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Only copy over the direct superclass of our terms from other ontologies #20

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Only copy over the direct superclass of our terms from other ontologies #20

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a6094c1
Only copy over the direct superclass of our terms from other ontologies
arteymix Nov 26, 2023
edc2588
Add missing homozygous definition from GENO
arteymix Nov 26, 2023
8dce3a3
Remove unnecessary XML namespaces
arteymix Nov 27, 2023
a5ffcca
Add a full OWL ontology with imports
arteymix Nov 27, 2023
c0bb38f
Ignore properties file and ROBOT JAR
arteymix Nov 27, 2023
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -4,3 +4,5 @@ TGEMO-Interim.OBO
TGEMO-Interim.OWL
.DS_Store
catalog-v001.xml
*.properties
robot.jar
51 changes: 51 additions & 0 deletions TGEMO-full.OWL
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@@ -0,0 +1,51 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://gemma.msl.ubc.ca/ont/TGEMO/"
xml:base="http://gemma.msl.ubc.ca/ont/TGEMO/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:so="http://purl.obolibrary.org/obo/so#"
xmlns:efo="http://www.ebi.ac.uk/efo/"
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:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:cito="http://purl.org/spar/cito/"
xmlns:core="http://purl.obolibrary.org/obo/uberon/core#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:efo3="http://www.ebi.ac.uk/efo/#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:obo1="http://purl.obolibrary.org/obo#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:chebi="http://purl.obolibrary.org/obo/chebi/"
xmlns:mondo="http://purl.obolibrary.org/obo/mondo#"
xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:vocab="https://w3id.org/semapv/vocab/"
xmlns:chebi2="http://purl.obolibrary.org/obo/chebi#"
xmlns:chebi5="http://purl.obolibrary.org/obo/chebi#2"
xmlns:chebi6="http://purl.obolibrary.org/obo/chebi#3"
xmlns:chebi7="http://purl.obolibrary.org/obo/chebi#1"
xmlns:refont="http://purl.obolibrary.org/obo/uberon/refont/"
xmlns:uberon="http://purl.obolibrary.org/obo/uberon#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:cellline="http://www.ebi.ac.uk/cellline#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:patterns="http://www.co-ode.org/patterns#"
xmlns:cellline4="http://www.ebi.ac.uk/cellline/"
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#">
<owl:Ontology rdf:about="http://gemma.msl.ubc.ca/ont/TGEMO">
<owl:imports rdf:resource="http://gemma.msl.ubc.ca/ont/TGEMO"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/clo.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/geno/releases/2023-10-08/geno.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/so/2021-11-22/so.owl"/>
<owl:imports rdf:resource="http://www.ebi.ac.uk/efo/releases/v3.60.0/efo.owl"/>
</owl:Ontology>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->

173 changes: 124 additions & 49 deletions TGEMO.OWL
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Expand Up @@ -2,47 +2,15 @@
<rdf:RDF xmlns="http://gemma.msl.ubc.ca/ont/TGEMO#"
xml:base="http://gemma.msl.ubc.ca/ont/TGEMO"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:so="http://purl.obolibrary.org/obo/so#"
xmlns:efo="http://www.ebi.ac.uk/efo/"
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:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:cito="http://purl.org/spar/cito/"
xmlns:core="http://purl.obolibrary.org/obo/uberon/core#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:efo3="http://www.ebi.ac.uk/efo/#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:obo1="http://purl.obolibrary.org/obo#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:chebi="http://purl.obolibrary.org/obo/chebi/"
xmlns:mondo="http://purl.obolibrary.org/obo/mondo#"
xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:vocab="https://w3id.org/semapv/vocab/"
xmlns:chebi2="http://purl.obolibrary.org/obo/chebi#"
xmlns:chebi5="http://purl.obolibrary.org/obo/chebi#2"
xmlns:chebi6="http://purl.obolibrary.org/obo/chebi#3"
xmlns:chebi7="http://purl.obolibrary.org/obo/chebi#1"
xmlns:refont="http://purl.obolibrary.org/obo/uberon/refont/"
xmlns:uberon="http://purl.obolibrary.org/obo/uberon#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:cellline="http://www.ebi.ac.uk/cellline#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:patterns="http://www.co-ode.org/patterns#"
xmlns:cellline4="http://www.ebi.ac.uk/cellline/"
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#">
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://gemma.msl.ubc.ca/ont/TGEMO">
<owl:versionIRI rdf:resource="http://gemma.msl.ubc.ca/ont/TGEMO"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/clo.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/geno.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro.owl"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/so.owl"/>
<owl:imports rdf:resource="http://www.geneontology.org/formats/oboInOwl"/>
<owl:imports rdf:resource="https://www.ebi.ac.uk/efo/efo.owl"/>
<dc:contributor>Guillaume Poirier-Morency</dc:contributor>
<dc:contributor>Mahan Rafieenaini</dc:contributor>
<dc:contributor>Paul Pavlidis</dc:contributor>
Expand Down Expand Up @@ -73,6 +41,48 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232"/>



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

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>



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

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>



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

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/language"/>



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

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/license"/>



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

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/rights"/>



<!-- http://www.geneontology.org/formats/oboInOwl#auto-generated-by -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#auto-generated-by"/>
Expand Down Expand Up @@ -103,6 +113,24 @@



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

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



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

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



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

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



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

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
Expand Down Expand Up @@ -141,6 +169,12 @@



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

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



<!-- http://www.geneontology.org/formats/oboInOwl#saved-by -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#saved-by"/>
Expand Down Expand Up @@ -237,6 +271,22 @@



<!-- http://purl.obolibrary.org/obo/RO_0000086 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000086">
<rdfs:label>has quality</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/RO_0002566 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002566">
<rdfs:label>causally influences</rdfs:label>
</owl:ObjectProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand Down Expand Up @@ -839,51 +889,76 @@



<!-- http://purl.obolibrary.org/obo/NCBITaxon_10116 -->
<!-- http://purl.obolibrary.org/obo/GENO_0000136 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/GENO_0000136">
<rdfs:label>homozygous</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0000510 -->
<!-- http://purl.obolibrary.org/obo/NCBITaxon_10090 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000510"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10090">
<rdfs:label>Mus musculus</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0000597 -->
<!-- http://purl.obolibrary.org/obo/SO_0000287 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000597"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000287">
<rdfs:label>fusion_gene</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0000604 -->
<!-- http://purl.obolibrary.org/obo/SO_0000288 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000604"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000288">
<rdfs:label>engineered_fusion_gene</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0002547 -->
<!-- http://purl.obolibrary.org/obo/SO_0002053 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0002547"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0002053">
<rdfs:label>gain_of_function_variant</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0002694 -->
<!-- http://www.ebi.ac.uk/efo/EFO_0000510 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000510">
<rdfs:label>genetic modification</rdfs:label>
</owl:Class>



<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0002694"/>
<!-- http://www.ebi.ac.uk/efo/EFO_0000604 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000604">
<rdfs:label>C57BL/10</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0004008 -->
<!-- http://www.ebi.ac.uk/efo/EFO_0002694 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0004008"/>
<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0002694">
<rdfs:label>experimental process</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/efo/EFO_0005181 -->
<!-- http://www.ebi.ac.uk/efo/EFO_0022483 -->

<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0005181"/>
<owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0022483">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
<rdfs:label>FVB</rdfs:label>
</owl:Class>
</rdf:RDF>


Expand Down