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Merge pull request #288 from pato-ontology/release-3dec2019
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Release 3 Dec 2019
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@matentzn
matentzn authored Dec 3, 2019
2 parents 42ec0b6 + 51f14f5 commit c1f137e
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458 changes: 244 additions & 214 deletions pato-base.json
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21 changes: 15 additions & 6 deletions pato-base.obo
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@@ -1,8 +1,5 @@
format-version: 1.2
data-version: pato/releases/2019-11-05/pato-base.owl
date: 07:02:2018 10:27
saved-by: segerdel
auto-generated-by: OBO-Edit 2.3.1
data-version: pato/releases/2019-12-03/pato-base.owl
subsetdef: abnormal_slim "Abnormal/normal slim"
subsetdef: absent_slim "Absent/present slim"
subsetdef: attribute_slim "Attribute slim"
Expand All @@ -15,6 +12,9 @@ subsetdef: scalar_slim "Scalar slim"
subsetdef: value_slim "Value slim"
default-namespace: quality
ontology: pato/pato-base
property_value: http://purl.org/dc/elements/1.1/description "An ontology of phenotypic qualities (properties, attributes or characteristics)." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "PATO - the Phenotype And Trait Ontology" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/ xsd:string

[Term]
id: PATO:0000000
Expand Down Expand Up @@ -8768,7 +8768,7 @@ is_a: PATO:0001377 ! polyploid
[Term]
id: PATO:0001384
name: hexaploid
def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid]
def: "A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes." [Wikipedia:http\://en.wikipedia.org/wiki/Hexaploid]
subset: cell_quality
subset: value_slim
is_a: PATO:0001377 ! polyploid
Expand Down Expand Up @@ -20420,6 +20420,15 @@ synonym: "structurally interrupted" EXACT []
is_a: PATO:0001241 ! physical object quality
created_by: http://orcid.org/0000-0001-5208-3432

[Term]
id: PATO:0040027
name: doubled haploid
def: "A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling." [Wikipedia:https\://en.wikipedia.org/wiki/Doubled_haploidy]
synonym: "double haploid" EXACT []
synonym: "double-haploid" EXACT []
is_a: PATO:0001393 ! euploid
created_by: http://orcid.org/0000-0001-5208-3432

[Term]
id: PATO:0045000
name: normal rate
Expand Down Expand Up @@ -21351,7 +21360,7 @@ creation_date: 2017-12-22T14:16:43Z
[Term]
id: PATO:0045075
name: normal variability of color
def: "A variability which is relatively normal or average" []
def: "A variability of color which is relatively normal or average" []
subset: value_slim
intersection_of: PATO:0001615 ! variant color
intersection_of: has_relative_magnitude PATO:0000461 ! normal
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77 changes: 43 additions & 34 deletions pato-base.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,14 +9,15 @@
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:pato="http://purl.obolibrary.org/obo/pato#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/pato/pato-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/pato/releases/2019-11-05/pato-base.owl"/>
<oboInOwl:auto-generated-by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBO-Edit 2.3.1</oboInOwl:auto-generated-by>
<oboInOwl:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">07:02:2018 10:27</oboInOwl:date>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/pato/releases/2019-12-03/pato-base.owl"/>
<dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An ontology of phenotypic qualities (properties, attributes or characteristics).</dc:description>
<dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PATO - the Phenotype And Trait Ontology</dc:title>
<terms:license rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://creativecommons.org/licenses/by/3.0/</terms:license>
<oboInOwl:default-namespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">quality</oboInOwl:default-namespace>
<oboInOwl:hasOBOFormatVersion rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.2</oboInOwl:hasOBOFormatVersion>
<oboInOwl:saved-by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">segerdel</oboInOwl:saved-by>
</owl:Ontology>


Expand Down Expand Up @@ -172,12 +173,6 @@



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

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#auto-generated-by"/>



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

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#consider">
Expand All @@ -198,12 +193,6 @@



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

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



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

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#default-namespace"/>
Expand Down Expand Up @@ -300,12 +289,6 @@



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

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



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

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
Expand Down Expand Up @@ -21307,7 +21290,7 @@ Association is weaker than correlation or proportionality. These relations may b

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0001384">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001377"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A polyploidy quality inhering in a bearer by virtue of the bearer&apos;s containing four homologous sets of chromosomes.</obo:IAO_0000115>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A polyploidy quality inhering in a bearer by virtue of the bearer&apos;s containing six homologous sets of chromosomes.</obo:IAO_0000115>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">quality</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PATO:0001384</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/pato#cell_quality"/>
Expand All @@ -21317,7 +21300,7 @@ Association is weaker than correlation or proportionality. These relations may b
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PATO_0001384"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A polyploidy quality inhering in a bearer by virtue of the bearer&apos;s containing four homologous sets of chromosomes.</owl:annotatedTarget>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A polyploidy quality inhering in a bearer by virtue of the bearer&apos;s containing six homologous sets of chromosomes.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wikipedia:http://en.wikipedia.org/wiki/Hexaploid</oboInOwl:hasDbXref>
</owl:Axiom>

Expand Down Expand Up @@ -49547,6 +49530,27 @@ height&apos;).</rdfs:comment>



<!-- http://purl.obolibrary.org/obo/PATO_0040027 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0040027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PATO_0001393"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A ploidy quality inhering in a bearer by virtue of the bearer&apos;s haploid cells undergo chromosome doubling.</obo:IAO_0000115>
<oboInOwl:created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://orcid.org/0000-0001-5208-3432</oboInOwl:created_by>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">double haploid</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">double-haploid</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">quality</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PATO:0040027</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">doubled haploid</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PATO_0040027"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A ploidy quality inhering in a bearer by virtue of the bearer&apos;s haploid cells undergo chromosome doubling.</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PATO_0045000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0045000">
Expand Down Expand Up @@ -51614,7 +51618,7 @@ height&apos;).</rdfs:comment>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A variability which is relatively normal or average</obo:IAO_0000115>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A variability of color which is relatively normal or average</obo:IAO_0000115>
<oboInOwl:created_by rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Luke Slater</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2017-12-22T14:16:43Z</oboInOwl:creation_date>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">quality</oboInOwl:hasOBONamespace>
Expand Down Expand Up @@ -52274,29 +52278,34 @@ height&apos;).</rdfs:comment>
-->

<owl:Class>
<owl:complementOf>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005634"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005929"/>
</owl:Restriction>
</owl:complementOf>
</owl:intersectionOf>
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0001405"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0001408"/>
</owl:Restriction>
</owl:equivalentClass>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005929"/>
<owl:Class>
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0005634"/>
</owl:Restriction>
</owl:complementOf>
<owl:equivalentClass>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0001408"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0001405"/>
</owl:Restriction>
</owl:equivalentClass>
</owl:Restriction>
</owl:Class>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
Expand Down
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