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Merge pull request #154 from information-artifact-ontology/release-12…
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…-10-2023

Update release files 12 oct 2023
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matentzn authored Oct 12, 2023
2 parents a3770d7 + 3e53426 commit 3686099
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50 changes: 47 additions & 3 deletions omo-full.json
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"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",
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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",
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4 changes: 2 additions & 2 deletions omo-full.obo
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@@ -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
Expand Down Expand Up @@ -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
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36 changes: 32 additions & 4 deletions omo-full.owl
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Expand Up @@ -12,7 +12,7 @@
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/omo/omo-full.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/omo/releases/2023-08-23/omo-full.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/omo/releases/2023-10-12/omo-full.owl"/>
<protege:defaultLanguage>en</protege:defaultLanguage>
<dc:contributor xml:lang="en">Adam Goldstein</dc:contributor>
<dc:contributor xml:lang="en">Alan Ruttenberg</dc:contributor>
Expand Down Expand Up @@ -52,7 +52,7 @@
<dc:description xml:lang="en">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).</dc:description>
<dc:title xml:lang="en">OBO Metadata Ontology</dc:title>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<owl:versionInfo>2023-08-23</owl:versionInfo>
<owl:versionInfo>2023-10-12</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -149,7 +149,7 @@ We don&apos;t have definitions of &apos;meaning&apos; or &apos;expression&apos;

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. </obo:IAO_0000116>
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.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
<rdfs:label xml:lang="en">definition</rdfs:label>
Expand Down Expand Up @@ -719,6 +719,34 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]



<!-- http://purl.obolibrary.org/obo/OMO_0003010 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0003010">
<obo:IAO_0000112>CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) &quot;paracetamol&quot;. In some cases such as this one, the INN might be the same as the ontology&apos;s primary label</obo:IAO_0000112>
<obo:IAO_0000115>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.</obo:IAO_0000115>
<obo:IAO_0000233 rdf:resource="https://github.com/information-artifact-ontology/ontology-metadata/issues/149"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-09-30</terms:created>
<rdfs:label>International Nonproprietary Name</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/OMO_0003011 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0003011">
<obo:IAO_0000112>nasopharynx (UBERON:0001728) has the latin name &quot;pars nasalis pharyngis</obo:IAO_0000112>
<obo:IAO_0000115>A synonym type for describing Latin term synonyms.</obo:IAO_0000115>
<obo:IAO_0000233 rdf:resource="https://github.com/information-artifact-ontology/ontology-metadata/issues/146"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-1773-2692"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-10-12</terms:created>
<rdfs:label>latin term</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
</owl:AnnotationProperty>



<!-- http://purl.org/dc/elements/1.1/contributor -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
Expand Down Expand Up @@ -1592,5 +1620,5 @@ No imports</obo:IAO_0000115>



<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

50 changes: 47 additions & 3 deletions omo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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",
Expand Down
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