "lbl" : "male gender role", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000010", + "lbl" : "human health care role", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question." + "val" : "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "male gender" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000009", - "lbl" : "female gender role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "female gender" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000010", - "lbl" : "human health care role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. " - }, - "comments" : [ "Mathias Brochhausen" ], - "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "health care role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33428,8 +33149,9 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A role borne by an organism being as the recipient of a health care service." + "val" : "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." }, + "comments" : [ "In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" @@ -33441,10 +33163,7 @@ "val" : "patient" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Patient" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "val" : "CAFE domain expert working group." } ] } }, { @@ -33452,36 +33171,35 @@ "lbl" : "health care provider organization role", "type" : "CLASS", "meta" : { - "comments" : [ "Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division)." ], + "definition" : { + "val" : "A role that inheres in an organization and that is realized by the providing of services in a health care encounter." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "lbl" : "collection of organisms", + "lbl" : "aggregate of objectual organisms", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An object aggregate of organisms." + "val" : "An object aggregate of objectual organisms." }, - "comments" : [ "Any arbitrary collection of organisms. They need not be of the same taxonomic class. " ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species." - } ] + "comments" : [ "Any arbitrary collection of organisms. They need not be of the same taxonomic class. " ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000023", "lbl" : "collection of humans", "type" : "CLASS", "meta" : { - "comments" : [ "An object aggregate all of whose components are human beings." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] + "definition" : { + "val" : "An object aggregate all of whose components are human beings." + } } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000025", @@ -33495,9 +33213,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33512,9 +33227,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan\nMathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33523,58 +33235,60 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organization social role that is realized by a health care process." + "val" : "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process" }, - "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] + "comments" : [ "Previous definition: An organization social role played by an organization in health care processes." ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000033", - "lbl" : "aggregate of organizations", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "lbl" : "human patient role", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An aggregate of organizations that have some feature in common, but is not itself an organization." - }, - "comments" : [ "It is often convenient to group organizations together that otherwise might not even interact with one another. " ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - } ] + "val" : "A patient role that inheres in a human being." + } } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000052", - "lbl" : "hospital function", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000033", + "lbl" : "aggregate of organizations", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population." + "val" : "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" }, + "comments" : [ "It is often convenient to group organizations together that otherwise might not even interact with one another. " ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "val" : "William R. Hogan\nAmanda Hicks" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "lbl" : "material entity role", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "lbl" : "organism role", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "lbl" : "Homo sapiens role", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "lbl" : "organization role", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000053", "lbl" : "school function", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A function inhering in a facility that manifests by the facility participating in providing formal education to a student population." + "val" : "A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33583,14 +33297,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care." + "val" : "A healthcare provider role that inheres in an organization and is realized by providing inpatient care." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33604,9 +33315,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33620,9 +33328,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33636,9 +33341,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33647,14 +33349,11 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A human social role that is realized by the process of formal education that the bearer undergoes." + "val" : "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33662,16 +33361,9 @@ "lbl" : "nursery school role", "type" : "CLASS", "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data.\n" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "preschool" } ] } }, { @@ -33679,16 +33371,9 @@ "lbl" : "primary school role", "type" : "CLASS", "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "primarySchool" } ] } }, { @@ -33706,9 +33391,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://de.wikipedia.org/wiki/Bauwerk" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" } ] } }, { @@ -33722,28 +33404,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000063", - "lbl" : "hospital facility", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A facility that is run by a hospital organization and is the bearer of a hospital function." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "HealthcareFacility" } ] } }, { @@ -33757,12 +33417,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "SchoolFacility" } ] } }, { @@ -33770,152 +33424,62 @@ "lbl" : "secondary school role", "type" : "CLASS", "meta" : { - "comments" : [ "Key motivating use case was Synthia synthetic population data." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "secondarySchool" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000074", - "lbl" : "housing unit", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function." - }, - "comments" : [ "Housing units are individuated by their residence functions." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "houses" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000076", - "lbl" : "household", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000086", + "lbl" : "human role within an organization", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function." + "val" : "A human social role that is created by a deontic declaration performed by an organization." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "Household" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000078", - "lbl" : "workplace facility", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "workplace" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000079", - "lbl" : "workplace function", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "human organizational role" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000098", - "lbl" : "racial identity datum", + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "lbl" : "human traveling information", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method." + "val" : "An information content entity that is about human travel." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/apollo_sv.owl/APOLLO_SV_0000040", - "val" : "race" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000102", - "lbl" : "health care facility", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/ufbmi/OMRSE/issues/79" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "lbl" : "identity datum", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "Jie Zheng" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Amanda Hicks" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method." } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000172", + "lbl" : "health care function", + "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002072", "lbl" : "role in human social processes", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A role inhering in an entity realized by social interactions in human society." + "val" : "A role that inheres in some entity that is realized in a social act." }, "comments" : [ "Previous definition: A role played by an entity in human social processes." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" @@ -34157,20 +33721,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001025", - "lbl" : "pressure", - "type" : "CLASS", - "meta" : { - "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147487103" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001241", "lbl" : "physical object quality", @@ -35618,7 +35168,7 @@ "val" : "http://www.geneontology.org/formats/oboInOwl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147487102" + "val" : "_:genid2147487128" } ] } }, { @@ -37349,74 +36899,38 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020012", - "lbl" : "obsolete_designates", + "id" : "http://purl.obolibrary.org/obo/IDO_0000660", + "lbl" : "results_in", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000228" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/IAO_0000219" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } + "propertyType" : "OBJECT" }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020013", - "lbl" : "is_borrowed_reference_to", + "id" : "http://purl.obolibrary.org/obo/OBIB_0000732", + "lbl" : "owns", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020014", - "lbl" : "is_fixing_reference_to", + "id" : "http://purl.obolibrary.org/obo/OBIB_0000735", + "lbl" : "is owned by", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the." + "val" : "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "Mathias Brochhausen" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020018", - "lbl" : "is designated by", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IDO_0000660", - "lbl" : "results_in", - "type" : "PROPERTY", - "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000293", "lbl" : "has_specified_input", @@ -37626,6 +37140,9 @@ "propertyType" : "OBJECT", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." }, { @@ -37634,11 +37151,15 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. " - } ] + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000732" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", - "lbl" : "is owned by", + "lbl" : "obsolete is owned by", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -37648,33 +37169,32 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/omrse.owl" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000735" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMRSE_00000068", + "lbl" : "is administered by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000070", "lbl" : "is enrolled in school", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000071", "lbl" : "is admitted to hospital", "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse.owl" - } ] - } + "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", "lbl" : "inheres in", @@ -41697,6 +41217,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. " @@ -42369,18 +41892,6 @@ "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020019", - "lbl" : "IUI", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION", - "meta" : { - "comments" : [ "An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "instance unique identifier" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0100001", "lbl" : "term replaced by", @@ -42472,10 +41983,6 @@ "val" : "https://github.com/oborel/obo-relations/wiki/ROAndTime" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", "type" : "PROPERTY", @@ -46137,30 +45644,6 @@ "sub" : "http://purl.obolibrary.org/obo/FBcv_0000787", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_49443", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_67135" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_55457", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_64854" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_64854", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_64989" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_64989", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_49443" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_67135", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/FMA_67165" - }, { - "sub" : "http://purl.obolibrary.org/obo/FMA_67165", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/GEO_000000001", "pred" : "is_a", @@ -47437,42 +46920,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020002", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020003", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020004", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020005", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000178" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020006" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020007", - "pred" : "http://purl.obolibrary.org/obo/RO_0000053", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020003" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020007" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020009", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "is_a", @@ -47481,14 +46928,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020010", "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020011", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020011", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020008" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020015", "pred" : "is_a", @@ -47500,7 +46939,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020017", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020015" + "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020020", "pred" : "is_a", @@ -47509,6 +46948,14 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0021003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/IAO_0021009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0021003" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", "pred" : "is_a", @@ -47836,7 +47283,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IDO_0000629", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/IDO_0000654", "pred" : "is_a", @@ -50084,7 +49531,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000245", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000425", "pred" : "is_a", @@ -50293,6 +49740,10 @@ "sub" : "http://purl.obolibrary.org/obo/OGMS_0000096", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + }, { + "sub" : "http://purl.obolibrary.org/obo/OGMS_0000097", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/OGMS_0000097", "pred" : "is_a", @@ -50327,48 +49778,44 @@ "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000026" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000001", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000007", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000007" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000009", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000007" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000010", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000010", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000011", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000010" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000011", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000015", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000027" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000015", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PCO_0000018" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000022" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", - "pred" : "http://purl.obolibrary.org/obo/RO_0002351", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000025", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000051" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000025", "pred" : "is_a", @@ -50376,27 +49823,63 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000026", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000026", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000027", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000025" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000052", + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" + "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000053", "pred" : "is_a", @@ -50408,7 +49891,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000055", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000025" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000056", "pred" : "is_a", @@ -50425,10 +49908,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000057", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000055" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000058", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000001" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000059", "pred" : "is_a", @@ -50446,49 +49925,51 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000061" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000063", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000102" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000062", + "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000068", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "09/09/2017" + } ] + } + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000062", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000053" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000065", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000055" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000074", + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000142", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000076", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000078", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000079", + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000172", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000098", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000132" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000102", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000172", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002072", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0000001", "pred" : "is_a", @@ -50537,10 +50018,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0001018", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001241" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0001025", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0001241", "pred" : "is_a", @@ -50577,10 +50054,6 @@ "sub" : "http://purl.obolibrary.org/obo/PCO_0000001", "pred" : "http://purl.obolibrary.org/obo/BFO_0000177", "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000104" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000018", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000022" }, { "sub" : "http://purl.obolibrary.org/obo/PCO_0000018", "pred" : "is_a", @@ -51046,17 +50519,9 @@ "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020012", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020013", + "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020018", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000293", "pred" : "subPropertyOf", @@ -51092,13 +50557,13 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" + "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { - "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", + "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000070", + "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { @@ -51813,6 +51278,14 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0000418", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/IAO_0000419" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000735" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBI_0000299", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000312" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0000052", "pred" : "inverseOf", @@ -51938,10 +51411,6 @@ "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0010002" } ], - "equivalentNodesSets" : [ { - "representativeNodeId" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "nodeIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000022", "http://purl.obolibrary.org/obo/PCO_0000000" ] - } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000006", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ] @@ -52464,16 +51933,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000312", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020010" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020005", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000178" ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020007", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0020006" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020003" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020010", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ], @@ -52540,6 +51999,41 @@ }, { "definedClassId" : "http://purl.obolibrary.org/obo/OBI_0001530", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0001173" ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000011" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/BFO_0000040" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000048" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0100026" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000049" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000052", + "fillerId" : "http://purl.obolibrary.org/obo/OBI_0000245" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000056", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000245" ], @@ -52554,6 +52048,27 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", "fillerId" : "http://purl.obolibrary.org/obo/OMRSE_00000055" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000062", + "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000061" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/BFO_0000034" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", + "fillerId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000172", + "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000054", + "fillerId" : "http://purl.obolibrary.org/obo/OGMS_0000097" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/VO_0000001", "genusIds" : [ "http://purl.obolibrary.org/obo/OBI_0000047" ], @@ -52601,6 +52116,36 @@ "pred" : "http://purl.obolibrary.org/obo/OBI_0000312", "obj" : "http://purl.obolibrary.org/obo/IAO_0000444" } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002351", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000052", + "allValuesFromEdges" : [ { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002072", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + } ] }, { "predicateId" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000057", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] @@ -52694,10 +52239,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000583", "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000582" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/IAO_0020013", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000293", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] @@ -52853,6 +52394,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/IAO_0000039", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OMRSE_00000070", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000057" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/OMRSE_00000071", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000056" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] diff --git a/apollo_sv.obo b/apollo_sv.obo index 194553b..4de3220 100644 --- a/apollo_sv.obo +++ b/apollo_sv.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-08-15 +data-version: releases/2024-12-24 subsetdef: attribute_slim "" subsetdef: common_anatomy "" subsetdef: gocheck_do_not_annotate "" @@ -48,11 +48,11 @@ property_value: dc:contributor "Mike Wagner" xsd:string property_value: dc:contributor "Shawn T. Brown" xsd:string property_value: dc:contributor "William R. Hogan" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: dc:title "Apollo Structured Vocabulary (Apollo-SV)" xsd:string -property_value: owl:versionInfo "2023-01-10" xsd:string -property_value: owl:versionInfo "2024-08-15" xsd:string +property_value: owl:versionInfo "2024-12-24" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-9881-1017" xsd:anyURI property_value: terms:description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string +property_value: terms:title "Apollo Structured Vocabulary (Apollo-SV)" xsd:string property_value: www:RTS_00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string property_value: www:RTS_00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string @@ -6876,36 +6876,6 @@ subset: camcur is_a: IAO:0000310 ! document property_value: IAO:0000412 "http://purl.org/obo/owl/flybase_vocab" xsd:string -[Term] -id: FMA:49443 -name: Anatomical cluster -is_a: FMA:67135 ! Anatomical structure - -[Term] -id: FMA:55457 -name: vocal fold -is_a: FMA:64854 ! Subdivision of larynx - -[Term] -id: FMA:64854 -name: Subdivision of larynx -is_a: FMA:64989 ! Heterogeneous cluster - -[Term] -id: FMA:64989 -name: Heterogeneous cluster -is_a: FMA:49443 ! Anatomical cluster - -[Term] -id: FMA:67135 -name: Anatomical structure -is_a: FMA:67165 ! Material anatomical entity - -[Term] -id: FMA:67165 -name: Material anatomical entity -is_a: BFO:0000040 ! material entity - [Term] id: GEO:000000001 name: geopolitical entity @@ -7321,7 +7291,6 @@ synonym: "virulence" RELATED [] synonym: "virus process" EXACT [GOC:bf, GOC:jl] xref: Wikipedia:Viral_life_cycle is_a: GO:0008150 ! biological process -property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0016301 @@ -7426,10 +7395,6 @@ synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI -property_value: RO:0002161 NCBITaxon:2 -property_value: RO:0002161 NCBITaxon:2157 -property_value: RO:0002161 NCBITaxon:4896 -property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -7523,7 +7488,6 @@ synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological process property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI -property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0048609 @@ -7589,7 +7553,6 @@ name: measurement unit label def: "A data item label that denotes a unit of measure." [] def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] is_a: IAO:0000009 ! datum label -property_value: APOLLO_SV:0000040 "unitId" xsd:string property_value: IAO:0000111 "measurement unit label" xsd:string property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -7604,14 +7567,10 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string id: IAO:0000005 name: objective specification def: "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] -def: "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved." [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000111 "objective specification" xsd:string property_value: IAO:0000112 "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." xsd:string -property_value: IAO:0000112 "purpose of a study; support of hypothesis, discovery of new information" xsd:string property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an\nnon realizable information entity which can serve as that proper part\nof a plan towards which the realization of the plan is directed.\"" xsd:string property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\"" xsd:string property_value: IAO:0000116 "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that." xsd:string property_value: IAO:0000116 "Answers the question, why did you do this experiment?" xsd:string @@ -7640,12 +7599,10 @@ property_value: IAO:0000119 "OBI_0000013" xsd:string [Term] id: IAO:0000007 name: action specification -def: "a directive information entity that describes an action the bearer will take" [] def: "A directive information entity that describes an action the bearer will take." [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000112 "Pour the contents of flask 1 into flask 2" xsd:string property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string @@ -7663,10 +7620,8 @@ name: datum label def: "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label" [] def: "An information content entity that is part of some data item and is used to partially define the denotation of that data item." [] is_a: IAO:0000030 ! information content entity -property_value: APOLLO_SV:0000040 "label" xsd:string property_value: IAO:0000111 "data item label" xsd:string property_value: IAO:0000111 "datum label" xsd:string -property_value: IAO:0000111 "label" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" xsd:string @@ -7793,32 +7748,24 @@ property_value: IAO:0000119 "OBI_0000058" xsd:string [Term] id: IAO:0000027 name: data item -def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "data item" xsd:string -property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string -property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string -property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000118 "data" xsd:string [Term] id: IAO:0000028 name: symbol -def: "a smallish, word-like datum..." [] def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "symbol" xsd:string @@ -7845,18 +7792,14 @@ property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string id: IAO:0000030 name: information content entity def: "A generically dependent continuant that is about some thing." [] -def: "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity" [] is_a: BFO:0000031 ! generically dependent continuant relationship: IAO:0000136 BFO:0000001 ! is about entity property_value: IAO:0000111 "information content entity" xsd:string property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string -property_value: IAO:0000119 "OBI_0000142" xsd:string property_value: IAO:0000119 "OBI_0000142" xsd:string [Term] @@ -7890,8 +7833,6 @@ def: "An information content entity whose concretizations indicate to their bear is_a: IAO:0000030 ! information content entity relationship: IAO:0000136 BFO:0000017 ! is about realizable entity property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be\nconcretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it." xsd:string property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string @@ -7975,7 +7916,6 @@ is_a: IAO:0000001 ! conditional specification property_value: IAO:0000111 "rule" xsd:string property_value: IAO:0000112 "example to be added" xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000114 IAO:0000124 property_value: IAO:0000116 "MSI" xsd:string property_value: IAO:0000117 "PRS" xsd:string property_value: IAO:0000119 "OBI_0500021" xsd:string @@ -8013,7 +7953,6 @@ is_obsolete: true [Term] id: IAO:0000064 name: algorithm -def: "A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "algorithm" xsd:string @@ -8162,10 +8101,8 @@ id: IAO:0000100 name: data set def: "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets." [] is_a: IAO:0000027 ! data item -property_value: APOLLO_SV:0000040 "dataSets" xsd:string property_value: IAO:0000111 "data set" xsd:string property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string @@ -8173,7 +8110,6 @@ property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 "group:OBI" xsd:string property_value: IAO:0000119 "OBI_0000042" xsd:string -property_value: IAO:0000119 "OBI_0000042" xsd:string [Term] id: IAO:0000101 @@ -8201,16 +8137,13 @@ property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000104 name: plan specification -def: "a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications." [] def: "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them -comment: 2/3/2009 Comment from OBI review.\n \n Action specification not well enough specified.\n Conditional specification not well enough specified.\n Question whether all plan specifications have objective specifications.\n \n Request that IAO either clarify these or change definitions not to use them is_a: IAO:0000033 ! directive information entity relationship: has_part IAO:0000005 ! objective specification relationship: has_part IAO:0000007 ! action specification property_value: IAO:0000111 "plan specification" xsd:string property_value: IAO:0000112 "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2014-03-31: A plan specification can have other parts, such as conditional specifications." xsd:string @@ -8242,7 +8175,6 @@ def: "A measurement datum is an information content entity that is a recording o is_a: IAO:0000027 ! data item property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string @@ -8266,7 +8198,6 @@ def: "A version number is an information content entity which is a sequence of c is_a: IAO:0000028 ! symbol property_value: IAO:0000111 "version number" xsd:string property_value: IAO:0000114 IAO:0000123 -property_value: IAO:0000114 IAO:0000124 property_value: IAO:0000116 "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version" xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string @@ -8329,7 +8260,6 @@ property_value: IAO:0000111 "material information bearer" xsd:string property_value: IAO:0000112 "a brain" xsd:string property_value: IAO:0000112 "a hard drive" xsd:string property_value: IAO:0000112 "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string -property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: IAO" xsd:string @@ -9886,7 +9816,6 @@ intersection_of: OBI:0000312 IAO:0020010 {all_only="true"} ! is_specified_output intersection_of: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process relationship: IAO:0000219 BFO:0000001 ! denotes entity relationship: OBI:0000312 IAO:0020010 ! is_specified_output_of identifier creating process -property_value: APOLLO_SV:0000040 "name" xsd:string property_value: dc:creator "Mathias Brochhausen" xsd:string property_value: IAO:0000111 "identifier" xsd:string property_value: IAO:0000117 "Justin Whorton" xsd:string @@ -9898,7 +9827,6 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020001 name: grapheme -def: "A grapheme is an information content entity that is a fundamental unit in a written language. " [] def: "An information content entity that is a fundamental unit in a written language." [] comment: Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there. is_a: IAO:0000030 ! information content entity @@ -9908,71 +9836,11 @@ property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Grapheme" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string -[Term] -id: IAO:0020002 -name: utterance -def: "An utterance is an information content entity that is a complete unit of speech in spoken language. " [] -is_a: IAO:0000030 ! information content entity -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Wikipedia: http://en.wikipedia.org/wiki/Utterance" xsd:string - -[Term] -id: IAO:0020003 -name: mechanical wave quality -def: "An attributive collection of qualities inhering in energy when transported through a medium in a wave." [] -is_a: BFO:0000019 ! quality -property_value: dc:creator "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020004 -name: writing quality -def: "is a quality that is the concretization of graphemes and inheres in a material object." [] -is_a: BFO:0000019 ! quality -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020005 -name: writing bearer -def: "is a material information bearer that bears the concretization of graphemes." [] -is_a: IAO:0000178 ! material information bearer -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000112 "pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting," xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020006 -name: portion of energy -is_a: BFO:0000004 ! independent continuant - -[Term] -id: IAO:0020007 -name: sound energy -def: "Energy that is transported in a sound wave." [] -is_a: IAO:0020006 ! portion of energy -relationship: RO:0000053 IAO:0020003 ! is bearer of mechanical wave quality -property_value: dc:creator "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0020008 -name: utterance energy -def: "Sound energy bearing the concretization of an utterance and being the output of an uttering process. " [] -is_a: IAO:0020007 ! sound energy - -[Term] -id: IAO:0020009 -name: oscillating -def: "Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states." [] -is_a: BFO:0000015 ! process -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Oscillation" xsd:string - [Term] id: IAO:0020010 name: identifier creating process -def: "A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] def: "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] +def: "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000299 IAO:0020000 ! has_specified_output identifier @@ -9985,16 +9853,6 @@ property_value: IAO:0000118 "dubbing process" xsd:string property_value: IAO:0000118 "naming" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string -[Term] -id: IAO:0020011 -name: utterance process -def: "is a planned process of making speech sounds which may or may not have an actual language involved. " [] -is_a: OBI:0000011 ! planned process -relationship: OBI:0000299 IAO:0020008 ! has_specified_output utterance energy -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://en.wiktionary.org/wiki/utter" xsd:string - [Term] id: IAO:0020015 name: personal name @@ -10015,12 +9873,10 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020016 name: given name -def: "A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name" [] def: "A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name" [] is_a: IAO:0020015 ! personal name property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "first name" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Given_name" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string @@ -10028,12 +9884,10 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020017 name: family name -def: "A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children." [] def: "An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children." [] -is_a: IAO:0020015 ! personal name +is_a: IAO:0020000 ! identifier property_value: IAO:0000117 "Justin Whorton" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "last name" xsd:string property_value: IAO:0000118 "surname" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Family_name" xsd:string @@ -10042,19 +9896,15 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA [Term] id: IAO:0020020 name: code set -def: "An information content entity that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate." [] +def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate." [] def: "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." [] comment: Code sets might include non-entities/things (e.g. missing thumbs). comment: Does not imply absence vs. presence of any taxonomy. comment: Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. -comment: Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories). comment: Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). -comment: Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). -comment: Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain. comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. -comment: The identifiers do not denote each other. comment: The information content entities do not denote each other. is_a: IAO:0000030 ! information content entity relationship: has_part IAO:0020000 ! identifier @@ -10074,6 +9924,22 @@ property_value: IAO:0000118 "coding system" xsd:string property_value: IAO:0000118 "controlled vocabulary" xsd:string property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IAO/issues/237" xsd:string +[Term] +id: IAO:0021003 +name: social act +def: "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." [] +comment: The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote. +is_a: OBI:0000011 ! planned process +property_value: IAO:0000112 "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" xsd:string +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string + +[Term] +id: IAO:0021009 +name: deontic declaration +def: "A social act that creates or revokes a deontic role." [] +is_a: IAO:0021003 ! social act +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string + [Term] id: IAO:8000000 name: ontology module @@ -10632,7 +10498,7 @@ property_value: IAO:0000117 "Lindsay Cowell" xsd:string id: IDO:0000629 name: host role def: "A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." [] -is_a: BFO:0000023 ! role +is_a: OMRSE:00000049 ! organism role property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000117 "Alexander Diehl" xsd:string property_value: IAO:0000117 "Lindsay Cowell" xsd:string @@ -15421,6 +15287,8 @@ property_value: IAO:0000116 "We are only considering successfully completed plan property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "branch derived" xsd:string +property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string +property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] @@ -15469,8 +15337,9 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string [Term] id: OBI:0000245 name: organization +def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] def: "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] -is_a: BFO:0000004 ! independent continuant +is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "organization" xsd:string property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -15829,6 +15698,7 @@ is_a: OBI:0000011 ! planned process relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective property_value: IAO:0000111 "data transformation" xsd:string property_value: IAO:0000112 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string +property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "Helen Parkinson" xsd:string @@ -16111,6 +15981,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string id: OGMS:0000097 name: health care encounter def: "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter" [] +is_a: OBI:0000011 ! planned process is_a: OGMS:0000096 ! health care process property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string @@ -16139,6 +16010,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ogms.owl" xsd:string [Term] id: OGMS:0000100 name: inpatient encounter +def: "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night." [] is_a: OGMS:0000097 ! health care encounter property_value: IAO:0000117 "Albert Goldfain" xsd:string property_value: IAO:0000119 "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" xsd:string @@ -16179,100 +16051,63 @@ id: OMRSE:00000001 name: human social role def: "A social role inhering in a human being." [] is_a: OMRSE:00000026 ! organism social role -relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens -property_value: IAO:0000117 "Mathias Brochhausen\n" xsd:string -property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000007 -name: gender role -def: "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." [] -is_a: BFO:0000023 ! role -property_value: APOLLO_SV:0000040 "sex" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Gender_role" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000008 -name: male gender role -def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question." [] -is_a: OMRSE:00000007 ! gender role +is_a: OMRSE:00000050 ! Homo sapiens role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "male gender" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000009 -name: female gender role -def: "A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question." [] -is_a: OMRSE:00000007 ! gender role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "female gender" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] id: OMRSE:00000010 name: human health care role -def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. " [] -comment: Mathias Brochhausen +def: "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis." [] is_a: OMRSE:00002072 ! role in human social processes +relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "health care role" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000011 name: patient role -def: "A human health care role that inheres in an organism [human?] as the recipient of a health care service." [] -def: "A role borne by an organism being as the recipient of a health care service." [] +def: "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." [] +comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. is_a: OMRSE:00000010 ! human health care role +is_a: OMRSE:00000049 ! organism role property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "patient" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Patient" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +property_value: IAO:0000119 "CAFE domain expert working group." xsd:string [Term] id: OMRSE:00000015 name: health care provider organization role -comment: Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). +def: "A role that inheres in an organization and that is realized by the providing of services in a health care encounter." [] is_a: OMRSE:00000027 ! organization health care role -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter +property_value: dc:contributor "Mathias Brochhausen" xsd:string +property_value: dc:creator "Amanda Hicks" xsd:string [Term] id: OMRSE:00000022 -name: collection of organisms -def: "An object aggregate of organisms." [] +name: aggregate of objectual organisms +def: "An object aggregate of objectual organisms." [] comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class. is_a: BFO:0000027 ! object aggregate -intersection_of: BFO:0000027 ! object aggregate -intersection_of: RO:0002351 OBI:0100026 ! has member organism -intersection_of: RO:0002351 OBI:0100026 {all_only="true"} ! has member organism -equivalent_to: PCO:0000000 ! PCO:collection of organisms -relationship: RO:0002351 OBI:0100026 ! has member organism -property_value: IAO:0000600 "This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species." xsd:string [Term] id: OMRSE:00000023 name: collection of humans -comment: An object aggregate all of whose components are human beings. -is_a: PCO:0000018 ! collection of organisms of the same species -intersection_of: OMRSE:00000022 ! collection of organisms -intersection_of: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens -intersection_of: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens -relationship: RO:0002351 NCBITaxon:9606 ! has member Homo sapiens -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +def: "An object aggregate all of whose components are human beings." [] +is_a: OMRSE:00000022 ! aggregate of objectual organisms +relationship: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens [Term] id: OMRSE:00000025 name: organization social role def: "A role in human social processes that inheres in an organization." [] comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. +is_a: OMRSE:00000051 ! organization role is_a: OMRSE:00002072 ! role in human social processes property_value: IAO:0000117 "William R. Hogan" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000026 @@ -16281,62 +16116,91 @@ def: "A role in human social processes that inheres in an organism." [] comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. comment: Previous definition: A role in human social processes played by an organism. -is_a: BFO:0000023 ! role -relationship: RO:0000052 OBI:0100026 ! inheres in organism +is_a: OMRSE:00000049 ! organism role +is_a: OMRSE:00002072 ! role in human social processes property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000027 name: organization health care role -def: "An organization social role that is realized by a health care process." [] +def: "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process" [] comment: Previous definition: An organization social role played by an organization in health care processes. is_a: OMRSE:00000025 ! organization social role -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string + +[Term] +id: OMRSE:00000030 +name: human patient role +def: "A patient role that inheres in a human being." [] +is_a: OMRSE:00000011 ! patient role +is_a: OMRSE:00000050 ! Homo sapiens role +intersection_of: OMRSE:00000011 ! patient role +intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens [Term] id: OMRSE:00000033 name: aggregate of organizations -def: "An aggregate of organizations that have some feature in common, but is not itself an organization." [] +def: "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" [] comment: It is often convenient to group organizations together that otherwise might not even interact with one another. -is_a: BFO:0000027 ! object aggregate -intersection_of: BFO:0000027 ! object aggregate -intersection_of: RO:0002351 OBI:0000245 ! has member organization -intersection_of: RO:0002351 OBI:0000245 {all_only="true"} ! has member organization +is_a: BFO:0000040 ! material entity relationship: RO:0002351 OBI:0000245 ! has member organization -property_value: IAO:0000117 "William R. Hogan" xsd:string +property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string [Term] -id: OMRSE:00000052 -name: hospital function -def: "A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population." [] -is_a: BFO:0000034 ! function -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +id: OMRSE:00000048 +name: material entity role +is_a: BFO:0000023 ! role +intersection_of: BFO:0000023 ! role +intersection_of: RO:0000052 BFO:0000040 ! inheres in material entity +relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity +relationship: RO:0000052 BFO:0000040 ! inheres in material entity + +[Term] +id: OMRSE:00000049 +name: organism role +is_a: OMRSE:00000048 ! material entity role +intersection_of: OMRSE:00000048 ! material entity role +intersection_of: RO:0000052 OBI:0100026 ! inheres in organism +relationship: RO:0000052 OBI:0100026 {all_only="true"} ! inheres in organism +relationship: RO:0000052 OBI:0100026 ! inheres in organism + +[Term] +id: OMRSE:00000050 +name: Homo sapiens role +is_a: OMRSE:00000049 ! organism role +intersection_of: OMRSE:00000049 ! organism role +intersection_of: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 ! inheres in Homo sapiens +relationship: RO:0000052 NCBITaxon:9606 {all_only="true"} ! inheres in Homo sapiens + +[Term] +id: OMRSE:00000051 +name: organization role +is_a: OMRSE:00000048 ! material entity role +intersection_of: BFO:0000023 ! role +intersection_of: RO:0000052 OBI:0000245 ! inheres in organization +relationship: RO:0000052 OBI:0000245 ! inheres in organization +relationship: RO:0000052 OBI:0000245 {all_only="true"} ! inheres in organization [Term] id: OMRSE:00000053 name: school function -def: "A function inhering in a facility that manifests by the facility participating in providing formal education to a student population." [] +def: "A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population." [] is_a: BFO:0000034 ! function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000054 name: hospital role -def: "A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care." [] +def: "A healthcare provider role that inheres in an organization and is realized by providing inpatient care." [] is_a: OMRSE:00000015 ! health care provider organization role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000055 name: school role -is_a: BFO:0000023 ! role +is_a: OMRSE:00000025 ! organization social role property_value: IAO:0000117 "An organization social role that inheres in an organization and is realized by providing formal education to students." xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000056 @@ -16347,7 +16211,6 @@ intersection_of: OBI:0000245 ! organization intersection_of: RO:0000053 OMRSE:00000054 ! is bearer of hospital role relationship: RO:0000053 OMRSE:00000054 ! is bearer of hospital role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000057 @@ -16358,33 +16221,24 @@ intersection_of: OBI:0000245 ! organization intersection_of: RO:0000053 OMRSE:00000055 ! is bearer of school role relationship: RO:0000053 OMRSE:00000055 ! is bearer of school role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000058 name: student role -def: "A human social role that is realized by the process of formal education that the bearer undergoes." [] -is_a: OMRSE:00000001 ! human social role +def: "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes." [] property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000059 name: nursery school role -comment: Key motivating use case was Synthia synthetic population data.\n is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "preschool" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000060 name: primary school role -comment: Key motivating use case was Synthia synthetic population data. is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "primarySchool" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000061 @@ -16395,111 +16249,68 @@ comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". is_a: BFO:0000040 ! material entity property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "http://de.wikipedia.org/wiki/Bauwerk" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000062 name: facility def: "An architectural structure that bears some function." [] is_a: OMRSE:00000061 ! architectural structure +intersection_of: OMRSE:00000061 ! architectural structure +intersection_of: RO:0000053 BFO:0000034 ! is bearer of function +relationship: OMRSE:00000068 OBI:0000245 {owl:versionInfo="09/09/2017"} ! is administered by organization +relationship: RO:0000053 BFO:0000034 ! is bearer of function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000063 -name: hospital facility -def: "A facility that is run by a hospital organization and is the bearer of a hospital function." [] -is_a: OMRSE:00000102 ! health care facility -property_value: APOLLO_SV:0000040 "HealthcareFacility" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000064 name: school facility def: "A facility that is run by a school organization and is the bearer of a school function." [] is_a: OMRSE:00000062 ! facility -property_value: APOLLO_SV:0000040 "SchoolFacility" xsd:string +relationship: RO:0000053 OMRSE:00000053 ! is bearer of school function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] id: OMRSE:00000065 name: secondary school role -comment: Key motivating use case was Synthia synthetic population data. is_a: OMRSE:00000055 ! school role -property_value: APOLLO_SV:0000040 "secondarySchool" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string [Term] -id: OMRSE:00000074 -name: housing unit -def: "A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function." [] -comment: Housing units are individuated by their residence functions. -is_a: BFO:0000040 ! material entity -property_value: APOLLO_SV:0000040 "houses" xsd:string +id: OMRSE:00000086 +name: human role within an organization +def: "A human social role that is created by a deontic declaration performed by an organization." [] property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +property_value: IAO:0000118 "human organizational role" xsd:string [Term] -id: OMRSE:00000076 -name: household -def: "A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function." [] -is_a: BFO:0000040 ! material entity -property_value: APOLLO_SV:0000040 "Household" xsd:string -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000078 -name: workplace facility -is_a: OMRSE:00000062 ! facility -property_value: APOLLO_SV:0000040 "workplace" xsd:string -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +id: OMRSE:00000142 +name: human traveling information +def: "An information content entity that is about human travel." [] +is_a: IAO:0000030 ! information content entity +intersection_of: IAO:0000030 ! information content entity +intersection_of: IAO:0000136 APOLLO_SV:00000532 ! is about human travel +relationship: IAO:0000136 APOLLO_SV:00000532 ! is about human travel +property_value: dc:contributor "Jie Zheng" xsd:string +property_value: dc:creator "Amanda Hicks" xsd:string +property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/issues/79" xsd:anyURI [Term] -id: OMRSE:00000079 -name: workplace function -def: "a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out" [] +id: OMRSE:00000172 +name: health care function is_a: BFO:0000034 ! function -property_value: IAO:0000117 "Amanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000098 -name: racial identity datum -def: "A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method." [] -is_a: OMRSE:00000132 ! identity datum -property_value: APOLLO_SV:0000040 "race" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000102 -name: health care facility -is_a: OMRSE:00000062 ! facility -property_value: IAO:0000117 "A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string - -[Term] -id: OMRSE:00000132 -name: identity datum -is_a: IAO:0000030 ! information content entity -property_value: dc:creator "Amanda Hicks" xsd:string -property_value: dc:creator "An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method." xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +intersection_of: BFO:0000034 ! function +intersection_of: BFO:0000054 OGMS:0000097 ! is realized by health care encounter +relationship: BFO:0000054 OGMS:0000097 ! is realized by health care encounter [Term] id: OMRSE:00002072 name: role in human social processes -def: "A role inhering in an entity realized by social interactions in human society." [] +def: "A role that inheres in some entity that is realized in a social act." [] comment: Previous definition: A role played by an entity in human social processes. -is_a: BFO:0000023 ! role +is_a: OMRSE:00000048 ! material entity role +relationship: RO:0000052 BFO:0000040 {all_only="true"} ! inheres in material entity property_value: dc:contributor "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl" xsd:string [Term] id: PATO:0000001 @@ -16619,13 +16430,6 @@ property_value: IAO:0000111 "physical quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl property_value: IAO:0000412 "http://purl.obolibrary.org/obo/pato.owl" xsd:string -[Term] -id: PATO:0001025 -name: pressure -namespace: quality -subset: attribute_slim -is_a: BFO:0000019 ! quality - [Term] id: PATO:0001241 name: physical object quality @@ -16729,7 +16533,6 @@ property_value: IAO:0000119 "ISBN:0878932739" xsd:string id: PCO:0000018 name: collection of organisms of the same species def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] -is_a: OMRSE:00000022 ! collection of organisms is_a: PCO:0000000 ! PCO:collection of organisms [Term] @@ -17993,41 +17796,6 @@ property_value: IAO:0000117 "Alan Ruttenberg" xsd:string domain: IAO:0000582 ! time stamped measurement datum is_a: has_part ! has part -[Typedef] -id: IAO:0020012 -name: obsolete_designates -def: "x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.." [] -property_value: dc:creator "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000228 -is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty -is_obsolete: true -replaced_by: IAO:0000219 - -[Typedef] -id: IAO:0020013 -name: is_borrowed_reference_to -def: "x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place." [] -property_value: dc:creator "Mathias Brochhausen" xsd:string -domain: IAO:0020000 ! identifier -range: BFO:0000001 ! entity -is_asymmetric: true - -[Typedef] -id: IAO:0020014 -name: is_fixing_reference_to -def: "x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the." [] -property_value: dc:creator "Mathias Brochhausen" xsd:string -is_asymmetric: true - -[Typedef] -id: IAO:0020018 -name: is designated by -def: "p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context." [] -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty -is_obsolete: true -is_asymmetric: true - [Typedef] id: IDO:0000660 name: results_in @@ -18076,6 +17844,7 @@ property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has_participant +inverse_of: OBI:0000312 ! is_specified_output_of [Typedef] id: OBI:0000308 @@ -18117,29 +17886,58 @@ property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/obi.owl" xsd:string +[Typedef] +id: OBIB:0000732 +name: owns +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal." xsd:string +inverse_of: OBIB:0000735 ! is owned by +is_asymmetric: true + +[Typedef] +id: OBIB:0000735 +name: is owned by +def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." [] +property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string +is_asymmetric: true + [Typedef] id: OMIABIS:0000008 +name: obsolete owns name: owns +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string property_value: IAO:0000600 "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. " xsd:string +is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty +is_obsolete: true +replaced_by: OBIB:0000732 [Typedef] id: OMIABIS:0000048 name: is owned by +name: obsolete is owned by def: "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b." [] property_value: IAO:0000119 "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204." xsd:string +property_value: IAO:0000119 "Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204." xsd:string property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +replaced_by: OBIB:0000735 + +[Typedef] +id: OMRSE:00000068 +name: is administered by +is_asymmetric: true [Typedef] id: OMRSE:00000070 name: is enrolled in school -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +range: OMRSE:00000057 ! school organization +is_asymmetric: true [Typedef] id: OMRSE:00000071 name: is admitted to hospital -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string +range: OMRSE:00000056 ! hospital organization [Typedef] id: RO:0000052 diff --git a/apollo_sv.owl b/apollo_sv.owl index 522bc60..0dac2c8 100644 --- a/apollo_sv.owl +++ b/apollo_sv.owl @@ -27,7 +27,7 @@ xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#" xmlns:ace_lexicon="http://attempto.ifi.uzh.ch/ace_lexicon#"> - + Amanda Hicks John Levander Josh Hanna @@ -36,14 +36,14 @@ Shawn T. Brown William R. Hogan Mathias Brochhausen - Apollo Structured Vocabulary (Apollo-SV) + https://orcid.org/0000-0002-9881-1017 An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. https://creativecommons.org/licenses/by/4.0/ + Apollo Structured Vocabulary (Apollo-SV) C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). - 2023-01-10 - 2024-08-15 + 2024-12-24 @@ -331,7 +331,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred label editor preferred label editor preferred term editor preferred term @@ -376,7 +375,6 @@ For the 1982-10-17 date, we suggest the dc:created annotation. PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 - has curation status has curation status @@ -408,6 +406,26 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -429,7 +447,6 @@ We also have the outstanding issue of how to aim different definitions to differ GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note editor note @@ -447,7 +464,6 @@ We also have the outstanding issue of how to aim different definitions to differ definition editor definition editor - term editor term editor @@ -467,7 +483,6 @@ We also have the outstanding issue of how to aim different definitions to differ Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label - alternative term alternative term @@ -485,7 +500,6 @@ We also have the outstanding issue of how to aim different definitions to differ Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source definition source @@ -511,7 +525,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note curator note @@ -827,16 +840,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - instance unique identifier - An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system. - IUI - - - - @@ -922,12 +925,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - - - - - @@ -2665,7 +2662,6 @@ Some currently missing phenomena that should be considered "about" are person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy http://purl.obolibrary.org/obo/iao.owl - is about is about @@ -2922,65 +2918,34 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + - - - x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.. - - - Mathias Brochhausen - obsolete_designates - true + + results_in - + - + + - - - - x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place. - Mathias Brochhausen - is_borrowed_reference_to - - - - - - - - - - x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the. - Mathias Brochhausen - is_fixing_reference_to - - - - - - - - - - - p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context. Mathias Brochhausen - is designated by - true + This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. + owns - + - - results_in + + + a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. + Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. + is owned by @@ -3037,6 +3002,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + has_specified_output has_specified_output @@ -3115,11 +3081,16 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + + Mathias Brochhausen Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. http://purl.obolibrary.org/obo/omrse.owl This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal. + + obsolete owns owns + true @@ -3130,8 +3101,20 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b. Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204. + Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204. http://purl.obolibrary.org/obo/omrse.owl + is owned by + obsolete is owned by + + + + + + + + + is administered by @@ -3139,8 +3122,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - http://purl.obolibrary.org/obo/omrse.owl + + + + + + + + is enrolled in school @@ -3150,7 +3139,13 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - http://purl.obolibrary.org/obo/omrse.owl + + + + + + + is admitted to hospital @@ -21307,60 +21302,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - - - - Anatomical cluster - - - - - - - - - vocal fold - - - - - - - - - Subdivision of larynx - - - - - - - - - Heterogeneous cluster - - - - - - - - - Anatomical structure - - - - - - - - - Material anatomical entity - - - - @@ -22239,7 +22180,6 @@ Date accessed: 2015-04-13 A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle. - GO:0022415 Wikipedia:Viral_life_cycle virus process @@ -22488,10 +22428,6 @@ Date accessed: 2015-04-13 Any biological process, occurring at the level of a multicellular organism, pertinent to its function. https://github.com/geneontology/go-ontology/issues/27189 - - - - jl 2012-09-19T16:07:47Z GO:0044707 @@ -22670,7 +22606,6 @@ Date accessed: 2015-04-13 Any process evolved to enable an interaction with an organism of a different species. https://github.com/geneontology/go-ontology/issues/20191 - interaction with another species interspecies interaction interspecies interaction between organisms @@ -22804,7 +22739,6 @@ of this, different, term. PERSON: Alan Ruttenberg PERSON: Melanie Courtot http://purl.obolibrary.org/obo/obi.owl - unitId measurement unit label @@ -22816,14 +22750,8 @@ of this, different, term. objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - purpose of a study; support of hypothesis, discovery of new information - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an -non realizable information entity which can serve as that proper part -of a plan towards which the realization of the plan is directed." 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? @@ -22863,9 +22791,7 @@ of a plan towards which the realization of the plan is directed." Pour the contents of flask 1 into flask 2 - A directive information entity that describes an action the bearer will take. - a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification @@ -22890,7 +22816,6 @@ of a plan towards which the realization of the plan is directed." data item label datum label - label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label @@ -22901,7 +22826,6 @@ of a plan towards which the realization of the plan is directed."9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. http://purl.obolibrary.org/obo/obi.owl - label data item label datum label @@ -23091,16 +23015,12 @@ Superclass was 'digital entity' - data item data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some @@ -23110,11 +23030,8 @@ process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert PERSON: Chris Stoeckert - PERSON: Jonathan Rees PERSON: Jonathan Rees data data item @@ -23132,7 +23049,6 @@ JAR: A data item is an approximately justified approximately true approximate be a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - a smallish, word-like datum... 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton @@ -23169,16 +23085,12 @@ JAR: A data item is an approximately justified approximately true approximate be information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. - A generically dependent continuant that is about some thing. - an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert PERSON: Chris Stoeckert - OBI_0000142 OBI_0000142 information content entity @@ -23241,10 +23153,7 @@ this case we explicitly refer to the singular form - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be -concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO @@ -23352,7 +23261,6 @@ superclass was 'digital document' rule example to be added - A rule is an executable which guides, defines, restricts actions. MSI PRS @@ -23407,7 +23315,6 @@ superclass was 'digital document' algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch @@ -23617,17 +23524,14 @@ XML document; The instructions in a XSD file" data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert - OBI_0000042 OBI_0000042 group:OBI - dataSets data set @@ -23682,10 +23586,8 @@ XML document; The instructions in a XSD file" plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. @@ -23701,13 +23603,6 @@ Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them - 2/3/2009 Comment from OBI review. - - Action specification not well enough specified. - Conditional specification not well enough specified. - Question whether all plan specifications have objective specifications. - - Request that IAO either clarify these or change definitions not to use them plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 @@ -23738,7 +23633,6 @@ superclass was 'digial entity' measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? @@ -23772,7 +23666,6 @@ Note: everybody agreed that identifier is probably a too general term. We howeve version number - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO @@ -23891,7 +23784,6 @@ Cons sometimes specifies a quality which is not a realizable. A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive - A material entity in which a concretization of an information content entity inheres. GROUP: IAO @@ -26528,7 +26420,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 - name Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier @@ -26541,7 +26432,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems - A grapheme is an information content entity that is a fundamental unit in a written language. An information content entity that is a fundamental unit in a written language. Justin Whorton http://en.wikipedia.org/wiki/Grapheme @@ -26553,222 +26443,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - - - - - An utterance is an information content entity that is a complete unit of speech in spoken language. - Mathias Brochhausen - Wikipedia: http://en.wikipedia.org/wiki/Utterance - Mathias Brochhausen - utterance - - - - - - - - - An attributive collection of qualities inhering in energy when transported through a medium in a wave. - Mathias Brochhausen - mechanical wave quality - - - - - - - - - is a quality that is the concretization of graphemes and inheres in a material object. - Mathias Brochhausen - Mathias Brochhausen - writing quality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting, - is a material information bearer that bears the concretization of graphemes. - Mathias Brochhausen - Mathias Brochhausen - writing bearer - - - - - - - - - portion of energy - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Energy that is transported in a sound wave. - Mathias Brochhausen - sound energy - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Sound energy bearing the concretization of an utterance and being the output of an uttering process. - utterance energy - - - - - - - - - Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states. - http://en.wikipedia.org/wiki/Oscillation - Mathias Brochhausen - oscillating - - - - @@ -26796,8 +26470,8 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. + An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen Mathias Brochhausen @@ -26810,31 +26484,6 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - - - - - - - - - - - - - - - - - is a planned process of making speech sounds which may or may not have an actual language involved. - Mathias Brochhausen - http://en.wiktionary.org/wiki/utter - Mathias Brochhausen - utterance process - - - - @@ -26869,10 +26518,8 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name Justin Whorton - Mathias Brochhausen Mathias Brochhausen first name http://en.wikipedia.org/wiki/Given_name @@ -26885,11 +26532,9 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - - A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. + An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. Justin Whorton - Mathias Brochhausen Mathias Brochhausen last name surname @@ -26910,7 +26555,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - An information content entity that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate. + An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate. An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. Alan Ruttenberg Justin Whorton @@ -26930,24 +26575,44 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta Code sets might include non-entities/things (e.g. missing thumbs). Does not imply absence vs. presence of any taxonomy. Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. - Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories). Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). - Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. - -When there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. - Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain. Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. - The identifiers do not denote each other. The information content entities do not denote each other. code set + + + + + Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom + A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. + Mathias Brochhausen + The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). +Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. +Thanks to W.R. Hogan for finding the Reinach quote. + social act + + + + + + + + + A social act that creates or revokes a deontic role. + Mathias Brochhausen + deontic declaration + + + + @@ -28111,7 +27776,7 @@ No imports - + @@ -38139,6 +37804,8 @@ No imports objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process @@ -38207,10 +37874,11 @@ objectives is a planned process. - + organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: @@ -38795,6 +38463,7 @@ This issue is outside the scope of OBI. data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + A data transformation is a process which produces output data from input data A planned process that produces output data from input data. @@ -39197,6 +38866,7 @@ See vaccination and antiviral treatment. + A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain @@ -39239,6 +38909,7 @@ See vaccination and antiviral treatment. + A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z @@ -39293,71 +38964,29 @@ See vaccination and antiviral treatment. - - - - - - + A social role inhering in a human being. - Mathias Brochhausen - + Mathias Brochhausen William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl human social role - - - - - A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Gender_role - http://purl.obolibrary.org/obo/omrse.owl - sex - gender role - - - - - - - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question. - Mathias Brochhausen - male gender - http://purl.obolibrary.org/obo/omrse.owl - male gender role - - - - - - - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question. - Mathias Brochhausen - female gender - http://purl.obolibrary.org/obo/omrse.owl - female gender role - - - - - A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. + + + + + + + A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. + Mathias Brochhausen William R. Hogan health care role - http://purl.obolibrary.org/obo/omrse.owl - Mathias Brochhausen human health care role @@ -39367,13 +38996,13 @@ See vaccination and antiviral treatment. - A human health care role that inheres in an organism [human?] as the recipient of a health care service. - A role borne by an organism being as the recipient of a health care service. + + A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter. Amanda Hicks Mathias Brochhausen patient - http://en.wikipedia.org/wiki/Patient - http://purl.obolibrary.org/obo/omrse.owl + CAFE domain expert working group. + In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. patient role @@ -39383,8 +39012,15 @@ See vaccination and antiviral treatment. - http://purl.obolibrary.org/obo/omrse.owl - Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). + + + + + + + A role that inheres in an organization and that is realized by the providing of services in a health care encounter. + Mathias Brochhausen + Amanda Hicks health care provider organization role @@ -39393,33 +39029,23 @@ See vaccination and antiviral treatment. - - - - - - - - - - - - - - - - - + + + + + + + + - An object aggregate of organisms. - This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species. + An object aggregate of objectual organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. - collection of organisms + aggregate of objectual organisms @@ -39427,30 +39053,14 @@ See vaccination and antiviral treatment. - - - - - - - - - - - - - - - - + - + - http://purl.obolibrary.org/obo/omrse.owl - An object aggregate all of whose components are human beings. + An object aggregate all of whose components are human beings. collection of humans @@ -39459,10 +39069,10 @@ See vaccination and antiviral treatment. + A role in human social processes that inheres in an organization. William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. @@ -39474,17 +39084,11 @@ Ditto for its current descendants. - - - - - - - + + A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. @@ -39499,55 +39103,196 @@ Ditto for its current descendants. - An organization social role that is realized by a health care process. - http://purl.obolibrary.org/obo/omrse.owl + An organization social role that, if realized, is realized by either a health care process or an ancillary health care process Previous definition: An organization social role played by an organization in health care processes. organization health care role + + + + + + + + + + + + + + + + + A patient role that inheres in a human being. + human patient role + + + + - + + + - + - + 2 + - + - An aggregate of organizations that have some feature in common, but is not itself an organization. - William R. Hogan + An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common + William R. Hogan +Amanda Hicks It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations - + - - - A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital function + + + + + + + + + + + + + + + + + + + + + + + + + + material entity role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Homo sapiens role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organization role @@ -39556,9 +39301,8 @@ Ditto for its current descendants. - A function inhering in a facility that manifests by the facility participating in providing formal education to a student population. + A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl school function @@ -39568,9 +39312,8 @@ Ditto for its current descendants. - A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care. + A healthcare provider role that inheres in an organization and is realized by providing inpatient care. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl hospital role @@ -39579,10 +39322,9 @@ Ditto for its current descendants. - + An organization social role that inheres in an organization and is realized by providing formal education to students. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl school role @@ -39611,7 +39353,6 @@ Ditto for its current descendants. An organization that is the bearer of a hospital role. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl hospital organization @@ -39640,7 +39381,6 @@ Ditto for its current descendants. An organization that is the bearer of a school role. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl school organization @@ -39649,10 +39389,29 @@ Ditto for its current descendants. - - A human social role that is realized by the process of formal education that the bearer undergoes. + + + + + + + + + + + + + + + + + + + + + + A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl student role @@ -39663,10 +39422,6 @@ Ditto for its current descendants. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - preschool - Key motivating use case was Synthia synthetic population data. - nursery school role @@ -39677,9 +39432,6 @@ Ditto for its current descendants. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - primarySchool - Key motivating use case was Synthia synthetic population data. primary school role @@ -39692,7 +39444,6 @@ Ditto for its current descendants. A material entity that is a human made strcuture with firm connection between its foundation and the ground. Mathias Brochhausen http://de.wikipedia.org/wiki/Bauwerk - http://purl.obolibrary.org/obo/omrse.owl "Building" is a subclass of this. This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". architectural structure @@ -39703,36 +39454,77 @@ Ditto for its current descendants. + + + + + + + + + + + + + + + + + + An architectural structure that bears some function. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl facility - - - - - - - - A facility that is run by a hospital organization and is the bearer of a hospital function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - HealthcareFacility - hospital facility - + + + + + + + + + 09/09/2017 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - SchoolFacility school facility @@ -39743,97 +39535,102 @@ Ditto for its current descendants. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - secondarySchool - Key motivating use case was Synthia synthetic population data. secondary school role - + - - - A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A human social role that is created by a deontic declaration performed by an organization. Amanda Hicks - https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household - http://purl.obolibrary.org/obo/omrse.owl - houses - Housing units are individuated by their residence functions. - housing unit + human organizational role + human role within an organization - - - - - A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function. - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Household - household - - - + - - - - - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace - workplace facility + + + + + + + + + + + + + + + + + + + + An information content entity that is about human travel. + https://github.com/ufbmi/OMRSE/issues/79 + Jie Zheng + Amanda Hicks + human traveling information - + - + + + + + + + + + + + + - a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace function - - - - - - - - - A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. - http://purl.obolibrary.org/obo/omrse.owl - race - racial identity datum - - - - - - - - - A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population. - http://purl.obolibrary.org/obo/omrse.owl - health care facility - - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - Amanda Hicks - An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method. - identity datum + + + + + + + health care function @@ -39841,10 +39638,15 @@ Ditto for its current descendants. - - A role inhering in an entity realized by social interactions in human society. + + + + + + + + A role that inheres in some entity that is realized in a social act. Matthew Diller - http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes @@ -40031,20 +39833,6 @@ Ditto for its current descendants. - - - - - - - - quality - - pressure - - - - @@ -40190,7 +39978,6 @@ Ditto for its current descendants. - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -41678,15 +41465,15 @@ This interpretation is *not* the same as an at-all-times relation - - - + + + @@ -42365,9 +42152,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42376,9 +42163,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42410,9 +42197,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42421,9 +42208,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42455,9 +42242,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42466,9 +42253,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42500,9 +42287,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42511,9 +42298,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42545,9 +42332,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42556,9 +42343,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -42590,7 +42377,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42601,7 +42388,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42618,7 +42405,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42628,7 +42415,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42646,7 +42433,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42657,7 +42444,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42674,7 +42461,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42684,7 +42471,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42701,7 +42488,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42712,7 +42499,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -42745,9 +42532,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42756,9 +42543,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42789,9 +42576,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42800,9 +42587,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42833,9 +42620,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42844,9 +42631,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42877,9 +42664,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42888,9 +42675,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -42922,8 +42709,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -42933,8 +42720,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 7e29de1..38d06a4 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -22,6 +22,7 @@ These are the current imports in APOLLO_SV | mf | http://purl.obolibrary.org/obo/mf.owl | slme | | go | http://purl.obolibrary.org/obo/go.owl | slme | | iao | http://purl.obolibrary.org/obo/iao.owl | mirror | +| omrse | http://purl.obolibrary.org/obo/omrse.owl | slme | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index e5ae862..3ef41b5 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -16,7 +16,7 @@ # 3. [Update repo to latest ODK](update_repo) # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 15f7592d9de34fe046ce12ec9f83ca39edbde7b087bef60e9c64a022551c8f57 +CONFIG_HASH= 4c4d6cc789d818fbe915ac259c1dd0e97c415ffd56c74ba1d7866e6691c26c0b # ---------------------------------------- @@ -165,7 +165,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro geo ido mf go iao +IMPORTS = ro geo ido mf go iao omrse IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -431,6 +431,14 @@ $(IMPORTDIR)/iao_import.owl: $(MIRRORDIR)/iao.owl $(IMPORTDIR)/iao_terms_combine if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi +## Module for ontology: omrse + +$(IMPORTDIR)/omrse_import.owl: $(MIRRORDIR)/omrse.owl $(IMPORTDIR)/omrse_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/omrse_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --method BOT \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi + .PHONY: refresh-imports refresh-imports: @@ -510,6 +518,14 @@ mirror-iao: | $(TMPDIR) $(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl +## ONTOLOGY: omrse +.PHONY: mirror-omrse +.PRECIOUS: $(MIRRORDIR)/omrse.owl +mirror-omrse: | $(TMPDIR) + curl -L $(OBOBASE)/omrse.owl --create-dirs -o $(TMPDIR)/omrse-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/omrse-download.owl -o $(TMPDIR)/$@.owl + + $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi diff --git a/src/ontology/apollo_sv-edit.owl b/src/ontology/apollo_sv-edit.owl index 79f6d20..dd69002 100644 --- a/src/ontology/apollo_sv-edit.owl +++ b/src/ontology/apollo_sv-edit.owl @@ -27,10 +27,11 @@ + - + Amanda Hicks John Levander Josh Hanna @@ -39,13 +40,13 @@ Shawn T. Brown William R. Hogan Mathias Brochhausen - Apollo Structured Vocabulary (Apollo-SV) + https://orcid.org/0000-0002-9881-1017 An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. https://creativecommons.org/licenses/by/4.0/ + Apollo Structured Vocabulary (Apollo-SV) C87985BA-6A8A-483A-A6B6-63975101F672 082D5D78-D916-457E-B4FD-365F86F45B30 When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI). - 2023-01-10 @@ -178,6 +179,7 @@ For the 1982-10-17 date, we suggest the dc:created annotation. + @@ -1037,6 +1039,7 @@ For example, the disposition of a piece of glass to bend light and the lattice s + @@ -1101,28 +1104,6 @@ For example, the disposition of a piece of glass to bend light and the lattice s http://purl.obolibrary.org/obo/omrse.owl is owned by - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - is enrolled in school - - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - is admitted to hospital - - - @@ -1550,6 +1531,7 @@ For example, the disposition of a piece of glass to bend light and the lattice s + @@ -24729,541 +24712,6 @@ See vaccination and antiviral treatment. url unique resource locator - - - - - - - - - - - - - - A social role inhering in a human being. - Mathias Brochhausen - - William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl - human social role - - - - - - - - - A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Gender_role - http://purl.obolibrary.org/obo/omrse.owl - sex - gender role - - - - - - - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question. - Mathias Brochhausen - male gender - http://purl.obolibrary.org/obo/omrse.owl - male gender role - - - - - - - - - A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question. - Mathias Brochhausen - female gender - http://purl.obolibrary.org/obo/omrse.owl - female gender role - - - - - - - - - A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis. - William R. Hogan - health care role - http://purl.obolibrary.org/obo/omrse.owl - Mathias Brochhausen - human health care role - - - - - - - - - A human health care role that inheres in an organism [human?] as the recipient of a health care service. - A role borne by an organism being as the recipient of a health care service. - Amanda Hicks - Mathias Brochhausen - patient - http://en.wikipedia.org/wiki/Patient - http://purl.obolibrary.org/obo/omrse.owl - patient role - - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). - health care provider organization role - - - - - - - - - - - - - - - - - - - - - - - - - An object aggregate of organisms. - This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species. - Any arbitrary collection of organisms. They need not be of the same taxonomic class. - collection of organisms - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - An object aggregate all of whose components are human beings. - collection of humans - - - - - - - - - A role in human social processes that inheres in an organization. - William R. Hogan - http://purl.obolibrary.org/obo/omrse.owl - Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. - -Ditto for its current descendants. - organization social role - - - - - - - - - - - - - - - A role in human social processes that inheres in an organism. - William R. Hogan -Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. - -Ditto for its current descendants. - Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. - Previous definition: A role in human social processes played by an organism. - organism social role - - - - - - - - - An organization social role that is realized by a health care process. - http://purl.obolibrary.org/obo/omrse.owl - Previous definition: An organization social role played by an organization in health care processes. - organization health care role - - - - - - - - - - - - - - - - - - - - - - - - An aggregate of organizations that have some feature in common, but is not itself an organization. - William R. Hogan - It is often convenient to group organizations together that otherwise might not even interact with one another. - aggregate of organizations - - - - - - - - - A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital function - - - - - - - - - A function inhering in a facility that manifests by the facility participating in providing formal education to a student population. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - school function - - - - - - - - - A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital role - - - - - - - - - An organization social role that inheres in an organization and is realized by providing formal education to students. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - school role - - - - - - - - - - - - - - - - - - - - An organization that is the bearer of a hospital role. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - hospital organization - - - - - - - - - - - - - - - - - - - - An organization that is the bearer of a school role. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - school organization - - - - - - - - - A human social role that is realized by the process of formal education that the bearer undergoes. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - student role - - - - - - - - - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - preschool - Key motivating use case was Synthia synthetic population data. - - nursery school role - - - - - - - - - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - primarySchool - Key motivating use case was Synthia synthetic population data. - primary school role - - - - - - - - - A material entity that is a human made strcuture with firm connection between its foundation and the ground. - Mathias Brochhausen - http://de.wikipedia.org/wiki/Bauwerk - http://purl.obolibrary.org/obo/omrse.owl - "Building" is a subclass of this. - This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". - architectural structure - - - - - - - - - An architectural structure that bears some function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - facility - - - - - - - - - A facility that is run by a hospital organization and is the bearer of a hospital function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - HealthcareFacility - hospital facility - - - - - - - - - A facility that is run by a school organization and is the bearer of a school function. - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - SchoolFacility - school facility - - - - - - - - - Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl - secondarySchool - Key motivating use case was Synthia synthetic population data. - secondary school role - - - - - - - - - A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function. - Amanda Hicks - https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household - http://purl.obolibrary.org/obo/omrse.owl - houses - Housing units are individuated by their residence functions. - housing unit - - - - - - - - - A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function. - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - Household - household - - - - - - - - - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace - workplace facility - - - - - - - - - a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out - Amanda Hicks - http://purl.obolibrary.org/obo/omrse.owl - workplace function - - - - - - - - - A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. - http://purl.obolibrary.org/obo/omrse.owl - race - racial identity datum - - - - - - - - - A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population. - http://purl.obolibrary.org/obo/omrse.owl - health care facility - - - - - - - - - http://purl.obolibrary.org/obo/omrse.owl - Amanda Hicks - An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method. - identity datum - - - - - - - - - A role inhering in an entity realized by social interactions in human society. - Matthew Diller - http://purl.obolibrary.org/obo/omrse/releases/2022-12-21/omrse.owl - Mathias Brochhausen - Previous definition: A role played by an entity in human social processes. - role in human social processes - - - @@ -26265,5 +25713,5 @@ np.average(range(1,11), weights=range(10,0,-1)) - + diff --git a/src/ontology/apollo_sv-odk.yaml b/src/ontology/apollo_sv-odk.yaml index 858b836..e02bdb3 100644 --- a/src/ontology/apollo_sv-odk.yaml +++ b/src/ontology/apollo_sv-odk.yaml @@ -37,6 +37,9 @@ import_group: slme_individuals: exclude - id: iao module_type: mirror + - id: omrse + module_type: slme + slme_individuals: exclude use_custom_import_module: TRUE robot_java_args: '-Xmx8G' custom_makefile_header: | diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index dc12057..47a4c3c 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -21,5 +21,7 @@ + + diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl index 43446e9..0af915a 100644 --- a/src/ontology/imports/geo_import.owl +++ b/src/ontology/imports/geo_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-08-17") + +Annotation(owl:versionInfo "2024-12-24") Declaration(Class()) Declaration(Class()) @@ -2700,7 +2700,7 @@ AnnotationAssertion(rdfs:label "g EquivalentClasses( ObjectIntersectionOf(ObjectComplementOf() ObjectAllValuesFrom( ) ObjectMinCardinality(2 ))) SubClassOf( ) -# Class: (aggregate of dependencies) +# Class: (group of dependencies) AnnotationAssertion( "An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common."@en) AnnotationAssertion( "Amanda Hicks"@en) diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl index ce8f7bd..ca0b9bd 100644 --- a/src/ontology/imports/go_import.owl +++ b/src/ontology/imports/go_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-08-17") + +Annotation( ) +Annotation(owl:versionInfo "2024-12-24") Declaration(Class()) Declaration(Class()) @@ -40,7 +40,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -310,7 +309,6 @@ AnnotationAssertion(rdfs:label "biol # Class: (viral process) AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") Annotation( "GOC:mah") "A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.") -AnnotationAssertion( ) AnnotationAssertion( "GO:0022415") AnnotationAssertion( "Wikipedia:Viral_life_cycle") AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") "virus process") @@ -408,10 +406,6 @@ SubClassOf( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "jl") AnnotationAssertion( "2012-09-19T16:07:47Z") AnnotationAssertion( "GO:0044707") @@ -505,7 +499,6 @@ SubClassOf( "GOC:cc") "Any process evolved to enable an interaction with an organism of a different species.") AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) -AnnotationAssertion( ) AnnotationAssertion( "interaction with another species") AnnotationAssertion( "interspecies interaction") AnnotationAssertion( "interspecies interaction between organisms") diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index b6fafce..3616221 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-08-17") +Annotation(owl:versionInfo "2024-12-24") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index 2497710..ca2ca7e 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-08-17") +Annotation(owl:versionInfo "2024-12-24") Declaration(Class()) Declaration(Class()) @@ -172,7 +172,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) diff --git a/src/ontology/imports/mf_import.owl b/src/ontology/imports/mf_import.owl index c2be049..8aab4bf 100644 --- a/src/ontology/imports/mf_import.owl +++ b/src/ontology/imports/mf_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-08-17") +Annotation(owl:versionInfo "2024-12-24") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/omrse_import.owl b/src/ontology/imports/omrse_import.owl new file mode 100644 index 0000000..c63dc8f --- /dev/null +++ b/src/ontology/imports/omrse_import.owl @@ -0,0 +1,4371 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-12-24") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) 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+Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(DataProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) 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+Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(rdfs:comment)) +Declaration(AnnotationProperty(rdfs:label)) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (BFO OWL specification label) + +AnnotationAssertion( "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en) +AnnotationAssertion( "Really of interest to developers only"@en) +AnnotationAssertion(rdfs:label "BFO OWL specification label"@en) + +# Annotation Property: (BFO CLIF specification label) + +AnnotationAssertion( "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en) +AnnotationAssertion( "Person:Alan Ruttenberg") +AnnotationAssertion( "Really of interest to developers only"@en) +AnnotationAssertion(rdfs:label "BFO CLIF specification label"@en) + +# Annotation Property: (editor preferred term) + +AnnotationAssertion( "editor preferred term"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "editor preferred label"@en) +AnnotationAssertion(rdfs:label "editor preferred term"@en) +AnnotationAssertion(rdfs:label "editor preferred term") + +# Annotation Property: (example of usage) + +AnnotationAssertion( "example of usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "example of usage"@en) +AnnotationAssertion(rdfs:label "example of usage") + +# Annotation Property: (has curation status) + +AnnotationAssertion( "has curation status"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "has curation status"@en) + +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "textual definition") + +# Annotation Property: (editor note) + +AnnotationAssertion( "editor note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "editor note"@en) + +# Annotation Property: (definition editor) + +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition editor"@en) +AnnotationAssertion(rdfs:label "term editor"@en) +AnnotationAssertion(rdfs:label "definition editor") + +# Annotation Property: (alternative label) + +AnnotationAssertion( "alternative label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "alternative label"@en) +AnnotationAssertion(rdfs:label "alternative term"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition source"@en) + +# Annotation Property: (has obsolescence reason) + +AnnotationAssertion( "has obsolescence reason"@en) +AnnotationAssertion( "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "has obsolescence reason"@en) + +# Annotation Property: (curator note) + +AnnotationAssertion( "curator note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "curator note"@en) + +# Annotation Property: (imported from) + +AnnotationAssertion( "imported from"@en) +AnnotationAssertion( ) +AnnotationAssertion( "For external terms/classes, the ontology from which the term was imported"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "imported from"@en) + +# Annotation Property: (expand expression to) + +AnnotationAssertion( "expand expression to"@en) +AnnotationAssertion( "ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" +"@en) +AnnotationAssertion( "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en) +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion(rdfs:label "expand expression to"@en) + +# Annotation Property: (OBO foundry unique label) + +AnnotationAssertion( "OBO foundry unique label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An alternative name for a class or property which is unique across the OBO Foundry."@en) +AnnotationAssertion( "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ."@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters"@en) +AnnotationAssertion( "PERSON:Chris Mungall"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion( "GROUP:OBO Foundry "@en) +AnnotationAssertion(rdfs:label "OBO foundry unique label"@en) + +# Annotation Property: (elucidation) + +AnnotationAssertion( "elucidation"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Barry Smith"@en) +AnnotationAssertion( "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "elucidation"@en) + +# Annotation Property: (has associated axiom(nl)) + +AnnotationAssertion( "has associated axiom(nl)"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "An axiom associated with a term expressed using natural language"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "has associated axiom(nl)"@en) + +# Annotation Property: (has associated axiom(fol)) + +AnnotationAssertion( "has associated axiom(fol)"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "An axiom expressed in first order logic using CLIF syntax"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "has associated axiom(fol)"@en) + +# Annotation Property: (term replaced by) + +AnnotationAssertion( "term replaced by"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) +AnnotationAssertion(rdfs:label "term replaced by"@en) + +# Annotation Property: (temporal interpretation) + +AnnotationAssertion( "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.") +AnnotationAssertion(rdfs:label "temporal interpretation"@en) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (is a defining property chain axiom) + +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL") +AnnotationAssertion(rdfs:label "is a defining property chain axiom") + +# Annotation Property: (is a defining property chain axiom where second argument is reflexive) + +AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.") +AnnotationAssertion(rdfs:label "is a defining property chain axiom where second argument is reflexive") + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (has broad synonym) + +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") + +# Annotation Property: (has exact synonym) + +AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") +AnnotationAssertion(rdfs:label "has exact synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") + +# Annotation Property: (has narrow synonym) + +AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") +AnnotationAssertion(rdfs:label "has narrow synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") + +# Annotation Property: (has related synonym) + +AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") +AnnotationAssertion(rdfs:label "has related synonym"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") + +# Annotation Property: rdfs:label (label) + +AnnotationAssertion(rdfs:label rdfs:label "label") + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (realized in) + +AnnotationAssertion( "realized in"@en) +AnnotationAssertion( "this disease is realized in this disease course"@en) +AnnotationAssertion( "this fragility is realized in this shattering"@en) +AnnotationAssertion( "this investigator role is realized in this investigation"@en) +AnnotationAssertion( "is realized by"@en) +AnnotationAssertion( "realized_in"@en) +AnnotationAssertion( "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realizes) + +AnnotationAssertion( "realizes"@en) +AnnotationAssertion( "this disease course realizes this disease"@en) +AnnotationAssertion( "this investigation realizes this investigator role"@en) +AnnotationAssertion( "this shattering realizes this fragility"@en) +AnnotationAssertion( "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (preceded by) + +AnnotationAssertion( "preceded by"@en) +AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) +AnnotationAssertion( "is preceded by"@en) +AnnotationAssertion( "preceded_by"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (precedes) + +AnnotationAssertion( "precedes"@en) +AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "precedes"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (occurs in) + +AnnotationAssertion( "occurs in"@en) +AnnotationAssertion( "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) +AnnotationAssertion( "occurs_in"@en) +AnnotationAssertion( "unfolds in"@en) +AnnotationAssertion( "unfolds_in"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "occurs in"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (contains process) + +AnnotationAssertion( "site of"@en) +AnnotationAssertion( "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) +AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "contains process"@en) + +# Object Property: (has measurement unit label) + +AnnotationAssertion(rdfs:label "has measurement unit label"@en) +SubObjectPropertyOf( ) +FunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (is about) + +AnnotationAssertion( "This document is about information artifacts and their representations"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A (currently) primitive relation that relates an information artifact to an entity."@en) +AnnotationAssertion( "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + +# Object Property: (denotes) + +AnnotationAssertion( "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named."@en) +AnnotationAssertion( "A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically"@en) +AnnotationAssertion( "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan"@en) +AnnotationAssertion(rdfs:comment ""@en) +AnnotationAssertion(rdfs:label "denotes"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is quality measurement of) + +AnnotationAssertion( "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q"@en) +AnnotationAssertion( "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later"@en) +AnnotationAssertion( "From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] + +This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. + +Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details. +-- +From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] + +unit of measure is a quality, e.g. the length of a ruler. + +[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] + +[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] + +a represents b means either a denotes b or a describes + +describe: +a describes b means a is about b and a allows an inference of at least one quality of b + +We have had a long discussion about denotes versus describes."@en) +AnnotationAssertion( "From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. + +a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality."@en) +AnnotationAssertion( "From the second meeting on IAO: + +An attempt at defining assay using Barry's \"reliability\" wording + +assay: +process and has_input some material entity +and has_output some information content entity +and which is such that instances of this process type reliably generate +outputs that describes the input."@en) +AnnotationAssertion( "This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. + +Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "is quality measurement of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (denoted by) + +AnnotationAssertion( "inverse of the relation 'denotes'"@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Mike Conlon"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "denoted by"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is duration of) + +AnnotationAssertion( ) +AnnotationAssertion( "relates a process to a time-measurement-datum that represents the duration of the process"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "is duration of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is quality measured as) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of the relation of is quality measurement of"@en) +AnnotationAssertion( "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "is quality measured as"@en) + +# Object Property: (has time stamp) + +AnnotationAssertion( ) +AnnotationAssertion( "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "has time stamp"@en) +SubObjectPropertyOf( ) +FunctionalObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion( "relates a time stamped measurement datum to the measurement datum that was measured"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "has measurement datum"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) + +# Object Property: (owns) + +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal."@en) +AnnotationAssertion(rdfs:label "owns"@en) +SubObjectPropertyOf( owl:topObjectProperty) +InverseObjectProperties( ) +AsymmetricObjectProperty() + +# Object Property: (is owned by) + +AnnotationAssertion( "a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b."@en) +AnnotationAssertion( "Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.") +AnnotationAssertion(rdfs:label "is owned by"@en) +AsymmetricObjectProperty() + +# Object Property: (has_specified_input) + +AnnotationAssertion( "has_specified_input"@en) +AnnotationAssertion( "has_specified_input") +AnnotationAssertion( "see is_input_of example_of_usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_input_of"@en) +AnnotationAssertion( "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Coutot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has_specified_input"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) + +# Object Property: (is_specified_input_of) + +AnnotationAssertion(rdfs:label "is_specified_input_of"@en) + +# Object Property: (has_specified_output) + +AnnotationAssertion( "has_specified_output"@en) +AnnotationAssertion( "has_specified_output") +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_output_of"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has_specified_output"@en) +EquivalentObjectProperties( ObjectInverseOf()) +SubObjectPropertyOf( ) +SubObjectPropertyOf( owl:topObjectProperty) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (is_specified_output_of) + +AnnotationAssertion( "is_specified_output_of"@en) +AnnotationAssertion( "is_specified_output_of") +AnnotationAssertion( ) +AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is_specified_output_of"@en) +AnnotationAssertion(rdfs:label "is_specified_output_of") +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (obsolete owns) + +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "obsolete owns") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) +SubObjectPropertyOf( ) + +# Object Property: (obsolete is owned by) + +AnnotationAssertion( "Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "obsolete is owned by") + +# Object Property: (is administered by) + +AnnotationAssertion(rdfs:label "is administered by"@en) +AsymmetricObjectProperty() + +# Object Property: (is enrolled in school) + +AnnotationAssertion(rdfs:label "is enrolled in school"@en) +AsymmetricObjectProperty() +ObjectPropertyDomain( ObjectSomeValuesFrom( )) +ObjectPropertyRange( ) + +# Object Property: (is admitted to hospital) + +AnnotationAssertion(rdfs:label "is admitted to hospital"@en) +SubObjectPropertyOf( owl:topObjectProperty) +ObjectPropertyDomain( ObjectSomeValuesFrom( )) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility is a characteristic of this vase"@en) +AnnotationAssertion( "this red color is a characteristic of this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") +AnnotationAssertion(rdfs:label "characteristic of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +FunctionalObjectProperty() + +# Object Property: (bearer_of) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "bearer_of"@en) +AnnotationAssertion(rdfs:label "has characteristic"@en) +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (participates in) + +AnnotationAssertion( "participates in"@en) +AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) +AnnotationAssertion( "this input material (or this output material) participates in this process"@en) +AnnotationAssertion( "this investigator participates in this investigation"@en) +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "participates_in"@en) +AnnotationAssertion(rdfs:label "participates in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has_participant) + +AnnotationAssertion( "has participant"@en) +AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) +AnnotationAssertion( "this investigation has participant this investigator"@en) +AnnotationAssertion( "this process has participant this input material (or this output material)"@en) +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) +AnnotationAssertion( "has_participant"@en) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion(rdfs:label "has participant"@en) +AnnotationAssertion(rdfs:label "has_participant") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is concretized as) + +AnnotationAssertion( "is concretized as"@en) +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion( "http://purl.obolibrary.org/obo/obi.owl") +AnnotationAssertion(rdfs:label "is concretized as"@en) +SubObjectPropertyOf( owl:topObjectProperty) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (concretizes) + +AnnotationAssertion( "concretizes"@en) +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion( "http://purl.obolibrary.org/obo/obi.owl") +AnnotationAssertion(rdfs:label "concretizes"@en) +SubObjectPropertyOf( owl:topObjectProperty) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion(rdfs:label "has quality"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion( "inverse of has disposition") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) + +# Object Property: (location of) + +AnnotationAssertion( "is location of"@en) +AnnotationAssertion( "my head is the location of my brain"@en) +AnnotationAssertion( "this cage is the location of this rat"@en) +AnnotationAssertion( "a relation between two independent continuants, the location and the target, in which the target is entirely within the location"@en) +AnnotationAssertion( "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/"@en) +AnnotationAssertion( "location_of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "location of"@en) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (located in) + +AnnotationAssertion( "located in"@en) +AnnotationAssertion( "my brain is located in my head"@en) +AnnotationAssertion( "this rat is located in this cage"@en) +AnnotationAssertion( "a relation between two independent continuants, the target and the location, in which the target is entirely within the location"@en) +AnnotationAssertion( "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus"@en) +AnnotationAssertion( "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/"@en) +AnnotationAssertion( "located_in"@en) +AnnotationAssertion( ) +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:located_in") +AnnotationAssertion(rdfs:label "located in"@en) +TransitiveObjectProperty() +ObjectPropertyDomain(Annotation( "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") ) +ObjectPropertyDomain( ObjectIntersectionOf( ObjectComplementOf())) +ObjectPropertyRange(Annotation( "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") ) +ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) + +# Object Property: (has regulatory component activity) + +AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has negative regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") +AnnotationAssertion(rdfs:label "has negative regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has positive regulatory component activity) + +AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") +AnnotationAssertion(rdfs:label "has positive regulatory component activity") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has component activity) + +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") +AnnotationAssertion(rdfs:label "has component activity") +SubObjectPropertyOf( ) + +# Object Property: (has component process) + +AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "has component process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulated by) + +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(rdfs:label "directly regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly negatively regulated by) + +AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly negatively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (directly positively regulated by) + +AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "directly positively regulated by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has effector activity) + +AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") +AnnotationAssertion(rdfs:label "has effector activity") +SubObjectPropertyOf( ) +FunctionalObjectProperty() + +# Object Property: (ends after) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) +AnnotationAssertion(rdfs:label "ends after"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately preceded by) + +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "starts_at_end_of") +AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately preceded by"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately precedes) + +AnnotationAssertion( ) +AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( "ends_at_start_of") +AnnotationAssertion( "meets") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) +AnnotationAssertion(rdfs:label "immediately precedes"@en) +SubObjectPropertyOf( ) + +# Object Property: (overlaps) + +AnnotationAssertion( ) +AnnotationAssertion( "x overlaps y if and only if there exists some z such that x has part z and z part of y") +AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "overlaps"@en) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (has component) + +AnnotationAssertion( ) +AnnotationAssertion( "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") +AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") +AnnotationAssertion( "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has component"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (regulates) + +AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "GO") +AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") +AnnotationAssertion( "regulates (processual)") +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulates) + +AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (positively regulates) + +AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (capable of) + +AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") +AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") +AnnotationAssertion( "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ") +AnnotationAssertion( ) +AnnotationAssertion( "has function realized in") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of part of) + +AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") +AnnotationAssertion( ) +AnnotationAssertion( "has function in") +AnnotationAssertion(rdfs:label "capable of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (obsolete has active participant) + +AnnotationAssertion( "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y") +AnnotationAssertion( ) +AnnotationAssertion( "has agent") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "obsolete has active participant") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) + +# Object Property: (temporally related to) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") +AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") +AnnotationAssertion(rdfs:label "temporally related to"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (starts) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of starts with") +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "Allen") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "starts"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (starts with) + +AnnotationAssertion( "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor") +AnnotationAssertion( ) +AnnotationAssertion( "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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.") +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "started by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "starts with"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (ends) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of ends with") +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ends"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (ends with) + +AnnotationAssertion( ) +AnnotationAssertion( "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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.") +AnnotationAssertion( ) +AnnotationAssertion( "Chris Mungall") +AnnotationAssertion( "finished by") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ends with"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (has start location) + +AnnotationAssertion( ) +AnnotationAssertion( "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y") +AnnotationAssertion( ) +AnnotationAssertion( "starts with process that occurs in") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has start location"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has end location) + +AnnotationAssertion( ) +AnnotationAssertion( "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y") +AnnotationAssertion( ) +AnnotationAssertion( "ends with process that occurs in") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has end location"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has input) + +AnnotationAssertion( ) +AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") +AnnotationAssertion( ) +AnnotationAssertion( "consumes") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has input"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (has output) + +AnnotationAssertion( ) +AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.") +AnnotationAssertion( ) +AnnotationAssertion( "produces") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has output"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (acts upstream of) + +AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") +AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within) + +AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") +AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") +AnnotationAssertion( "affects") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, positive effect) + +AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") +AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of, negative effect) + +AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (characteristic of part of) + +AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") +AnnotationAssertion( "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of") +AnnotationAssertion( ) +AnnotationAssertion( "inheres in part of") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "characteristic of part of"@en) +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (mereotopologically related to) + +AnnotationAssertion( "A mereological relationship or a topological relationship") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mereotopologically related to"@en) + +# Object Property: (enables) + +AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") +AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") +AnnotationAssertion( ) +AnnotationAssertion( "catalyzes") +AnnotationAssertion( "executes") +AnnotationAssertion( "has") +AnnotationAssertion( "is catalyzing") +AnnotationAssertion( "is executing") +AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enables"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (functionally related to) + +AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") +AnnotationAssertion( ) +AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") +AnnotationAssertion(rdfs:label "functionally related to"@en) + +# Object Property: (part of structure that is capable of) + +AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") +AnnotationAssertion( ) +AnnotationAssertion( "false"^^xsd:boolean) +AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) +SubObjectPropertyOf( ) + +# Object Property: (involved in) + +AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") +AnnotationAssertion( ) +AnnotationAssertion( "actively involved in") +AnnotationAssertion( "enables part of") +AnnotationAssertion(rdfs:label "involved in"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (enabled by) + +AnnotationAssertion( "inverse of enables") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (regulated by) + +AnnotationAssertion( "inverse of regulates") +AnnotationAssertion( ) +AnnotationAssertion( "regulated by (processual)") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulated by"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (negatively regulated by) + +AnnotationAssertion( "inverse of negatively regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (positively regulated by) + +AnnotationAssertion( "inverse of positively regulates") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulated by"@en) +SubObjectPropertyOf( ) + +# Object Property: (member of) + +AnnotationAssertion( "An organism that is a member of a population of organisms") +AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") +AnnotationAssertion( "is member of") +AnnotationAssertion( "member part of") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "member of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has member) + +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has member"@en) +SubObjectPropertyOf( ) +IrreflexiveObjectProperty() + +# Object Property: (input of) + +AnnotationAssertion( "inverse of has input") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "input of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (output of) + +AnnotationAssertion( "inverse of has output") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "output of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( "inverse of upstream of") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (immediately causally downstream of) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (indirectly positively regulates) + +AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly activates") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (indirectly negatively regulates) + +AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "indirectly inhibits") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (causally related to) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") +AnnotationAssertion( "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types.") +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causally related to"@en) + +# Object Property: (causally upstream of) + +AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (immediately causally upstream of) + +AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within) + +AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") +AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") +AnnotationAssertion( ) +AnnotationAssertion( "influences (processual)") +AnnotationAssertion( "affects") +AnnotationAssertion(rdfs:label "causally upstream of or within") +SubObjectPropertyOf( ) +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (causally downstream of or within) + +AnnotationAssertion( "inverse of causally upstream of or within") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causally downstream of or within") +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (involved in regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (involved in positive regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in positive regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in negative regulation of) + +AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "involved in negative regulation of") +SubObjectPropertyOf( ) + +# Object Property: (involved in or involved in regulation of) + +AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") +AnnotationAssertion( "OWL does not allow defining object properties via a Union") +AnnotationAssertion( ) +AnnotationAssertion( "involved in or reguates") +AnnotationAssertion(rdfs:label "involved in or involved in regulation of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (is active in) + +AnnotationAssertion( "A protein that enables activity in a cytosol.") +AnnotationAssertion(Annotation( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") +AnnotationAssertion( ) +AnnotationAssertion( "executes activity in") +AnnotationAssertion( "enables activity in") +AnnotationAssertion(rdfs:comment "") +AnnotationAssertion(rdfs:label "is active in") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Is_active_in"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (interacts with) + +AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) +AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion( ) +AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") +AnnotationAssertion( "in pairwise interaction with") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interacts with") +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) +SymmetricObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (molecularly interacts with) + +AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") +AnnotationAssertion( ) +AnnotationAssertion( "binds") +AnnotationAssertion( "molecularly binds with") +AnnotationAssertion(rdfs:label "molecularly interacts with") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) +SubObjectPropertyOf( ) +SymmetricObjectProperty() + +# Object Property: (phosphorylates) + +AnnotationAssertion( "Axiomatization to GO to be added later") +AnnotationAssertion( ) +AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") +AnnotationAssertion(rdfs:label "phosphorylates") +SubObjectPropertyOf( ) + +# Object Property: (directly regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "molecularly controls") +AnnotationAssertion(rdfs:label "directly regulates activity of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly negatively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly inhibits") +AnnotationAssertion( "molecularly decreases activity of") +AnnotationAssertion(rdfs:label "directly negatively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly positively regulates activity of) + +AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly activates") +AnnotationAssertion( "molecularly increases activity of") +AnnotationAssertion(rdfs:label "directly positively regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (helper property (not for use in curation)) + +AnnotationAssertion( ) +AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") +AnnotationAssertion(rdfs:label "helper property (not for use in curation)") + +# Object Property: (has part that occurs in) + +AnnotationAssertion( "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part that occurs in") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is kinase activity) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "is kinase activity") +SubObjectPropertyOf( ) + +# Object Property: (causal agent in process) + +AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal agent in process") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (causal relation between processes) + +AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between processes") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (depends on) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "depends on") +AnnotationAssertion(rdfs:seeAlso ) + +# Object Property: (causal relation between entities) + +AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion(rdfs:label "causal relation between entities") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (causally influenced by) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influenced by (entity-centric)") +AnnotationAssertion(rdfs:label "causally influenced by") +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "interaction relation helper property") +AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (molecular interaction relation helper property) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "molecular interaction relation helper property") +SubObjectPropertyOf( ) + +# Object Property: (causally influences) + +AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "causally influences (entity-centric)") +AnnotationAssertion(rdfs:label "causally influences") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (directly regulates) + +AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "directly regulates (processual)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly regulates") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has part structure that is capable of) + +AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") +AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part structure that is capable of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causal relation between material entity and a process) + +AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") +AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "causal relation between material entity and a process") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (capable of regulating) + +AnnotationAssertion( "pyrethroid -> growth") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of negatively regulating) + +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of negatively regulating") +SubObjectPropertyOf( ) + +# Object Property: (capable of positively regulating) + +AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") +AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "capable of positively regulating") +SubObjectPropertyOf( ) + +# Object Property: (process has causal agent) + +AnnotationAssertion( "Inverse of 'causal agent in process'") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "process has causal agent") +SubObjectPropertyOf( ) + +# Object Property: (directly positively regulates) + +AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly positively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly positively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (directly negatively regulates) + +AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "directly negatively regulates (process to process)") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "directly negatively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (produces) + +AnnotationAssertion( ) +AnnotationAssertion( "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") +AnnotationAssertion(rdfs:label "produces"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (produced by) + +AnnotationAssertion( ) +AnnotationAssertion( "a produced_by b iff some process that occurs_in b has_output a.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "produced by"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realized in response to stimulus) + +AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") +AnnotationAssertion( ) +AnnotationAssertion( "2017-12-26T19:45:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "realized in response to stimulus") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (enables subfunction) + +AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "enables subfunction") +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, positive effect) + +AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (acts upstream of, negative effect) + +AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "acts upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, negative effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) +SubObjectPropertyOf( ) + +# Object Property: (causally upstream of or within, positive effect) + +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) +SubObjectPropertyOf( ) + +# Object Property: (realized in response to) + +AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") +AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") +AnnotationAssertion( "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") +AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "triggered by process") +AnnotationAssertion(rdfs:label "realized in response to"@en) +AnnotationAssertion(rdfs:seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (generically depends on) + +AnnotationAssertion( "Genetic information generically depend on molecules of DNA.") +AnnotationAssertion( "The novel *War and Peace* generically depends on this copy of the novel.") +AnnotationAssertion( "The pattern shared by chess boards generically depends on any chess board.") +AnnotationAssertion( "The score of a symphony g-depends on a copy of the score.") +AnnotationAssertion( "This pdf file generically depends on this server.") +AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion( "g-depends on") +AnnotationAssertion(rdfs:label "generically depends on") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is carrier of) + +AnnotationAssertion( "Molecules of DNA are carriers of genetic information.") +AnnotationAssertion( "This copy of *War and Peace* is carrier of the novel written by Tolstoy.") +AnnotationAssertion( "This hard drive is carrier of these data items.") +AnnotationAssertion( "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion(rdfs:label "is carrier of"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (regulates activity of) + +AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates activity of") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (indirectly causally upstream of) + +AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") +AnnotationAssertion( ) +AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) +SubObjectPropertyOf( ) + +# Object Property: (indirectly regulates) + +AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") +AnnotationAssertion( ) +AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "indirectly regulates"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (device utilizes material) + +AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") +AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") +AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") +AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) +AnnotationAssertion( "utilizes") +AnnotationAssertion(rdfs:label "device utilizes material"@en) + +# Object Property: (regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "regulates characteristic") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (positively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "positively regulates characteristic") +SubObjectPropertyOf( ) + +# Object Property: (negatively regulates characteristic) + +AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "negatively regulates characteristic") +SubObjectPropertyOf( ) + + +############################ +# Data Properties +############################ + +# Data Property: (has measurement value) + +AnnotationAssertion(rdfs:label "has measurement value"@en) +FunctionalDataProperty() +DataPropertyDomain( ) +DataPropertyRange( xsd:double) + + + +############################ +# Classes +############################ + +# Class: (software development) + +AnnotationAssertion( "A planned process that has specified output a software product and that involves the creation of source code."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion( "http://en.wikipedia.org/wiki/Software_development") +AnnotationAssertion( "A planned process resulting in a software product involving the creation of source code."@en) +AnnotationAssertion(rdfs:label "software development"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) + +# Class: (count) + +AnnotationAssertion( "A measurement datum that is the output of counting."@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "A measurement datum that is the output of counting."@en) +AnnotationAssertion(rdfs:label "count"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (counting) + +AnnotationAssertion( "The planned process of finding the number of elements in a finite set of objects."@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Counting") +AnnotationAssertion( "The planned process of finding the number of elements in a finite set of objects."@en) +AnnotationAssertion(rdfs:label "counting"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (geographical movement of organism) + +AnnotationAssertion( "A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification."@en) +AnnotationAssertion( "Matthew Diller") +AnnotationAssertion( "William R. Hogan") +AnnotationAssertion( "A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification."@en) +AnnotationAssertion(rdfs:label "geographical movement of organism"@en) +SubClassOf( ) + +# Class: (source code repository) + +AnnotationAssertion( "software source code version control repository"@en) +AnnotationAssertion( "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc."@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion(rdfs:comment "Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based"@en) +AnnotationAssertion(rdfs:label "source code repository"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) + +# Class: (compiling software) + +AnnotationAssertion( "process of compiling software"@en) +AnnotationAssertion( "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions."@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion(rdfs:comment "It's compiling \"software\" (scare quotes) and not \"source code\" because you can compile Java bytecode to machine code, and Java bytecode is not technically \"source code\". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.)."@en) +AnnotationAssertion(rdfs:comment "Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code."@en) +AnnotationAssertion(rdfs:label "compiling software"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectUnionOf( )) ObjectSomeValuesFrom( ))) + +# Class: (human travel) + +AnnotationAssertion( "A geographical migration of an organism belonging to the species Homo sapiens."@en) +AnnotationAssertion( "Matthew Diller") +AnnotationAssertion( "William R. Hogan") +AnnotationAssertion(rdfs:label "human travel"@en) +SubClassOf( ) + +# Class: (dataset creating) + +AnnotationAssertion( "creating a data set"@en) +AnnotationAssertion( "A planned process that has a data set as its specified output."@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion( "data set creation"@en) +AnnotationAssertion( "dataset creation"@en) +AnnotationAssertion(rdfs:label "dataset creating"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (entity) + +AnnotationAssertion( "entity") +AnnotationAssertion( "Entity") +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") Annotation(rdfs:seeAlso ) "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) +AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "continuant") +AnnotationAssertion( "Continuant") +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (occurrent) + +AnnotationAssertion( "occurrent") +AnnotationAssertion( "Occurrent") +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) +AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) +AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "ic") +AnnotationAssertion( "IndependentContinuant") +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) +AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") +AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (spatial region) + +AnnotationAssertion( "s-region") +AnnotationAssertion( "SpatialRegion") +AnnotationAssertion( "BFO 2 Reference: Spatial regions do not participate in processes."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional."@en) +AnnotationAssertion(Annotation( ) "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])"@en) +AnnotationAssertion(Annotation( ) "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "spatial region"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (temporal region) + +AnnotationAssertion( "t-region") +AnnotationAssertion( "TemporalRegion") +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional"@en) +AnnotationAssertion(Annotation( ) "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])"@en) +AnnotationAssertion(Annotation( ) "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])"@en) +AnnotationAssertion(Annotation( ) "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "temporal region"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (process) + +AnnotationAssertion( "process") +AnnotationAssertion( "Process") +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion( "disposition") +AnnotationAssertion( "Disposition") +AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) +AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) +AnnotationAssertion(Annotation( ) "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"@en) +AnnotationAssertion(Annotation( ) "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "realizable") +AnnotationAssertion( "RealizableEntity") +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizable"@en) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion( "quality") +AnnotationAssertion( "Quality") +AnnotationAssertion( "the ambient temperature of this portion of air"@en) +AnnotationAssertion( "the color of a tomato"@en) +AnnotationAssertion( "the length of the circumference of your waist"@en) +AnnotationAssertion( "the mass of this piece of gold."@en) +AnnotationAssertion( "the shape of your nose"@en) +AnnotationAssertion( "the shape of your nostril"@en) +AnnotationAssertion(Annotation( ) "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"@en) +AnnotationAssertion(Annotation( ) "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (characteristic) + +AnnotationAssertion( "sdc") +AnnotationAssertion( "SpecificallyDependentContinuant") +AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion( "the disposition of this fish to decay"@en) +AnnotationAssertion( "the function of this heart: to pump blood"@en) +AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the shape of this hole."@en) +AnnotationAssertion( "the smell of this portion of mozzarella"@en) +AnnotationAssertion( "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) +AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "characteristic"@en) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/OBOFoundry/COB/issues/65") +AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "role") +AnnotationAssertion( "Role") +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (fiat object part) + +AnnotationAssertion( "fiat-object-part") +AnnotationAssertion( "FiatObjectPart") +AnnotationAssertion( "or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29"@en) +AnnotationAssertion( "the FMA:regional parts of an intact human body."@en) +AnnotationAssertion( "the Western hemisphere of the Earth"@en) +AnnotationAssertion( "the division of the brain into regions"@en) +AnnotationAssertion( "the division of the planet into hemispheres"@en) +AnnotationAssertion( "the dorsal and ventral surfaces of the body"@en) +AnnotationAssertion( "the upper and lower lobes of the left lung"@en) +AnnotationAssertion( "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions"@en) +AnnotationAssertion(Annotation( ) "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "fiat object part"@en) +SubClassOf( ) + +# Class: (object aggregate) + +AnnotationAssertion( "object-aggregate") +AnnotationAssertion( "ObjectAggregate") +AnnotationAssertion( "a collection of cells in a blood biobank."@en) +AnnotationAssertion( "a swarm of bees is an aggregate of members who are linked together through natural bonds"@en) +AnnotationAssertion( "a symphony orchestra"@en) +AnnotationAssertion( "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)"@en) +AnnotationAssertion( "defined by fiat: the aggregate of members of an organization"@en) +AnnotationAssertion( "defined through physical attachment: the aggregate of atoms in a lump of granite"@en) +AnnotationAssertion( "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container"@en) +AnnotationAssertion( "defined via attributive delimitations such as: the patients in this hospital"@en) +AnnotationAssertion( "the aggregate of bearings in a constant velocity axle joint"@en) +AnnotationAssertion( "the aggregate of blood cells in your body"@en) +AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) +AnnotationAssertion( "the restaurants in Palo Alto"@en) +AnnotationAssertion( "your collection of Meissen ceramic plates."@en) +AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.") +AnnotationAssertion(Annotation( ) "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "object aggregate"@en) +SubClassOf( ) + +# Class: (site) + +AnnotationAssertion( "site") +AnnotationAssertion( "Site") +AnnotationAssertion( "Manhattan Canyon)"@en) +AnnotationAssertion( "a hole in the interior of a portion of cheese"@en) +AnnotationAssertion( "a rabbit hole"@en) +AnnotationAssertion( "an air traffic control region defined in the airspace above an airport"@en) +AnnotationAssertion( "the Grand Canyon"@en) +AnnotationAssertion( "the Piazza San Marco"@en) +AnnotationAssertion( "the cockpit of an aircraft"@en) +AnnotationAssertion( "the hold of a ship"@en) +AnnotationAssertion( "the interior of a kangaroo pouch"@en) +AnnotationAssertion( "the interior of the trunk of your car"@en) +AnnotationAssertion( "the interior of your bedroom"@en) +AnnotationAssertion( "the interior of your office"@en) +AnnotationAssertion( "the interior of your refrigerator"@en) +AnnotationAssertion( "the lumen of your gut"@en) +AnnotationAssertion( "your left nostril (a fiat part – the opening – of your left nasal cavity)"@en) +AnnotationAssertion(Annotation( ) "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "site"@en) +SubClassOf( ) + +# Class: (object) + +AnnotationAssertion( "object") +AnnotationAssertion( "Object") +AnnotationAssertion( "atom"@en) +AnnotationAssertion( "cell"@en) +AnnotationAssertion( "cells and organisms"@en) +AnnotationAssertion( "engineered artifacts"@en) +AnnotationAssertion( "grain of sand"@en) +AnnotationAssertion( "molecule"@en) +AnnotationAssertion( "organelle"@en) +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "planet"@en) +AnnotationAssertion( "solid portions of matter"@en) +AnnotationAssertion( "star"@en) +AnnotationAssertion( "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting."@en) +AnnotationAssertion( "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)."@en) +AnnotationAssertion( "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47"@en) +AnnotationAssertion( "BFO 2 Reference: an object is a maximal causally unified material entity"@en) +AnnotationAssertion( "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74"@en) +AnnotationAssertion(Annotation( ) "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "object"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "gdc") +AnnotationAssertion( "GenericallyDependentContinuant") +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion( "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) +AnnotationAssertion(Annotation( ) "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(Annotation( ) "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:comment "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (function) + +AnnotationAssertion( "function") +AnnotationAssertion( "Function") +AnnotationAssertion( "the function of a hammer to drive in nails"@en) +AnnotationAssertion( "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) +AnnotationAssertion( "the function of amylase in saliva to break down starch into sugar"@en) +AnnotationAssertion( "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) +AnnotationAssertion(Annotation( ) "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) + +# Class: (one-dimensional temporal region) + +AnnotationAssertion( "1d-t-region") +AnnotationAssertion( "OneDimensionalTemporalRegion") +AnnotationAssertion( "the temporal region during which a process occurs."@en) +AnnotationAssertion( "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)."@en) +AnnotationAssertion(Annotation( ) "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "one-dimensional temporal region"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "material") +AnnotationAssertion( "MaterialEntity") +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) +AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (immaterial entity) + +AnnotationAssertion( "immaterial") +AnnotationAssertion( "ImmaterialEntity") +AnnotationAssertion( "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "immaterial entity"@en) +SubClassOf( ) + +# Class: (process profile) + +AnnotationAssertion( "process-profile") +AnnotationAssertion( "ProcessProfile") +AnnotationAssertion( "On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels"@en) +AnnotationAssertion( "One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance."@en) +AnnotationAssertion( "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on."@en) +AnnotationAssertion(Annotation( ) "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])"@en) +AnnotationAssertion(Annotation( ) "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] ") +AnnotationAssertion(Annotation( ) "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process profile"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (history) + +AnnotationAssertion( "history") +AnnotationAssertion( "History") +AnnotationAssertion(Annotation( ) "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "history"@en) +SubClassOf( ) + +# Class: (molecular_function) + +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") +AnnotationAssertion( "molecular function") +AnnotationAssertion( "GO:0003674") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:comment "This is the same as GO molecular function") +AnnotationAssertion(rdfs:label "gene product or complex activity"@en) +AnnotationAssertion(rdfs:label "molecular_function") +SubClassOf( ) +DisjointClasses( ) + +# Class: (behavior) + +AnnotationAssertion(Annotation( "GOC:ems") Annotation( "GOC:jl") Annotation( "ISBN:0395448956") Annotation( "PMID:20160973") "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.") +AnnotationAssertion( "Wikipedia:Behavior") +AnnotationAssertion(rdfs:comment "1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. +2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).") +AnnotationAssertion(rdfs:label "behavior") +SubClassOf( ) + +# Class: (biological_process) + +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T15:05:24Z") +AnnotationAssertion( "Wikipedia:Biological_process") +AnnotationAssertion( "biological process") +AnnotationAssertion( "physiological process") +AnnotationAssertion( "single organism process") +AnnotationAssertion( "single-organism process") +AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:comment "A biological process is an evolved process") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "biological process"@en) +AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) +DisjointClasses( ) + +# Class: (kinase activity) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") +AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") +AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") +AnnotationAssertion( "phosphokinase activity") +AnnotationAssertion( "GO:0016301") +AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") +AnnotationAssertion(rdfs:label "kinase activity") +SubClassOf( ) +SubClassOf( ObjectHasSelf()) + +# Class: (conditional specification) + +AnnotationAssertion( "conditional specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that specifies what should happen if the trigger condition is fulfilled."@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion( "OBI_0000349"@en) +AnnotationAssertion(rdfs:label "conditional specification"@en) +SubClassOf( ) + +# Class: (measurement unit label) + +AnnotationAssertion( "measurement unit label"@en) +AnnotationAssertion( "Examples of measurement unit labels are liters, inches, weight per volume."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en) +AnnotationAssertion( "2009-03-16: provenance: a term measurement unit was +proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and +Cristian Cocos, and subsequently moved to IAO where the objective for +which the original term was defined was satisfied with the definition +of this, different, term."@en) +AnnotationAssertion( "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "measurement unit label"@en) +SubClassOf( ) + +# Class: (objective specification) + +AnnotationAssertion( "objective specification"@en) +AnnotationAssertion( "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en) +AnnotationAssertion( "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\""@en) +AnnotationAssertion( "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that."@en) +AnnotationAssertion( "Answers the question, why did you do this experiment?"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Barry Smith"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Jennifer Fostel"@en) +AnnotationAssertion( "goal specification"@en) +AnnotationAssertion( "OBI Plan and Planned Process/Roles Branch"@en) +AnnotationAssertion( "OBI_0000217"@en) +AnnotationAssertion(rdfs:label "objective specification"@en) +SubClassOf( ) + +# Class: (action specification) + +AnnotationAssertion( "Pour the contents of flask 1 into flask 2"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an action the bearer will take."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion(rdfs:label "action specification"@en) +SubClassOf( ) + +# Class: (datum label) + +AnnotationAssertion( "datum label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label"@en) +AnnotationAssertion( "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion( "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. +") +AnnotationAssertion(rdfs:label "datum label"@en) +SubClassOf( ) + +# Class: (software) + +AnnotationAssertion( "software"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit."@en) +AnnotationAssertion( "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "GROUP: OBI"@en) +AnnotationAssertion(rdfs:label "software"@en) +SubClassOf( ) + +# Class: (information carrier) + +AnnotationAssertion( "information carrier"@en) +AnnotationAssertion( "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A quality of an information bearer that imparts the information content"@en) +AnnotationAssertion( "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'."@en) +AnnotationAssertion( "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "information carrier"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) +AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) +AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "data"@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (symbol) + +AnnotationAssertion( "symbol"@en) +AnnotationAssertion( "a serial number such as \"12324X\""@en) +AnnotationAssertion( "a stop sign"@en) +AnnotationAssertion( "a written proper name such as \"OBI\""@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity."@en) +AnnotationAssertion( "20091104, MC: this needs work and will most probably change"@en) +AnnotationAssertion( "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)."@en) +AnnotationAssertion( "PERSON: James A. Overton"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "based on Oxford English Dictionary"@en) +AnnotationAssertion(rdfs:label "symbol"@en) +SubClassOf( ) + +# Class: (numeral) + +AnnotationAssertion( "numeral"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A symbol that denotes a number."@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion(rdfs:label "numeral"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)."@en) +AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000142"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (scalar measurement datum) + +AnnotationAssertion( "10 feet. 3 ml."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en) +AnnotationAssertion( "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in +this case we explicitly refer to the singular form"@en) +AnnotationAssertion( "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "scalar measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectMinCardinality(1 )) +SubClassOf( DataMinCardinality(1 )) + +# Class: (directive information entity) + +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion( "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it."@en) +AnnotationAssertion( "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en) +AnnotationAssertion( "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion(rdfs:label "directive information entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (graph) + +AnnotationAssertion( "graph"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "OBI_0000240"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "graph"@en) +SubClassOf( ) + +# Class: (rule) + +AnnotationAssertion( "rule"@en) +AnnotationAssertion( "example to be added"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A rule is an executable which guides, defines, restricts actions."@en) +AnnotationAssertion( "MSI"@en) +AnnotationAssertion( "PRS"@en) +AnnotationAssertion( "OBI_0500021"@en) +AnnotationAssertion( "PRS"@en) +AnnotationAssertion(rdfs:label "rule"@en) +SubClassOf( ) + +# Class: (algorithm) + +AnnotationAssertion( "algorithm"@en) +AnnotationAssertion( "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata."@en) +AnnotationAssertion( "Philippe Rocca-Serra"@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI_0000270"@en) +AnnotationAssertion( "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)"@en) +AnnotationAssertion(rdfs:label "algorithm"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (source code module) + +AnnotationAssertion( "source code module"@en) +AnnotationAssertion( "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A source code module is a directive information entity that specifies, using a programming language, some algorithm."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000039"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "source code module"@en) +SubClassOf( ) + +# Class: (data set) + +AnnotationAssertion( "data set"@en) +AnnotationAssertion( "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) +AnnotationAssertion( "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type"@en) +AnnotationAssertion( "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000042"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "data set"@en) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (plan specification) + +AnnotationAssertion( "plan specification"@en) +AnnotationAssertion( "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion( "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2014-03-31: A plan specification can have other parts, such as conditional specifications."@en) +AnnotationAssertion( "2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231."@en) +AnnotationAssertion( "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Clint Dowland"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion( "OBI_0000344"@en) +AnnotationAssertion(rdfs:comment "2/3/2009 Comment from OBI review. + +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. + +Request that IAO either clarify these or change definitions not to use them"@en) +AnnotationAssertion(rdfs:label "plan specification"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (measurement datum) + +AnnotationAssertion( "measurement datum"@en) +AnnotationAssertion( "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en) +AnnotationAssertion( "2/2/2009 is_specified_output of some assay?"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000305"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "measurement datum"@en) +SubClassOf( ) + +# Class: (material information bearer) + +AnnotationAssertion( "material information bearer"@en) +AnnotationAssertion( "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier."@en) +AnnotationAssertion( "a brain"@en) +AnnotationAssertion( "a hard drive"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity in which a concretization of an information content entity inheres."@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion(rdfs:label "material information bearer"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (textual entity) + +AnnotationAssertion( "textual entity"@en) +AnnotationAssertion( "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc."@en) +AnnotationAssertion( "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc."@en) +AnnotationAssertion( "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "text"@en) +AnnotationAssertion(rdfs:label "textual entity"@en) +SubClassOf( ) + +# Class: (figure) + +AnnotationAssertion( "figure"@en) +AnnotationAssertion( "Any picture, diagram or table"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "figure"@en) +SubClassOf( ) + +# Class: (diagram) + +AnnotationAssertion( "diagram"@en) +AnnotationAssertion( "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A figure that expresses one or more propositions"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "diagram"@en) +SubClassOf( ) + +# Class: (document) + +AnnotationAssertion( "document"@en) +AnnotationAssertion( "A journal article, patent application, laboratory notebook, or a book"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A collection of information content entities intended to be understood together as a whole"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "document"@en) +SubClassOf( ) + +# Class: (publication) + +AnnotationAssertion( "publication"@en) +AnnotationAssertion( "journal article, newspaper story, book, etc."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A document that is the output of a publishing process."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jie Zheng"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "published document"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Revisit the term in Octorber 2020. Improve the defintion."@en) +AnnotationAssertion(rdfs:label "publication"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (length measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A scalar measurement datum that is the result of measurement of length quality"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "length measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (time measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A scalar measurement datum that is the result of measuring a temporal interval"@en) +AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "time measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectAllValuesFrom( ) ObjectAllValuesFrom( ))) + +# Class: (publishing process) + +AnnotationAssertion( ) +AnnotationAssertion( "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free."@en) +AnnotationAssertion( "Person: Jie Zheng"@en) +AnnotationAssertion( "https://en.wikipedia.org/wiki/Publishing") +AnnotationAssertion( ) +AnnotationAssertion( "VEuPathDB"@en) +AnnotationAssertion(rdfs:label "publishing process"@en) +SubClassOf( ) + +# Class: (documenting) + +AnnotationAssertion( "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A planned process in which a document is created or added to by including the specified input in it."@en) +AnnotationAssertion( "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape"@en) +AnnotationAssertion( "Bjoern Peters"@en) +AnnotationAssertion( "wikipedia http://en.wikipedia.org/wiki/Documenting"@en) +AnnotationAssertion(rdfs:label "documenting"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (centrally registered identifier symbol) + +AnnotationAssertion( "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "CRID symbol") +AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) +AnnotationAssertion(rdfs:label "centrally registered identifier symbol"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (centrally registered identifier) + +AnnotationAssertion( "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs."@en) +AnnotationAssertion( "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')."@en) +AnnotationAssertion( "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation."@en) +AnnotationAssertion( "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "CRID") +AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) +AnnotationAssertion(rdfs:label "centrally registered identifier"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) + +# Class: (centrally registered identifier registry) + +AnnotationAssertion( "PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. "@en) +AnnotationAssertion( ) +AnnotationAssertion( "A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process."@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "CRID registry") +AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) +AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) +AnnotationAssertion(rdfs:label "centrally registered identifier registry"@en) +SubClassOf( ) + +# Class: (time stamped measurement datum) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "time stamped measurement datum"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (time sampled measurement data set) + +AnnotationAssertion( "pmid:20604925 - time-lapse live cell microscopy"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "experimental time series"@en) +AnnotationAssertion(rdfs:label "time sampled measurement data set"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (software application) + +AnnotationAssertion( ) +AnnotationAssertion( "A software application is software that can be directly executed by some processing unit."@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "PERSON: Michel Dumontier"@en) +AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/80"@en) +AnnotationAssertion(rdfs:label "software application"@en) +SubClassOf( ) + +# Class: (identifier) + +AnnotationAssertion( "identifier"@en) +AnnotationAssertion( "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) +AnnotationAssertion( "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "proper name"@en) +AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion(rdfs:comment "Sep 29, 2016: The current definition has been amended from the previous version: \"A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.\" to more accuratly reflect the necessary and sufficient condition on the class. (MB)"@en) +AnnotationAssertion(rdfs:label "identifier"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (identifier creating process) + +AnnotationAssertion( "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) +AnnotationAssertion( "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "dubbing process"@en) +AnnotationAssertion( "naming"@en) +AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion(rdfs:label "identifier creating process"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (personal name) + +AnnotationAssertion( "A personal name is a proper name identifying an individual person."@en) +AnnotationAssertion( "An identifier referring to an individual entity that is ascribed personhood by the user of the identifier."@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Personal_name") +AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) +AnnotationAssertion(rdfs:comment "Personal names \"today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names.\" (http://en.wikipedia.org/wiki/Personal_name)"@en) +AnnotationAssertion(rdfs:comment "Personal names to not include names of fictional characters, e.g. Sherlock Holmes."@en) +AnnotationAssertion(rdfs:comment "Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)"@en) +AnnotationAssertion(rdfs:label "personal name"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) +SubClassOf( ) + +# Class: (code set) + +AnnotationAssertion( "An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate."@en) +AnnotationAssertion( "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Justin Whorton"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "code map"@en) +AnnotationAssertion( "code system"@en) +AnnotationAssertion( "codeset"@en) +AnnotationAssertion( "coding system"@en) +AnnotationAssertion( "controlled vocabulary"@en) +AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) +AnnotationAssertion( "Alan Ruttenberg") +AnnotationAssertion( "Clint Dowland") +AnnotationAssertion( "Matt Diller") +AnnotationAssertion( "Sarah Bost") +AnnotationAssertion( "William R. Hogan") +AnnotationAssertion(rdfs:comment "Code sets might include non-entities/things (e.g. missing thumbs)."@en) +AnnotationAssertion(rdfs:comment "Does not imply absence vs. presence of any taxonomy."@en) +AnnotationAssertion(rdfs:comment "Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities."@en) +AnnotationAssertion(rdfs:comment "Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. + +When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean)."@en) +AnnotationAssertion(rdfs:comment "For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs)."@en) +AnnotationAssertion(rdfs:comment "For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets."@en) +AnnotationAssertion(rdfs:comment "Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain."@en) +AnnotationAssertion(rdfs:comment "The information content entities do not denote each other."@en) +AnnotationAssertion(rdfs:label "code set"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (social act) + +AnnotationAssertion( "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom"@en) +AnnotationAssertion( "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived."@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion(rdfs:comment "The phrase \"in need of being perceived\" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: \"The command is according to its essence in need of being heard (vernehmungsbedürtig\". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target.\" (A. Reinach: The Apriori Foundations of the Civil Law.\" Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). +Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. +Thanks to W.R. Hogan for finding the Reinach quote."@en) +AnnotationAssertion(rdfs:label "social act"@en) +SubClassOf( ) + +# Class: (deontic declaration) + +AnnotationAssertion( "A social act that creates or revokes a deontic role.") +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion(rdfs:label "deontic declaration"@en) +SubClassOf( ) + +# Class: (Homo sapiens) + +AnnotationAssertion( "Homo sapiens"@en) +AnnotationAssertion( "human being") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Homo sapiens"@en) +SubClassOf( ) + +# Class: (planned process) + +AnnotationAssertion( "planned process"@en) +AnnotationAssertion( "planned process") +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) +AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "planned process"@en) +SubClassOf( ) + +# Class: (investigation) + +AnnotationAssertion( "investigation"@en) +AnnotationAssertion( "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "investigation"@en) +SubClassOf( ) + +# Class: (organization) + +AnnotationAssertion( "organization"@en) +AnnotationAssertion( "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) +AnnotationAssertion( "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "PERSON: Susanna Sansone") +AnnotationAssertion( "GROUP: OBI") +AnnotationAssertion(rdfs:label "organization"@en) +SubClassOf( ) + +# Class: (study design execution) + +AnnotationAssertion( "study design execution") +AnnotationAssertion( "a planned process that carries out a study design") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "study design execution") +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "animal"@en) +AnnotationAssertion( "fungus"@en) +AnnotationAssertion( "plant"@en) +AnnotationAssertion( "virus"@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") +AnnotationAssertion( "13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI.") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) +AnnotationAssertion(rdfs:label "organism"@en) +SubClassOf( ) + +# Class: (data transformation) + +AnnotationAssertion( "data transformation"@en) +AnnotationAssertion( "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process that produces output data from input data."@en) +AnnotationAssertion( "Elisabetta Manduchi"@en) +AnnotationAssertion( "Helen Parkinson"@en) +AnnotationAssertion( "James Malone"@en) +AnnotationAssertion( "Melanie Courtot"@en) +AnnotationAssertion( "Richard Scheuermann"@en) +AnnotationAssertion( "Ryan Brinkman"@en) +AnnotationAssertion( "Tina Hernandez-Boussard"@en) +AnnotationAssertion( "Philippe Rocca-Serra") +AnnotationAssertion( "data analysis"@en) +AnnotationAssertion( "data processing"@en) +AnnotationAssertion( "Branch editors"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "data transformation"@en) +SubClassOf( ) + +# Class: (study design) + +AnnotationAssertion( "study design"@en) +AnnotationAssertion( "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "study design"@en) +SubClassOf( ) + +# Class: (health care encounter) + +AnnotationAssertion( "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter"@en) +AnnotationAssertion( "Albert Goldfain") +AnnotationAssertion( "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6") +AnnotationAssertion( "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label "health care encounter") +SubClassOf( ) + +# Class: (inpatient encounter) + +AnnotationAssertion( "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night."@en) +AnnotationAssertion( "Albert Goldfain") +AnnotationAssertion( "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6") +AnnotationAssertion( "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label "inpatient encounter") +SubClassOf( ) + +# Class: (human social role) + +AnnotationAssertion( "A social role inhering in a human being."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion(rdfs:label "human social role"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (human health care role) + +AnnotationAssertion( "A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis."@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "health care role"@en) +AnnotationAssertion(rdfs:label "human health care role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (patient role) + +AnnotationAssertion( "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter."@en) +AnnotationAssertion( "Amanda Hicks"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "patient"@en) +AnnotationAssertion( "CAFE domain expert working group."@en) +AnnotationAssertion(rdfs:comment "In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications."@en) +AnnotationAssertion(rdfs:label "patient role"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (health care provider organization role) + +AnnotationAssertion( "A role that inheres in an organization and that is realized by the providing of services in a health care encounter."@en) +AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "Amanda Hicks") +AnnotationAssertion(rdfs:label "health care provider organization role"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (aggregate of objectual organisms) + +AnnotationAssertion( "An object aggregate of objectual organisms."@en) +AnnotationAssertion(rdfs:comment "Any arbitrary collection of organisms. They need not be of the same taxonomic class. "@en) +AnnotationAssertion(rdfs:label "aggregate of objectual organisms"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( ObjectIntersectionOf( ))) + +# Class: (collection of humans) + +AnnotationAssertion( "An object aggregate all of whose components are human beings."@en) +AnnotationAssertion(rdfs:label "collection of humans"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (organization social role) + +AnnotationAssertion( "A role in human social processes that inheres in an organization."@en) +AnnotationAssertion( "William R. Hogan"@en) +AnnotationAssertion(rdfs:comment "Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. + +Ditto for its current descendants."@en) +AnnotationAssertion(rdfs:label "organization social role"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (organism social role) + +AnnotationAssertion( "A role in human social processes that inheres in an organism."@en) +AnnotationAssertion( "William R. Hogan +Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:comment "Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. + +Ditto for its current descendants."@en) +AnnotationAssertion(rdfs:comment "Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc."@en) +AnnotationAssertion(rdfs:comment "Previous definition: A role in human social processes played by an organism."@en) +AnnotationAssertion(rdfs:label "organism social role"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (organization health care role) + +AnnotationAssertion( "An organization social role that, if realized, is realized by either a health care process or an ancillary health care process"@en) +AnnotationAssertion(rdfs:comment "Previous definition: An organization social role played by an organization in health care processes."@en) +AnnotationAssertion(rdfs:label "organization health care role"@en) +SubClassOf( ) + +# Class: (human patient role) + +AnnotationAssertion( "A patient role that inheres in a human being."@en) +AnnotationAssertion(rdfs:label "human patient role"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (aggregate of organizations) + +AnnotationAssertion( "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common"@en) +AnnotationAssertion( "William R. Hogan +Amanda Hicks"@en) +AnnotationAssertion(rdfs:comment "It is often convenient to group organizations together that otherwise might not even interact with one another. "@en) +AnnotationAssertion(rdfs:label "aggregate of organizations"@en) +EquivalentClasses( ObjectIntersectionOf(ObjectComplementOf() ObjectAllValuesFrom( ) ObjectMinCardinality(2 ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (material entity role) + +AnnotationAssertion(rdfs:label "material entity role"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (organism role) + +AnnotationAssertion(rdfs:label "organism role"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (Homo sapiens role) + +AnnotationAssertion(rdfs:label "Homo sapiens role"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (organization role) + +AnnotationAssertion(rdfs:label "organization role"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (school function) + +AnnotationAssertion( "A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "school function"@en) +SubClassOf( ) + +# Class: (hospital role) + +AnnotationAssertion( "A healthcare provider role that inheres in an organization and is realized by providing inpatient care."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "hospital role"@en) +SubClassOf( ) + +# Class: (school role) + +AnnotationAssertion( "An organization social role that inheres in an organization and is realized by providing formal education to students."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "school role"@en) +SubClassOf( ) + +# Class: (hospital organization) + +AnnotationAssertion( "An organization that is the bearer of a hospital role."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "hospital organization"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (school organization) + +AnnotationAssertion( "An organization that is the bearer of a school role."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "school organization"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (student role) + +AnnotationAssertion( "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "student role"@en) +SubClassOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (nursery school role) + +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "nursery school role"@en) +SubClassOf( ) + +# Class: (primary school role) + +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "primary school role"@en) +SubClassOf( ) + +# Class: (architectural structure) + +AnnotationAssertion( "A material entity that is a human made strcuture with firm connection between its foundation and the ground."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion( "http://de.wikipedia.org/wiki/Bauwerk"@en) +AnnotationAssertion(rdfs:comment "\"Building\" is a subclass of this. "@en) +AnnotationAssertion(rdfs:comment "This type of entity is referred to as \"Bauwerk\" or \"Bauliche Anlage\"."@en) +AnnotationAssertion(rdfs:label "architectural structure"@en) +SubClassOf( ) + +# Class: (facility) + +AnnotationAssertion( "An architectural structure that bears some function."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "facility"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf(Annotation(owl:versionInfo "09/09/2017") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (school facility) + +AnnotationAssertion( "A facility that is run by a school organization and is the bearer of a school function."@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "school facility"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (secondary school role) + +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:label "secondary school role"@en) +SubClassOf( ) + +# Class: (human role within an organization) + +AnnotationAssertion( "A human social role that is created by a deontic declaration performed by an organization."@en) +AnnotationAssertion( "Amanda Hicks"@en) +AnnotationAssertion( "human organizational role"@en) +AnnotationAssertion(rdfs:label "human role within an organization"@en) +SubClassOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))))) + +# Class: (human traveling information) + +AnnotationAssertion( "An information content entity that is about human travel."@en) +AnnotationAssertion( "https://github.com/ufbmi/OMRSE/issues/79"^^xsd:anyURI) +AnnotationAssertion( "Jie Zheng") +AnnotationAssertion( "Amanda Hicks") +AnnotationAssertion(rdfs:label "human traveling information"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (health care function) + +AnnotationAssertion(rdfs:label "health care function"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (role in human social processes) + +AnnotationAssertion( "A role that inheres in some entity that is realized in a social act."@en) +AnnotationAssertion( "Matthew Diller"@en) +AnnotationAssertion( "Mathias Brochhausen"@en) +AnnotationAssertion(rdfs:comment "Previous definition: A role played by an entity in human social processes."@en) +AnnotationAssertion(rdfs:label "role in human social processes"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") +AnnotationAssertion( "PATO:0000001") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + +# Class: (morphology) + +AnnotationAssertion( "morphology") +AnnotationAssertion( "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "morphology") +SubClassOf( ) + +# Class: (length) + +AnnotationAssertion( "length") +AnnotationAssertion( "A 1-D extent quality which is equal to the distance between two points.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "length") +SubClassOf( ) + +# Class: (mass) + +AnnotationAssertion( "mass") +AnnotationAssertion( "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "mass") +SubClassOf( ) + +# Class: (physical quality) + +AnnotationAssertion( "physical quality") +AnnotationAssertion( "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "physical quality") +SubClassOf( ) + +# Class: (physical object quality) + +AnnotationAssertion( "physical object quality") +AnnotationAssertion( "A quality which inheres in a continuant.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "physical object quality") +SubClassOf( ) + +# Class: (length unit) + +AnnotationAssertion( "length unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "length unit") +SubClassOf( ) + +# Class: (time unit) + +AnnotationAssertion( "time unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "time unit") +SubClassOf( ) + + +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( ) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) + +# Individual: (out of scope) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") +AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(rdfs:label "out of scope") + + +SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +) \ No newline at end of file diff --git a/src/ontology/imports/omrse_terms.txt b/src/ontology/imports/omrse_terms.txt new file mode 100644 index 0000000..139597f --- /dev/null +++ b/src/ontology/imports/omrse_terms.txt @@ -0,0 +1,2 @@ + + diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index a699580..2b0cd8b 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-08-17") +Annotation(owl:versionInfo "2024-12-24") Declaration(Class()) Declaration(Class()) @@ -223,7 +223,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty())