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Update #152

Merged
merged 34 commits into from
Sep 15, 2022
Merged

Update #152

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dda4311
Add GO based terms, ref #141 ref #142 ref #143.
seger Aug 10, 2021
3c525d9
New metaplastic and neoplastic terms, ref #146.
seger Aug 25, 2021
e194565
Additional width terms, ref #145.
seger Aug 31, 2021
f7ddd11
Consistent cilium size terms, ref #139.
seger Sep 6, 2021
f181157
Replace temp edematous terms, ref #138.
seger Sep 6, 2021
f27ef15
Run release pipeline.
seger Sep 7, 2021
214fb2b
New whole organism mass terms, ref #144.
seger Oct 14, 2021
27cf8ae
Run release pipeline.
seger Oct 14, 2021
6b16ab1
Add new GO metabolism terms, ref #150.
seger Jun 1, 2022
d7e0b65
Add publication as a comment.
seger Jul 25, 2022
5f1fd8f
Add GO based terms, ref #141 ref #142 ref #143.
seger Aug 10, 2021
5e1f503
New metaplastic and neoplastic terms, ref #146.
seger Aug 25, 2021
13adae4
Additional width terms, ref #145.
seger Aug 31, 2021
a992d07
Consistent cilium size terms, ref #139.
seger Sep 6, 2021
cb94bc6
Replace temp edematous terms, ref #138.
seger Sep 6, 2021
dc1d179
Run release pipeline.
seger Sep 7, 2021
863b73d
New whole organism mass terms, ref #144.
seger Oct 14, 2021
63fc3db
Run release pipeline.
seger Oct 14, 2021
a85aa22
Add new GO metabolism terms, ref #150.
seger Jun 1, 2022
d3c07fb
Add publication as a comment.
seger Jul 25, 2022
9001c94
Merge branch 'update' of https://github.com/obophenotype/xenopus-phen…
seger Aug 3, 2022
fb72932
Run release pipeline.
seger Aug 11, 2022
63b8ded
New body axis phenotypes, ref #147.
seger Aug 25, 2022
27aeecc
Obsolete body axis terms.
seger Aug 26, 2022
f132a04
BP phenotypes for new XAO terms.
seger Aug 26, 2022
ddce422
histone BP temrs, ref #153.
seger Aug 26, 2022
685e1bb
Replacement cilium motiliy terms, ref #154.
seger Aug 26, 2022
c09cb21
Obsolete cilium motility terms.
seger Aug 26, 2022
a630721
Phenotypes for new XAO classes.
seger Sep 14, 2022
2e3cf90
rm release artefacts.
seger Sep 14, 2022
ba668d1
New release.
seger Sep 14, 2022
18b4623
Fix patterns.
seger Sep 15, 2022
6d19819
Fix patterns.
seger Sep 15, 2022
99a30b5
New release.
seger Sep 15, 2022
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9 changes: 9 additions & 0 deletions .gitignore
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Expand Up @@ -50,3 +50,12 @@ src/patterns/reserved_iris.txt
src/patterns/tmp
src/patterns/xpo.csv
src/ontology/reports/trailing-whitespace-violation.csv
xpo-full.json
xpo-full.obo
xpo-full.owl
xpo-simple.json
xpo-simple.obo
xpo-simple.owl
xpo.json
xpo.obo
xpo.owl
3,330 changes: 2,753 additions & 577 deletions patterns/definitions.owl
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53 changes: 48 additions & 5 deletions patterns/pattern.owl
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139 changes: 81 additions & 58 deletions src/ontology/Makefile
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4 changes: 2 additions & 2 deletions src/ontology/imports/bfo_import.owl
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Expand Up @@ -10,9 +10,9 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/xpo/imports/bfo_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/bfo_import.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/bfo_import.owl"/>
<dc:source rdf:resource="http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
</owl:Ontology>


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4 changes: 2 additions & 2 deletions src/ontology/imports/chebi_import.owl
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Expand Up @@ -10,8 +10,8 @@
xmlns:chebi="http://purl.obolibrary.org/obo/chebi#3"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/xpo/imports/chebi_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/chebi_import.owl"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/chebi_import.owl"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
</owl:Ontology>


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72,177 changes: 43,206 additions & 28,971 deletions src/ontology/imports/go_import.owl
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28 changes: 26 additions & 2 deletions src/ontology/imports/iao_import.owl
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Expand Up @@ -10,9 +10,9 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/xpo/imports/iao_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/iao_import.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/iao_import.owl"/>
<dc:source rdf:resource="http://purl.obolibrary.org/obo/iao/2020-12-09/iao.owl"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -874,6 +874,30 @@ Previous. An information content entity is a non-realizable information entity t



<!-- http://purl.obolibrary.org/obo/PATO_0000125 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000125">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001018"/>
<obo:IAO_0000111>mass</obo:IAO_0000111>
<obo:IAO_0000115>A physical quality that inheres in a bearer by virtue of the proportion of the bearer&apos;s amount of matter.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label>mass</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0001018 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001018">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001241"/>
<obo:IAO_0000111>physical quality</obo:IAO_0000111>
<obo:IAO_0000115>A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
<rdfs:label>physical quality</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/PATO_0001241 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001241">
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16 changes: 9 additions & 7 deletions src/ontology/imports/nbo_import.owl
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Expand Up @@ -19,9 +19,9 @@
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/xpo/imports/nbo_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2021-03-05/imports/nbo_import.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/xpo/releases/2022-09-15/imports/nbo_import.owl"/>
<dc:source rdf:resource="http://purl.obolibrary.org/obo/nbo/releases/2021-02-15/nbo.owl"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-03-05</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-09-15</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -498,7 +498,9 @@

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

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym"/>
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym">
<rdfs:label>has_narrow_synonym</rdfs:label>
</owl:AnnotationProperty>



Expand Down Expand Up @@ -2926,7 +2928,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0009605"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:hb</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>GOC:hb</oboInOwl:hasDbXref>
</owl:Axiom>


Expand All @@ -2947,7 +2949,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0009612"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:hb</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>GOC:hb</oboInOwl:hasDbXref>
</owl:Axiom>


Expand All @@ -2971,7 +2973,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/GO_0009628"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GOC:hb</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>GOC:hb</oboInOwl:hasDbXref>
</owl:Axiom>


Expand Down Expand Up @@ -3834,7 +3836,7 @@ For example, A and B may be gene products and binding of B by A positively regul
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PATO_0000161"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A quality of a single process inhering in a bearer by virtue of the bearer&apos;s occurrence per unit time.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PATOC:melissa</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PATOC:melissa</oboInOwl:hasDbXref>
</owl:Axiom>


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