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Change SynonymType to SynonymTypeProperty #158

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Nov 2, 2023
Merged

Change SynonymType to SynonymTypeProperty #158

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3110f09
Change SynonymType to SynonymTypeProperty
matentzn Oct 26, 2023
c976707
Merge branch 'master' into matentzn-patch-1
matentzn Nov 2, 2023
6c7b90d
Update annotation_properties.tsv
matentzn Nov 2, 2023
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28 changes: 14 additions & 14 deletions src/ontology/omo-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -590,7 +590,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>abbreviation</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -603,7 +603,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>ambiguous synonym</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -616,7 +616,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>dubious synonym</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -630,7 +630,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>layperson synonym</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -644,7 +644,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>plural form</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -658,7 +658,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>UK spelling synonym</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -671,7 +671,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>misspelling</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -684,7 +684,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>misnomer</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -698,7 +698,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-07-25</terms:created>
<rdfs:label>previous name</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -712,7 +712,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-07-27</terms:created>
<rdfs:label>legal name</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -726,7 +726,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<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"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand All @@ -740,7 +740,7 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]
<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"/>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>


Expand Down Expand Up @@ -853,9 +853,9 @@ EquivalentTo: xsd:integer[&gt; 2151 , &lt;= 2300]



<!-- http://www.geneontology.org/formats/oboInOwl#SynonymType -->
<!-- http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymType"/>
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>



Expand Down
26 changes: 13 additions & 13 deletions src/templates/annotation_properties.tsv
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Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
relation id (required) type label (required) definition (required) parent property contributon ORCID (required) Date created (required) example of use term tracker item exact synonym
ID TYPE AT rdfs:label^^xsd:string AT IAO:0000115^^xsd:string SP % AI dc:contributor AT dc:created^^xsd:date AT IAO:0000112^^xsd:string AI IAO:0000233 AT oboInOwl:hasExactSynonym^^xsd:string
OMO:0003000 owl:AnnotationProperty abbreviation A synonym type for describing abbreviations or initalisms oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003001 owl:AnnotationProperty ambiguous synonym A synonym type for describing ambiguous synonyms oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003002 owl:AnnotationProperty dubious synonym A synonym type for describing dubious synonyms oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003003 owl:AnnotationProperty layperson synonym A synonym type for describing layperson or colloquial synonyms oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003004 owl:AnnotationProperty plural form A synonym type for describing pluralization synonyms oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003005 owl:AnnotationProperty UK spelling synonym A synonym type for describing UK spelling variants oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003006 owl:AnnotationProperty misspelling A synonym type for common misspellings oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/132
OMO:0003007 owl:AnnotationProperty misnomer A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/133
OMO:0003008 owl:AnnotationProperty previous name A synonym type for names that have been used as primary labels in the past. oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-07-25 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/139
OMO:0003009 owl:AnnotationProperty legal name A synonym type for the legal entity name oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-07-27 The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College https://github.com/information-artifact-ontology/ontology-metadata/issues/141
OMO:0003010 owl:AnnotationProperty International Nonproprietary Name 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. oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-09-30 "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" https://github.com/information-artifact-ontology/ontology-metadata/issues/149 INN
OMO:0003011 owl:AnnotationProperty latin term A synonym type for describing Latin term synonyms. oboInOwl:SynonymType https://orcid.org/0000-0002-1773-2692 2023-10-12 nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis" https://github.com/information-artifact-ontology/ontology-metadata/issues/146
OMO:0003012 owl:AnnotationProperty acronym A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. oboInOwl:SynonymType https://orcid.org/0000-0003-4423-4370 2023-11-01 NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. https://github.com/information-artifact-ontology/ontology-metadata/issues/135
OMO:0003000 owl:AnnotationProperty abbreviation A synonym type for describing abbreviations or initalisms oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003001 owl:AnnotationProperty ambiguous synonym A synonym type for describing ambiguous synonyms oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003002 owl:AnnotationProperty dubious synonym A synonym type for describing dubious synonyms oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003003 owl:AnnotationProperty layperson synonym A synonym type for describing layperson or colloquial synonyms oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003004 owl:AnnotationProperty plural form A synonym type for describing pluralization synonyms oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003005 owl:AnnotationProperty UK spelling synonym A synonym type for describing UK spelling variants oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) https://github.com/information-artifact-ontology/ontology-metadata/issues/122
OMO:0003006 owl:AnnotationProperty misspelling A synonym type for common misspellings oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/132
OMO:0003007 owl:AnnotationProperty misnomer A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-03-03 https://github.com/information-artifact-ontology/ontology-metadata/issues/133
OMO:0003008 owl:AnnotationProperty previous name A synonym type for names that have been used as primary labels in the past. oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-07-25 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/139
OMO:0003009 owl:AnnotationProperty legal name A synonym type for the legal entity name oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-07-27 The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College https://github.com/information-artifact-ontology/ontology-metadata/issues/141
OMO:0003010 owl:AnnotationProperty International Nonproprietary Name 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. oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-09-30 "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" https://github.com/information-artifact-ontology/ontology-metadata/issues/149 INN
OMO:0003011 owl:AnnotationProperty latin term A synonym type for describing Latin term synonyms. oboInOwl:SynonymTypeProperty https://orcid.org/0000-0002-1773-2692 2023-10-12 nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis" https://github.com/information-artifact-ontology/ontology-metadata/issues/146
OMO:0003012 owl:AnnotationProperty acronym A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. oboInOwl:SynonymTypeProperty https://orcid.org/0000-0003-4423-4370 2023-11-01 NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. https://github.com/information-artifact-ontology/ontology-metadata/issues/135
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