From 3e534262642051c38de72c8f32d37078faa9ca13 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 12 Oct 2023 14:05:06 +0300 Subject: [PATCH] Update release files 12 oct 2023 --- omo-full.json | 50 +++++++++++++++++++++++++++++++++++++++++++++++--- omo-full.obo | 4 ++-- omo-full.owl | 36 ++++++++++++++++++++++++++++++++---- omo.json | 50 +++++++++++++++++++++++++++++++++++++++++++++++--- omo.obo | 4 ++-- omo.owl | 36 ++++++++++++++++++++++++++++++++---- 6 files changed, 162 insertions(+), 18 deletions(-) diff --git a/omo-full.json b/omo-full.json index 2bc5c7f..6c16c6c 100644 --- a/omo-full.json +++ b/omo-full.json @@ -121,9 +121,9 @@ "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-23" + "val" : "2023-10-12" } ], - "version" : "http://purl.obolibrary.org/obo/omo/releases/2023-08-23/omo-full.json" + "version" : "http://purl.obolibrary.org/obo/omo/releases/2023-10-12/omo-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", @@ -626,7 +626,7 @@ "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. " + "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_0000117", "val" : "PERSON:Daniel Schober" @@ -1823,6 +1823,50 @@ "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://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has broad synonym", diff --git a/omo-full.obo b/omo-full.obo index aa022a9..d89eed1 100644 --- a/omo-full.obo +++ b/omo-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: omo/releases/2023-08-23/omo-full.owl +data-version: omo/releases/2023-10-12/omo-full.owl ontology: omo/omo-full property_value: defaultLanguage "en" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Adam Goldstein" xsd:string @@ -40,7 +40,7 @@ property_value: http://purl.org/dc/elements/1.1/contributor "Yongqun (Oliver) He property_value: http://purl.org/dc/elements/1.1/description "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)." xsd:string property_value: http://purl.org/dc/elements/1.1/title "OBO Metadata Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ -property_value: owl:versionInfo "2023-08-23" xsd:string +property_value: owl:versionInfo "2023-10-12" xsd:string [Term] id: IAO:0000027 diff --git a/omo-full.owl b/omo-full.owl index 14e4bc6..303e27e 100644 --- a/omo-full.owl +++ b/omo-full.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Adam Goldstein Alan Ruttenberg @@ -52,7 +52,7 @@ An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). OBO Metadata Ontology - 2023-08-23 + 2023-10-12 @@ -149,7 +149,7 @@ 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. +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> definition @@ -719,6 +719,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + 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 + + + + + @@ -1592,5 +1620,5 @@ No imports - + diff --git a/omo.json b/omo.json index e84fa33..eafb26a 100644 --- a/omo.json +++ b/omo.json @@ -121,9 +121,9 @@ "val" : "https://creativecommons.org/publicdomain/zero/1.0/" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2023-08-23" + "val" : "2023-10-12" } ], - "version" : "http://purl.obolibrary.org/obo/omo/releases/2023-08-23/omo.json" + "version" : "http://purl.obolibrary.org/obo/omo/releases/2023-10-12/omo.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", @@ -626,7 +626,7 @@ "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. " + "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_0000117", "val" : "PERSON:Daniel Schober" @@ -1823,6 +1823,50 @@ "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://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has broad synonym", diff --git a/omo.obo b/omo.obo index bfcec75..1fd005a 100644 --- a/omo.obo +++ b/omo.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2023-08-23 +data-version: releases/2023-10-12 ontology: omo property_value: defaultLanguage "en" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Adam Goldstein" xsd:string @@ -40,7 +40,7 @@ property_value: http://purl.org/dc/elements/1.1/contributor "Yongqun (Oliver) He property_value: http://purl.org/dc/elements/1.1/description "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)." xsd:string property_value: http://purl.org/dc/elements/1.1/title "OBO Metadata Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ -property_value: owl:versionInfo "2023-08-23" xsd:string +property_value: owl:versionInfo "2023-10-12" xsd:string [Term] id: IAO:0000027 diff --git a/omo.owl b/omo.owl index 4072bf3..a1b31b6 100644 --- a/omo.owl +++ b/omo.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Adam Goldstein Alan Ruttenberg @@ -52,7 +52,7 @@ An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). OBO Metadata Ontology - 2023-08-23 + 2023-10-12 @@ -149,7 +149,7 @@ 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. +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> definition @@ -719,6 +719,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + 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 + + + + + @@ -1592,5 +1620,5 @@ No imports - +