From 960ed85a1d1da2f13c7ddbe07c372941d42372e2 Mon Sep 17 00:00:00 2001 From: Matt Diller Date: Tue, 9 Jan 2024 21:41:05 -0500 Subject: [PATCH] Preparing release 2024-01-09. --- omrse-base.json | 88 ++----- omrse-base.obo | 37 +-- omrse-base.owl | 202 ++++---------- omrse-full.json | 604 +++++++++++++++++++++++++++++++++--------- omrse-full.obo | 153 +++++++---- omrse-full.owl | 688 ++++++++++++++++++++++++++++------------------- omrse.json | 604 +++++++++++++++++++++++++++++++++--------- omrse.obo | 149 +++++++---- omrse.owl | 689 +++++++++++++++++++++++++++++------------------- 9 files changed, 2054 insertions(+), 1160 deletions(-) diff --git a/omrse-base.json b/omrse-base.json index 32767b3..576ed17 100644 --- a/omrse-base.json +++ b/omrse-base.json @@ -56,6 +56,9 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/description", "val" : "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "Ontology for Modeling and Representation of Social Entities" }, { "pred" : "http://purl.org/dc/elements/1.1/type", "val" : "http://purl.obolibrary.org/obo/IAO_8000001" @@ -65,14 +68,11 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's \"meaningful use\" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#label", - "val" : "Ontology for Modeling and Representation of Social Entities" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-10-08" + "val" : "2024-01-10" } ], - "version" : "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse-base.json" + "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-01-10/omrse-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -194,7 +194,7 @@ "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. " + "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", @@ -2045,7 +2045,7 @@ "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000168", - "lbl" : "questions asking process", + "lbl" : "obsolete questions asking process", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { @@ -2072,7 +2072,7 @@ "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000173", - "lbl" : "material information bearer of question text plus answer set", + "lbl" : "obsolete material information bearer of question text plus answer set", "type" : "CLASS", "meta" : { "deprecated" : true @@ -2087,14 +2087,14 @@ "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000176", - "lbl" : "identity question asking process", + "lbl" : "obsolete identity question asking process", "type" : "CLASS", "meta" : { "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000177", - "lbl" : "ethnic identity question asking process", + "lbl" : "obsolete ethnic identity question asking process", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { @@ -2105,7 +2105,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000178", - "lbl" : "race identity question asking process", + "lbl" : "obsolete race identity question asking process", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { @@ -5789,6 +5789,14 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000097", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000038" + }, { + "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_00000100", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000132" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000102", "pred" : "is_a", @@ -6013,6 +6021,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000132", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000179" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000133", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000132" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000134", "pred" : "is_a", @@ -6185,14 +6197,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000168", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000168", - "pred" : "http://purl.obolibrary.org/obo/RO_0000057", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000168", - "pred" : "http://purl.obolibrary.org/obo/RO_0000057", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000173" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000169", "pred" : "is_a", @@ -6472,15 +6476,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000230", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMIABIS_0001025" + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000701" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000231", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMIABIS_0001035" + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000710" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000232", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMIABIS_0000060" + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000667" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000233", "pred" : "is_a", @@ -7005,46 +7009,6 @@ }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000067", "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000011" ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000098", - "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000132" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000100", - "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000132" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000133", - "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000132" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000142", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ], diff --git a/omrse-base.obo b/omrse-base.obo index 707338d..f1c5b89 100644 --- a/omrse-base.obo +++ b/omrse-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: omrse/releases/2023-10-08/omrse-base.owl +data-version: omrse/releases/2024-01-10/omrse-base.owl remark: This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's \"meaningful use\" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt ontology: omrse/omrse-base property_value: http://purl.org/dc/elements/1.1/contributor "Barry Smith" xsd:string @@ -20,10 +20,10 @@ property_value: http://purl.org/dc/elements/1.1/creator "Shariq Tariq" xsd:strin property_value: http://purl.org/dc/elements/1.1/creator "Swetha Garimalla" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "William Hogan" xsd:string property_value: http://purl.org/dc/elements/1.1/description "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Ontology for Modeling and Representation of Social Entities" xsd:string property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2023-10-08" xsd:string -name: Ontology for Modeling and Representation of Social Entities +property_value: owl:versionInfo "2024-01-10" xsd:string [Term] id: GO:0003674 @@ -107,7 +107,7 @@ property_value: IAO:0000118 "female gender" 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. " [] +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 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string @@ -774,6 +774,7 @@ is_a: BFO:0000038 id: OMRSE:00000098 name: obsolete 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 ! obsolete identity datum is_obsolete: true replaced_by: racial identity information content entity @@ -785,6 +786,7 @@ name: racial identification process id: OMRSE:00000100 name: obsolete ethnic identity datum def: "An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method." [] +is_a: OMRSE:00000132 ! obsolete identity datum property_value: IAO:0000117 "Amanda Hicks" xsd:string is_obsolete: true replaced_by: ethnic identity information content entity @@ -1032,6 +1034,7 @@ replaced_by: social identity information content entity id: OMRSE:00000133 name: obsolete gender identity datum def: "A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method." [] +is_a: OMRSE:00000132 ! obsolete identity datum property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string is_obsolete: true replaced_by: gender identity information content entity @@ -1227,7 +1230,7 @@ id: OMRSE:00000163 name: response to a question asking process comment: Note that not all responses to a question asking process are answers. For example, a refusal to answer is not an answer. A refusal to answer is also not a specified output of the question asking process since it does not acheive the objective of asking the question, which is to get an answer. is_a: IAO:0000030 -relationship: RO:0000056 OMRSE:00000168 ! questions asking process +relationship: RO:0000056 OMRSE:00000168 ! obsolete questions asking process [Term] id: OMRSE:00000164 @@ -1251,10 +1254,8 @@ relationship: BFO:0000066 OMRSE:00000074 ! housing unit [Term] id: OMRSE:00000168 -name: questions asking process +name: obsolete questions asking process is_a: ObsoleteClass -relationship: RO:0000057 NCBITaxon:9606 -relationship: RO:0000057 OMRSE:00000173 ! material information bearer of question text plus answer set is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000198 @@ -1286,7 +1287,7 @@ intersection_of: BFO:0000054 OGMS:0000097 [Term] id: OMRSE:00000173 -name: material information bearer of question text plus answer set +name: obsolete material information bearer of question text plus answer set is_a: BFO:0000040 is_obsolete: true @@ -1302,21 +1303,21 @@ is_a: OMRSE:00000163 ! response to a question asking process [Term] id: OMRSE:00000176 -name: identity question asking process -is_a: OMRSE:00000168 ! questions asking process +name: obsolete identity question asking process +is_a: OMRSE:00000168 ! obsolete questions asking process is_obsolete: true [Term] id: OMRSE:00000177 -name: ethnic identity question asking process -is_a: OMRSE:00000176 ! identity question asking process +name: obsolete ethnic identity question asking process +is_a: OMRSE:00000176 ! obsolete identity question asking process is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000199 [Term] id: OMRSE:00000178 -name: race identity question asking process -is_a: OMRSE:00000176 ! identity question asking process +name: obsolete race identity question asking process +is_a: OMRSE:00000176 ! obsolete identity question asking process is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000200 @@ -1849,7 +1850,7 @@ property_value: IAO:0000117 "S. Clint Dowland" xsd:string id: OMRSE:00000230 name: county smoking survey plan specification def: "A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county." [] -is_a: OMIABIS:0001025 +is_a: OBIB:0000701 property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string @@ -1863,7 +1864,7 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string id: OMRSE:00000231 name: county smoking survey execution def: "A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county." [] -is_a: OMIABIS:0001035 +is_a: OBIB:0000710 property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string @@ -1877,7 +1878,7 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string id: OMRSE:00000232 name: county smoking survey data def: "Survey data that is the specified output of a county smoking survey execution." [] -is_a: OMIABIS:0000060 +is_a: OBIB:0000667 property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string diff --git a/omrse-base.owl b/omrse-base.owl index acae0b6..77957ba 100644 --- a/omrse-base.owl +++ b/omrse-base.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Barry Smith Chris Stoeckert Daniel Welch @@ -32,11 +32,11 @@ Swetha Garimalla William Hogan The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. + Ontology for Modeling and Representation of Social Entities https://creativecommons.org/licenses/by/4.0/ This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt - Ontology for Modeling and Representation of Social Entities - 2023-10-08 + 2024-01-10 @@ -194,6 +194,12 @@ + + + + + + @@ -910,6 +916,24 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope + + + + + + + + + + + + + + + + + + @@ -958,24 +982,6 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - - - - - - - - - - - - - @@ -1166,7 +1172,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - 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 @@ -2876,30 +2882,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - + 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. racial identity information content entity obsolete racial identity datum @@ -2935,30 +2918,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - + An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. Amanda Hicks ethnic identity information content entity @@ -3539,30 +3499,6 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - 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. social identity information content entity @@ -3576,30 +3512,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - + A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method. gender identity information content entity Amanda Hicks @@ -4094,20 +4007,8 @@ Somehow involves skilled nursing encounters - - - - - - - - - - - - http://purl.obolibrary.org/obo/OMRSE_00000198 - questions asking process + obsolete questions asking process true @@ -4188,7 +4089,7 @@ Somehow involves skilled nursing encounters - material information bearer of question text plus answer set + obsolete material information bearer of question text plus answer set true @@ -4216,7 +4117,7 @@ Somehow involves skilled nursing encounters - identity question asking process + obsolete identity question asking process true @@ -4227,7 +4128,7 @@ Somehow involves skilled nursing encounters http://purl.obolibrary.org/obo/OMRSE_00000199 - ethnic identity question asking process + obsolete ethnic identity question asking process true @@ -4238,7 +4139,7 @@ Somehow involves skilled nursing encounters http://purl.obolibrary.org/obo/OMRSE_00000200 - race identity question asking process + obsolete race identity question asking process true @@ -4484,22 +4385,6 @@ Somehow involves skilled nursing encounters - - - - - - - - - - - - - - - - A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output. S. Clint Dowland Mathias Brochhausen @@ -5039,7 +4924,7 @@ Somehow involves skilled nursing encounters - + The Alachua county smoking survey plan specification. A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county. Mathias Brochhausen @@ -5068,7 +4953,7 @@ Somehow involves skilled nursing encounters - + The Alachua county smoking survey execution. A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county. Mathias Brochhausen @@ -5092,7 +4977,7 @@ Somehow involves skilled nursing encounters - + The Alachua county smoking survey data. Survey data that is the specified output of a county smoking survey execution. Mathias Brochhausen @@ -7080,6 +6965,15 @@ It indicates that a person has completed only early childhood education and noth imported from + + true + + + true + + + true + diff --git a/omrse-full.json b/omrse-full.json index b51b99a..614b038 100644 --- a/omrse-full.json +++ b/omrse-full.json @@ -56,20 +56,20 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/description", "val" : "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "Ontology for Modeling and Representation of Social Entities" }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's \"meaningful use\" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#label", - "val" : "Ontology for Modeling and Representation of Social Entities" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-10-08" + "val" : "2024-01-10" } ], - "version" : "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse-full.json" + "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-01-10/omrse-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", @@ -189,6 +189,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ready for release" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { @@ -228,6 +231,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "pending final vetting" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { @@ -388,6 +394,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "requires discussion" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" @@ -418,6 +427,28 @@ "val" : "https://orcid.org/0000-0001-5208-3432" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0001002", + "lbl" : "domain entity does not exist", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "http://orcid.org/0000-0002-4142-7153" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/136" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", + "val" : "https://orcid.org/0000-0002-4142-7153" + } ] + } }, { "id" : "http://purl.obolibary.org/obo/IAO_0021001", "lbl" : "obsolete_deontic document act", @@ -726,6 +757,7 @@ "definition" : { "val" : "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])" }, + "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "ic" @@ -947,6 +979,7 @@ "definition" : { "val" : "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])" }, + "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "process" @@ -1150,6 +1183,7 @@ "definition" : { "val" : "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])" }, + "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "sdc" @@ -1563,6 +1597,7 @@ "definition" : { "val" : "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])" }, + "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "gdc" @@ -1827,6 +1862,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { @@ -1950,7 +1988,7 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", + "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } @@ -1993,6 +2031,9 @@ }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { @@ -2355,7 +2396,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "val" : "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.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "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." ], @@ -2384,7 +2425,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", + "val" : "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.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "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." ], @@ -3975,6 +4016,9 @@ }, { "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. " @@ -10053,6 +10097,47 @@ "id" : "http://purl.obolibrary.org/obo/OAE_0004334", "lbl" : "has_MedDRA_id", "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/OBIB_0000667", + "lbl" : "survey data", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A data item that contains the outcome of a survey." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alice Nzinga" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBIB_0000701", + "lbl" : "survey plan specification", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A plan specification that is realized by process of gathering information (e.g. by asking questions)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Alice Nzinga" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Mathias Brochhausen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OBIB_0000710", + "lbl" : "survey execution", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A planned process that realizes the concretization of a survey to generate an output(survey data.)" + } + } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000011", "lbl" : "planned process", @@ -10537,6 +10622,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000732" } ], "deprecated" : true } @@ -10548,6 +10636,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000733" } ], "deprecated" : true } @@ -10559,6 +10650,9 @@ "basicPropertyValues" : [ { "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_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000735" } ] } }, { @@ -10572,7 +10666,11 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - } ] + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000667" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0001025", @@ -10585,12 +10683,23 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" - } ] + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000701" + } ], + "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0001035", "lbl" : "obsolete survey execution", - "type" : "CLASS" + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/OBIB_0000710" + } ], + "deprecated" : true + } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001001", "lbl" : "logical characteristic of object property", @@ -10629,6 +10738,258 @@ "val" : "https://orcid.org/0000-0002-8688-6599" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for describing abbreviations or initalisms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003001", + "lbl" : "ambiguous synonym", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for describing ambiguous synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "lbl" : "dubious synonym", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for describing dubious synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "lbl" : "layperson synonym", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for describing layperson or colloquial synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for describing pluralization synonyms" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003005", + "lbl" : "UK spelling synonym", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for describing UK spelling variants" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003006", + "lbl" : "misspelling", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for common misspellings" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/132" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003007", + "lbl" : "misnomer", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/133" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-03-03" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003008", + "lbl" : "previous name", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for names that have been used as primary labels in the past." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/139" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-07-25" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003009", + "lbl" : "legal name", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for the legal entity name" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/141" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-07-27" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003010", + "lbl" : "International Nonproprietary Name", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) \"paracetamol\". In some cases such as this one, the INN might be the same as the ontology's primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/149" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-09-30" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "lbl" : "latin term", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A synonym type for describing Latin term synonyms." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "nasopharynx (UBERON:0001728) has the latin name \"pars nasalis pharyngis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/146" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-1773-2692" + }, { + "pred" : "http://purl.org/dc/terms/created", + "val" : "2023-10-12" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000000", "lbl" : "social security number", @@ -10738,7 +11099,7 @@ "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. " + "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", @@ -10933,7 +11294,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000024", - "lbl" : "role in human social processes", + "lbl" : "obsolete role in human social processes", "type" : "CLASS", "meta" : { "definition" : { @@ -10943,9 +11304,6 @@ "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" } ], "deprecated" : true } @@ -12599,7 +12957,7 @@ "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000168", - "lbl" : "questions asking process", + "lbl" : "obsolete questions asking process", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { @@ -12626,7 +12984,7 @@ "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000173", - "lbl" : "material information bearer of question text plus answer set", + "lbl" : "obsolete material information bearer of question text plus answer set", "type" : "CLASS", "meta" : { "deprecated" : true @@ -12641,14 +12999,14 @@ "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000176", - "lbl" : "identity question asking process", + "lbl" : "obsolete identity question asking process", "type" : "CLASS", "meta" : { "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000177", - "lbl" : "ethnic identity question asking process", + "lbl" : "obsolete ethnic identity question asking process", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { @@ -12659,7 +13017,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000178", - "lbl" : "race identity question asking process", + "lbl" : "obsolete race identity question asking process", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { @@ -15907,6 +16265,9 @@ "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/2023-10-08/omrse.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" @@ -16124,10 +16485,10 @@ "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147485260" + "val" : "_:genid2147485205" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147485261" + "val" : "_:genid2147485206" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" @@ -16280,6 +16641,9 @@ }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } }, { @@ -16674,7 +17038,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" @@ -16691,7 +17055,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" @@ -16708,7 +17072,7 @@ "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" @@ -16722,7 +17086,7 @@ "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" @@ -16738,7 +17102,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" @@ -16752,7 +17116,7 @@ "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" @@ -16765,11 +17129,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" @@ -16782,11 +17146,11 @@ "meta" : { "definition" : { "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" @@ -16799,12 +17163,12 @@ "meta" : { "definition" : { "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" @@ -17296,6 +17660,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "consumes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { @@ -17316,6 +17683,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "produces" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { @@ -17353,7 +17723,7 @@ "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { @@ -17372,6 +17742,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { @@ -17389,6 +17762,9 @@ }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { @@ -17471,6 +17847,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enables" } ] } }, { @@ -17524,7 +17903,7 @@ "val" : "enables part of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { @@ -17539,6 +17918,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { @@ -17701,6 +18083,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { @@ -17720,6 +18105,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { @@ -17883,7 +18271,7 @@ "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { @@ -17899,6 +18287,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { @@ -18377,6 +18768,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { @@ -18397,6 +18791,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { @@ -18483,7 +18880,7 @@ "val" : "2018-01-26T23:49:30Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" } ] } }, { @@ -18501,6 +18898,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:51Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" } ] } }, { @@ -18523,7 +18923,7 @@ "val" : "2018-01-26T23:53:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" } ] } }, { @@ -18546,7 +18946,7 @@ "val" : "2018-01-26T23:53:22Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { @@ -18563,6 +18963,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { @@ -18579,6 +18982,9 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { @@ -18607,7 +19013,7 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", @@ -18712,7 +19118,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" @@ -18728,7 +19134,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:08:01Z" @@ -18845,7 +19251,7 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/iao/d-acts/dev/d-acts.owl#obligee_role", + "id" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligee_role", "lbl" : "obsolete obligee role", "type" : "CLASS", "meta" : { @@ -18859,7 +19265,7 @@ "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/iao/d-acts/dev/d-acts.owl#obligor_role", + "id" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligor_role", "lbl" : "obsolete obligor role", "type" : "CLASS", "meta" : { @@ -20284,7 +20690,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020027", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000024" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021000", "pred" : "is_a", @@ -20513,6 +20919,18 @@ "sub" : "http://purl.obolibrary.org/obo/OAE_0002807", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OAE_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBIB_0000667", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000027" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBIB_0000701", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000104" + }, { + "sub" : "http://purl.obolibrary.org/obo/OBIB_0000710", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/OBI_0000011", "pred" : "is_a", @@ -20697,10 +21115,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000020", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000024", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000024", "pred" : "is_a", @@ -21275,14 +21689,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000132", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000179" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000133", "pred" : "is_a", @@ -21475,22 +21881,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000166", "pred" : "http://purl.obolibrary.org/obo/BFO_0000066", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000074" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000168", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000168", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000168", - "pred" : "http://purl.obolibrary.org/obo/RO_0000057", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000168", - "pred" : "http://purl.obolibrary.org/obo/RO_0000057", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000173" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000169", "pred" : "is_a", @@ -21627,10 +22021,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000195", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002069" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000196", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000196", "pred" : "is_a", @@ -21774,23 +22164,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000230", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMIABIS_0001025" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000231", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000701" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000231", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMIABIS_0001035" + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000710" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000232", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000232", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMIABIS_0000060" + "obj" : "http://purl.obolibrary.org/obo/OBIB_0000667" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000232", "pred" : "http://purl.obolibrary.org/obo/OBI_0000312", @@ -22312,11 +22694,11 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" }, { - "sub" : "http://purl.obolibrary.org/obo/iao/d-acts/dev/d-acts.owl#obligee_role", + "sub" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligee_role", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { - "sub" : "http://purl.obolibrary.org/obo/iao/d-acts/dev/d-acts.owl#obligor_role", + "sub" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligor_role", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { @@ -22399,6 +22781,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMO_0001000", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMO_0001002", + "pred" : "type", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000225" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", "pred" : "subPropertyOf", @@ -22518,7 +22904,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000020", "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" + "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000021", "pred" : "subPropertyOf", @@ -23424,46 +23810,6 @@ }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000067", "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000011" ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000098", - "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000132" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000100", - "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000132" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000132", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000133", - "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000132" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020022" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/IAO_0000136", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000142", "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0000030" ], diff --git a/omrse-full.obo b/omrse-full.obo index 7cd8dca..08e8ada 100644 --- a/omrse-full.obo +++ b/omrse-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: omrse/releases/2023-10-08/omrse-full.owl +data-version: omrse/releases/2024-01-10/omrse-full.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -26,9 +26,9 @@ property_value: http://purl.org/dc/elements/1.1/creator "Shariq Tariq" xsd:strin property_value: http://purl.org/dc/elements/1.1/creator "Swetha Garimalla" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "William Hogan" xsd:string property_value: http://purl.org/dc/elements/1.1/description "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Ontology for Modeling and Representation of Social Entities" xsd:string property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string -property_value: owl:versionInfo "2023-10-08" xsd:string -name: Ontology for Modeling and Representation of Social Entities +property_value: owl:versionInfo "2024-01-10" xsd:string [Term] id: APOLLO_SV:00000008 @@ -170,8 +170,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +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. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant @@ -269,6 +269,7 @@ id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string @@ -356,6 +357,7 @@ id: BFO:0000020 name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +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. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant @@ -519,6 +521,7 @@ id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] def: "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])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +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. is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant property_value: BFO:0000179 "gdc" xsd:string @@ -759,7 +762,6 @@ property_value: IAO:0000117 "Amanda Hicks" xsd:string id: GO:0003674 name: molecular_function def: "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." [GOC:pdt] -def: "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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt] 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. synonym: "molecular function" EXACT [] is_a: BFO:0000034 ! function @@ -776,7 +778,6 @@ is_a: GO:0008150 ! biological_process id: GO:0008150 name: biological_process def: "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." [GOC:pdt] -def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] @@ -3305,7 +3306,7 @@ replaced_by: claimant role (IAO:0021013) id: IAO:0020027 name: owner role def: "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role." [] -is_a: OMRSE:00000024 ! obsolete role in human social processes +is_a: OMRSE:00002072 ! role in human social processes property_value: IAO:0000112 "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "https://github.com/d-acts/d-acts/issues/29" xsd:string @@ -3896,6 +3897,28 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string +[Term] +id: OBIB:0000667 +name: survey data +def: "A data item that contains the outcome of a survey." [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Alice Nzinga" xsd:string +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string + +[Term] +id: OBIB:0000701 +name: survey plan specification +def: "A plan specification that is realized by process of gathering information (e.g. by asking questions)." [] +is_a: IAO:0000104 ! plan specification +property_value: IAO:0000117 "Alice Nzinga" xsd:string +property_value: IAO:0000117 "Mathias Brochhausen" xsd:string + +[Term] +id: OBIB:0000710 +name: survey execution +def: "A planned process that realizes the concretization of a survey to generate an output(survey data.)" [] +is_a: OBI:0000011 ! planned process + [Term] id: OGMS:0000097 name: health care encounter @@ -3930,6 +3953,8 @@ name: obsolete survey data is_a: ObsoleteClass property_value: IAO:0000117 "Alice Nzinga" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +is_obsolete: true +replaced_by: OBIB:0000667 [Term] id: OMIABIS:0001025 @@ -3937,11 +3962,15 @@ name: obsolete survey plan specification is_a: ObsoleteClass property_value: IAO:0000117 "Alice Nzinga" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string +is_obsolete: true +replaced_by: OBIB:0000701 [Term] id: OMIABIS:0001035 name: obsolete survey execution is_a: ObsoleteClass +is_obsolete: true +replaced_by: OBIB:0000710 [Term] id: OMRSE:00000000 @@ -4016,7 +4045,7 @@ property_value: IAO:0000118 "female gender" 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. " [] +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 ! realized in health care encounter property_value: IAO:0000117 "Mathias Brochhausen" xsd:string @@ -4115,20 +4144,17 @@ id: OMRSE:00000023 name: collection of humans def: "An object aggregate all of whose components are human beings." [] comment: An object aggregate all of whose components are human beings. -is_a: OMRSE:00000022 ! aggregate of objectual organisms +is_a: OMRSE:00000022 ! collection of organisms relationship: OMRSE:00000020 NCBITaxon:9606 ! obsolete is-aggregate-of Homo sapiens relationship: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens [Term] id: OMRSE:00000024 name: obsolete role in human social processes -name: role in human social processes def: "A role inhering in an entity realized by social interactions in human society." [] comment: Previous definition: A role played by an entity in human social processes. -is_a: BFO:0000023 ! role is_a: ObsoleteClass property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse.owl" xsd:string is_obsolete: true [Term] @@ -4956,8 +4982,6 @@ id: OMRSE:00000132 name: obsolete identity datum def: "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." [] is_a: OMRSE:00000179 ! answer to identity question -relationship: BFO:0000050 IAO:0020022 ! part of documented identity -relationship: IAO:0000136 NCBITaxon:9606 ! is about Homo sapiens property_value: http://purl.org/dc/elements/1.1/creator "Amanda Hicks" xsd:string is_obsolete: true replaced_by: social identity information content entity @@ -5167,7 +5191,7 @@ id: OMRSE:00000163 name: response to a question asking process comment: Note that not all responses to a question asking process are answers. For example, a refusal to answer is not an answer. A refusal to answer is also not a specified output of the question asking process since it does not acheive the objective of asking the question, which is to get an answer. is_a: IAO:0000030 ! information content entity -relationship: RO:0000056 OMRSE:00000168 ! participates in questions asking process +relationship: RO:0000056 OMRSE:00000168 ! participates in obsolete questions asking process [Term] id: OMRSE:00000164 @@ -5191,11 +5215,8 @@ relationship: BFO:0000066 OMRSE:00000074 ! occurs in housing unit [Term] id: OMRSE:00000168 -name: questions asking process -is_a: BFO:0000003 ! occurrent +name: obsolete questions asking process is_a: ObsoleteClass -relationship: RO:0000057 NCBITaxon:9606 ! has_participant Homo sapiens -relationship: RO:0000057 OMRSE:00000173 ! has_participant material information bearer of question text plus answer set is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000198 @@ -5228,7 +5249,7 @@ relationship: BFO:0000054 OGMS:0000097 ! realized in health care encounter [Term] id: OMRSE:00000173 -name: material information bearer of question text plus answer set +name: obsolete material information bearer of question text plus answer set is_a: BFO:0000040 ! material entity is_obsolete: true @@ -5244,21 +5265,21 @@ is_a: OMRSE:00000163 ! response to a question asking process [Term] id: OMRSE:00000176 -name: identity question asking process -is_a: OMRSE:00000168 ! questions asking process +name: obsolete identity question asking process +is_a: OMRSE:00000168 ! obsolete questions asking process is_obsolete: true [Term] id: OMRSE:00000177 -name: ethnic identity question asking process -is_a: OMRSE:00000176 ! identity question asking process +name: obsolete ethnic identity question asking process +is_a: OMRSE:00000176 ! obsolete identity question asking process is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000199 [Term] id: OMRSE:00000178 -name: race identity question asking process -is_a: OMRSE:00000176 ! identity question asking process +name: obsolete race identity question asking process +is_a: OMRSE:00000176 ! obsolete identity question asking process is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/OMRSE_00000200 @@ -5408,7 +5429,6 @@ property_value: IAO:0000117 "Matthew Diller" xsd:string id: OMRSE:00000196 name: obsolete expression of preferred language def: "A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output." [] -is_a: OBI:0000011 ! planned process is_a: OMRSE:00000192 ! obsolete communication property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string @@ -5791,7 +5811,7 @@ property_value: IAO:0000117 "S. Clint Dowland" xsd:string id: OMRSE:00000230 name: county smoking survey plan specification def: "A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county." [] -is_a: OMIABIS:0001025 ! obsolete survey plan specification +is_a: OBIB:0000701 ! survey plan specification property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string @@ -5805,8 +5825,7 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string id: OMRSE:00000231 name: county smoking survey execution def: "A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county." [] -is_a: BFO:0000015 ! process -is_a: OMIABIS:0001035 ! obsolete survey execution +is_a: OBIB:0000710 ! survey execution property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Matthew Diller" xsd:string @@ -5820,8 +5839,7 @@ property_value: IAO:0000117 "Mathias Brochhausen" xsd:string id: OMRSE:00000232 name: county smoking survey data def: "Survey data that is the specified output of a county smoking survey execution." [] -is_a: BFO:0000002 ! continuant -is_a: OMIABIS:0000060 ! obsolete survey data +is_a: OBIB:0000667 ! survey data relationship: OBI:0000312 OMRSE:00000231 ! is_specified_output_of county smoking survey execution property_value: http://purl.org/dc/elements/1.1/contributor "Hansi Zhang" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Jiang Bian" xsd:string @@ -6769,6 +6787,7 @@ is_a: OMRSE:00000048 ! material entity role relationship: RO:0000052 BFO:0000040 {all_only="true"} ! characteristic of material entity property_value: http://purl.org/dc/elements/1.1/contributor "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string +property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl" xsd:string [Term] id: OOSTT:00000074 @@ -6883,7 +6902,7 @@ id: PCO:0000020 name: family def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. -is_a: OMRSE:00000022 ! aggregate of objectual organisms +is_a: OMRSE:00000022 ! collection of organisms property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string property_value: IAO:0000119 "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173" xsd:string @@ -6961,6 +6980,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -7019,7 +7039,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -7056,6 +7076,7 @@ property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 @@ -7380,6 +7401,7 @@ name: obsolete owns property_value: IAO:0000117 "Mathias Brochhausen" xsd:string is_a: ObsoleteProperty is_obsolete: true +replaced_by: OBIB:0000732 [Typedef] id: OMIABIS:0000009 @@ -7387,18 +7409,20 @@ name: obsolete administrates property_value: IAO:0000117 "Mathias Brochhausen" xsd:string is_a: ObsoleteProperty is_obsolete: true +replaced_by: OBIB:0000733 [Typedef] id: OMIABIS:0000048 name: obsolete is owned by property_value: IAO:0000119 "Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204." xsd:string +replaced_by: OBIB:0000735 [Typedef] id: OMRSE:00000020 +name: is-aggregate-of name: obsolete is-aggregate-of comment: We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.\n property_value: IAO:0000231 "BFO relation takes precedence." xsd:string -is_a: ObsoleteProperty is_obsolete: true [Typedef] @@ -7562,6 +7586,7 @@ name: has participant name: has_participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -7773,7 +7798,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -7783,7 +7808,7 @@ def: "A relationship that holds between a GO molecular function and a component 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'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -7793,7 +7818,7 @@ def: "A relationship that holds between a GO molecular function and a component 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'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -7801,7 +7826,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -7811,44 +7836,44 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -8146,6 +8171,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has_participant @@ -8162,6 +8188,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has_participant inverse_of: RO:0002353 ! output of @@ -8183,7 +8210,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -8196,6 +8223,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -8207,6 +8235,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -8245,6 +8274,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -8273,7 +8303,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -8285,6 +8315,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has_participant is_a: RO:0002328 ! functionally related to @@ -8382,6 +8413,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -8397,6 +8429,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -8498,11 +8531,12 @@ is_a: RO:0002500 ! causal agent in process [Typedef] id: RO:0002432 name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "executes activity in" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000066 {RO:0002581="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002328 ! functionally related to @@ -8750,6 +8784,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -8763,6 +8798,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -8813,7 +8849,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -8824,6 +8860,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -8835,7 +8872,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -8848,7 +8885,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -8859,6 +8896,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -8867,6 +8905,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -8886,7 +8925,7 @@ is_obsolete: true id: RO:0009501 name: realized in response to def: "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." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -8942,7 +8981,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -8951,7 +8990,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] diff --git a/omrse-full.owl b/omrse-full.owl index 031abc5..50d4a27 100644 --- a/omrse-full.owl +++ b/omrse-full.owl @@ -5,6 +5,7 @@ xmlns:obo="http://purl.obolibrary.org/obo/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:www="http://www.referent-tracking.com/" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:foaf="http://xmlns.com/foaf/0.1/" @@ -18,7 +19,7 @@ xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Barry Smith Chris Stoeckert Daniel Welch @@ -37,10 +38,10 @@ Swetha Garimalla William Hogan The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations. + Ontology for Modeling and Representation of Social Entities https://creativecommons.org/licenses/by/4.0/ This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt - Ontology for Modeling and Representation of Social Entities - 2023-10-08 + 2024-01-10 @@ -110,6 +111,7 @@ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage example of usage @@ -164,6 +166,26 @@ 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> @@ -645,6 +667,170 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initalisms + + + 2023-03-03 + abbreviation + + + + + + + + + A synonym type for describing ambiguous synonyms + + + 2023-03-03 + ambiguous synonym + + + + + + + + + A synonym type for describing dubious synonyms + + + 2023-03-03 + dubious synonym + + + + + + + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + + 2023-03-03 + layperson synonym + + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + + + + + + + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + + 2023-03-03 + UK spelling synonym + + + + + + + + + A synonym type for common misspellings + + + 2023-03-03 + misspelling + + + + + + + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + + 2023-03-03 + misnomer + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + @@ -921,12 +1107,24 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -939,6 +1137,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -951,6 +1155,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -963,6 +1173,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1014,6 +1230,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1045,6 +1267,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -1095,6 +1329,23 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + - + BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. + is-aggregate-of obsolete is-aggregate-of true @@ -2113,6 +2370,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has_participant @@ -2422,7 +2680,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -2435,7 +2693,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -2449,7 +2707,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -2461,7 +2719,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -2476,7 +2734,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -2488,7 +2746,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -2497,7 +2755,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -2508,7 +2766,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -2516,7 +2774,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -2527,7 +2785,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -2535,7 +2793,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -2546,7 +2804,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -2555,7 +2813,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -3010,6 +3268,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope has input + https://wiki.geneontology.org/Has_input @@ -3032,6 +3291,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope has output + https://wiki.geneontology.org/Has_output @@ -3066,7 +3326,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -3083,6 +3343,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3098,6 +3359,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope causally upstream of, negative effect + @@ -3171,6 +3433,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope 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. enables + https://wiki.geneontology.org/Enables @@ -3229,7 +3492,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -3243,6 +3506,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope enabled by + https://wiki.geneontology.org/Enabled_by @@ -3398,6 +3662,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -3425,6 +3690,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -3610,6 +3876,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different enables activity in is active in + https://wiki.geneontology.org/Is_active_in @@ -3624,8 +3891,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -4025,6 +4292,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -4042,6 +4310,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -4129,7 +4398,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -4147,6 +4416,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -4166,7 +4436,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -4186,7 +4456,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -4199,6 +4469,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4211,6 +4482,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -4260,7 +4532,7 @@ For example, A and B may be gene products and binding of B by A positively regul triggered by process - RO:cjm + @@ -4325,7 +4597,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -4338,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -4358,7 +4630,7 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -4985,13 +5257,13 @@ For example, A and B may be gene products and binding of B by A positively regul an organism the bottom right portion of a human torso the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) 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]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -5282,6 +5554,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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]) 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) (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] + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -5506,6 +5779,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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]) 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. (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] + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -5810,6 +6084,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -6341,7 +6616,6 @@ Note: this definition was taken over from "geopolitical organization". 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. - 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular function GO:0003674 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. @@ -6353,12 +6627,6 @@ Note: this definition was taken over from "geopolitical organization". 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. 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. - GOC:pdt - @@ -6390,7 +6658,6 @@ Note: this definition was taken over from "geopolitical organization". 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. - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -6408,12 +6675,6 @@ Note: this definition was taken over from "geopolitical organization". 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. GOC:pdt - - - - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - GOC:pdt - @@ -10821,7 +11082,7 @@ Is part_of the appropriate relation to use for data items and documented identit - + Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role. Mathias Brochhausen @@ -11646,6 +11907,40 @@ http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some intervention + + + + + A data item that contains the outcome of a survey. + Alice Nzinga + Mathias Brochhausen + survey data + + + + + + + + + A plan specification that is realized by process of gathering information (e.g. by asking questions). + Alice Nzinga + Mathias Brochhausen + survey plan specification + + + + + + + + + A planned process that realizes the concretization of a survey to generate an output(survey data.) + survey execution + + + + @@ -11872,7 +12167,9 @@ edited date: 30 SEPT 2015 Alice Nzinga Mathias Brochhausen + obsolete survey data + true @@ -11883,7 +12180,9 @@ edited date: 30 SEPT 2015 Alice Nzinga Mathias Brochhausen + obsolete survey plan specification + true @@ -11892,7 +12191,9 @@ edited date: 30 SEPT 2015 + obsolete survey execution + true @@ -12071,7 +12372,7 @@ edited date: 30 SEPT 2015 - 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 @@ -12334,14 +12635,11 @@ edited date: 30 SEPT 2015 - A role inhering in an entity realized by social interactions in human society. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl Previous definition: A role played by an entity in human social processes. obsolete role in human social processes - role in human social processes true @@ -13052,7 +13350,7 @@ Note: this definition was taken over from "geopolitical organization". - + @@ -13063,14 +13361,14 @@ Note: this definition was taken over from "geopolitical organization". Mathias Brochhausen facility - + - + 09/09/2017 @@ -13888,42 +14186,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. racial identity information content entity obsolete racial identity datum @@ -13959,42 +14222,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. Amanda Hicks ethnic identity information content entity @@ -14558,54 +14786,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. social identity information content entity Amanda Hicks @@ -14618,42 +14799,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method. gender identity information content entity Amanda Hicks @@ -15162,22 +15308,9 @@ Somehow involves skilled nursing encounters - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OMRSE_00000198 - questions asking process + obsolete questions asking process true @@ -15264,7 +15397,7 @@ Somehow involves skilled nursing encounters - material information bearer of question text plus answer set + obsolete material information bearer of question text plus answer set true @@ -15292,7 +15425,7 @@ Somehow involves skilled nursing encounters - identity question asking process + obsolete identity question asking process true @@ -15303,7 +15436,7 @@ Somehow involves skilled nursing encounters http://purl.obolibrary.org/obo/OMRSE_00000199 - ethnic identity question asking process + obsolete ethnic identity question asking process true @@ -15314,7 +15447,7 @@ Somehow involves skilled nursing encounters http://purl.obolibrary.org/obo/OMRSE_00000200 - race identity question asking process + obsolete race identity question asking process true @@ -15559,24 +15692,7 @@ Somehow involves skilled nursing encounters - - - - - - - - - - - - - - - - - A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output. S. Clint Dowland Mathias Brochhausen @@ -16115,7 +16231,7 @@ Somehow involves skilled nursing encounters - + The Alachua county smoking survey plan specification. A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county. Mathias Brochhausen @@ -16144,8 +16260,7 @@ Somehow involves skilled nursing encounters - - + @@ -16180,8 +16295,7 @@ Somehow involves skilled nursing encounters - - + @@ -18261,6 +18375,7 @@ It indicates that a person has completed only early childhood education and noth A role that inheres in some entity that is realized in a social act. Matthew Diller + http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes @@ -18501,9 +18616,9 @@ It indicates that a person has completed only early childhood education and noth - + - + A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. Sarah Bost @@ -18513,9 +18628,9 @@ It indicates that a person has completed only early childhood education and noth - + - + A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. Sarah Bost @@ -18592,6 +18707,7 @@ It indicates that a person has completed only early childhood education and noth ready for release + 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." ready for release @@ -18625,6 +18741,7 @@ It indicates that a person has completed only early childhood education and noth pending final vetting + 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. pending final vetting @@ -18756,6 +18873,7 @@ It indicates that a person has completed only early childhood education and noth requires discussion + 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. Alan Ruttenberg group:OBI @@ -18778,6 +18896,20 @@ It indicates that a person has completed only early childhood education and noth + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initalisms + + + 2023-03-03 + abbreviation + + + + + + + + + A synonym type for describing ambiguous synonyms + + + 2023-03-03 + ambiguous synonym + + + + + + + + + A synonym type for describing dubious synonyms + + + 2023-03-03 + dubious synonym + + + + + + + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + + 2023-03-03 + layperson synonym + + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + + + + + + + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + + 2023-03-03 + UK spelling synonym + + + + + + + + + A synonym type for common misspellings + + + 2023-03-03 + misspelling + + + + + + + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + + 2023-03-03 + misnomer + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + @@ -921,12 +1107,24 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -939,6 +1137,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -951,6 +1155,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -963,6 +1173,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1014,6 +1230,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -1045,6 +1267,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -1095,6 +1329,23 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + - + BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. + is-aggregate-of obsolete is-aggregate-of true @@ -2113,6 +2370,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has_participant @@ -2422,7 +2680,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -2435,7 +2693,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -2449,7 +2707,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -2461,7 +2719,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -2476,7 +2734,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -2488,7 +2746,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -2497,7 +2755,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -2508,7 +2766,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -2516,7 +2774,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -2527,7 +2785,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -2535,7 +2793,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -2546,7 +2804,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -2555,7 +2813,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -3010,6 +3268,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope has input + https://wiki.geneontology.org/Has_input @@ -3032,6 +3291,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope has output + https://wiki.geneontology.org/Has_output @@ -3066,7 +3326,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -3083,6 +3343,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -3098,6 +3359,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope causally upstream of, negative effect + @@ -3171,6 +3433,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope 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. enables + https://wiki.geneontology.org/Enables @@ -3229,7 +3492,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -3243,6 +3506,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope enabled by + https://wiki.geneontology.org/Enabled_by @@ -3398,6 +3662,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -3425,6 +3690,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -3610,6 +3876,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different enables activity in is active in + https://wiki.geneontology.org/Is_active_in @@ -3624,8 +3891,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + + @@ -4025,6 +4292,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -4042,6 +4310,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -4129,7 +4398,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -4147,6 +4416,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -4166,7 +4436,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -4186,7 +4456,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -4199,6 +4469,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -4211,6 +4482,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -4260,7 +4532,7 @@ For example, A and B may be gene products and binding of B by A positively regul triggered by process - RO:cjm + @@ -4325,7 +4597,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -4338,7 +4610,7 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -4358,7 +4630,7 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -4985,13 +5257,13 @@ For example, A and B may be gene products and binding of B by A positively regul an organism the bottom right portion of a human torso the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) 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]) 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]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -5282,6 +5554,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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]) 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) (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] + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -5506,6 +5779,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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]) 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. (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] + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -5810,6 +6084,7 @@ For example, A and B may be gene products and binding of B by A positively regul 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. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -6341,7 +6616,6 @@ Note: this definition was taken over from "geopolitical organization". 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. - 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular function GO:0003674 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. @@ -6353,12 +6627,6 @@ Note: this definition was taken over from "geopolitical organization". 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. 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. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. - GOC:pdt - @@ -6390,7 +6658,6 @@ Note: this definition was taken over from "geopolitical organization". 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. - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process @@ -6408,12 +6675,6 @@ Note: this definition was taken over from "geopolitical organization". 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. GOC:pdt - - - - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - GOC:pdt - @@ -10821,7 +11082,7 @@ Is part_of the appropriate relation to use for data items and documented identit - + Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role. Mathias Brochhausen @@ -11646,6 +11907,40 @@ http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some intervention + + + + + A data item that contains the outcome of a survey. + Alice Nzinga + Mathias Brochhausen + survey data + + + + + + + + + A plan specification that is realized by process of gathering information (e.g. by asking questions). + Alice Nzinga + Mathias Brochhausen + survey plan specification + + + + + + + + + A planned process that realizes the concretization of a survey to generate an output(survey data.) + survey execution + + + + @@ -11872,7 +12167,9 @@ edited date: 30 SEPT 2015 Alice Nzinga Mathias Brochhausen + obsolete survey data + true @@ -11883,7 +12180,9 @@ edited date: 30 SEPT 2015 Alice Nzinga Mathias Brochhausen + obsolete survey plan specification + true @@ -11892,7 +12191,9 @@ edited date: 30 SEPT 2015 + obsolete survey execution + true @@ -12071,7 +12372,7 @@ edited date: 30 SEPT 2015 - 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 @@ -12334,14 +12635,11 @@ edited date: 30 SEPT 2015 - A role inhering in an entity realized by social interactions in human society. Mathias Brochhausen - http://purl.obolibrary.org/obo/omrse.owl Previous definition: A role played by an entity in human social processes. obsolete role in human social processes - role in human social processes true @@ -13052,7 +13350,7 @@ Note: this definition was taken over from "geopolitical organization". - + @@ -13063,14 +13361,14 @@ Note: this definition was taken over from "geopolitical organization". Mathias Brochhausen facility - + - + 09/09/2017 @@ -13888,42 +14186,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. racial identity information content entity obsolete racial identity datum @@ -13959,42 +14222,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method. Amanda Hicks ethnic identity information content entity @@ -14558,54 +14786,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. social identity information content entity Amanda Hicks @@ -14618,42 +14799,7 @@ last accessed June 30, 2015 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method. gender identity information content entity Amanda Hicks @@ -15162,22 +15308,9 @@ Somehow involves skilled nursing encounters - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OMRSE_00000198 - questions asking process + obsolete questions asking process true @@ -15264,7 +15397,7 @@ Somehow involves skilled nursing encounters - material information bearer of question text plus answer set + obsolete material information bearer of question text plus answer set true @@ -15292,7 +15425,7 @@ Somehow involves skilled nursing encounters - identity question asking process + obsolete identity question asking process true @@ -15303,7 +15436,7 @@ Somehow involves skilled nursing encounters http://purl.obolibrary.org/obo/OMRSE_00000199 - ethnic identity question asking process + obsolete ethnic identity question asking process true @@ -15314,7 +15447,7 @@ Somehow involves skilled nursing encounters http://purl.obolibrary.org/obo/OMRSE_00000200 - race identity question asking process + obsolete race identity question asking process true @@ -15559,24 +15692,7 @@ Somehow involves skilled nursing encounters - - - - - - - - - - - - - - - - - A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output. S. Clint Dowland Mathias Brochhausen @@ -16115,7 +16231,7 @@ Somehow involves skilled nursing encounters - + The Alachua county smoking survey plan specification. A survey plan specification that aims to collect information about the smoking behavior or lack thereof of a population on a county level. Concretization of a smoking survey plan that is stratified by county. Mathias Brochhausen @@ -16144,8 +16260,7 @@ Somehow involves skilled nursing encounters - - + @@ -16180,7 +16295,7 @@ Somehow involves skilled nursing encounters - + @@ -18260,6 +18375,7 @@ It indicates that a person has completed only early childhood education and noth A role that inheres in some entity that is realized in a social act. Matthew Diller + http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes @@ -18500,9 +18616,9 @@ It indicates that a person has completed only early childhood education and noth - + - + A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. Sarah Bost @@ -18512,9 +18628,9 @@ It indicates that a person has completed only early childhood education and noth - + - + A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. Sarah Bost @@ -18591,6 +18707,7 @@ It indicates that a person has completed only early childhood education and noth ready for release + 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." ready for release @@ -18624,6 +18741,7 @@ It indicates that a person has completed only early childhood education and noth pending final vetting + 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. pending final vetting @@ -18755,6 +18873,7 @@ It indicates that a person has completed only early childhood education and noth requires discussion + 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. Alan Ruttenberg group:OBI @@ -18777,6 +18896,20 @@ It indicates that a person has completed only early childhood education and noth + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + +