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working on #3803
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fixing eqs, clarifying definition for when we mean hindlimb autopod, increasing consistency of labels
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@sbello
sbello committed Aug 8, 2023
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38 changes: 23 additions & 15 deletions src/ontology/mp-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -19779,14 +19779,16 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000572> "abnormal autopod morphology")
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000572> <http://purl.obolibrary.org/obo/MP_0002109>)

# Class: <http://purl.obolibrary.org/obo/MP_0000573> (enlarged hind paws)
# Class: <http://purl.obolibrary.org/obo/MP_0000573> (increased hindlimb autopod size)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "J:51296") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0000573> "larger than average size of the rear feet")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000573> "increased hind paw size")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000573> "enlarged hind paws")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0000573> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0000573> "MP:0000573")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000573> "enlarged hind paws")
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000573> <http://purl.obolibrary.org/obo/MP_0000572>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000573> "increased hindlimb autopod size")
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000573> <http://purl.obolibrary.org/obo/MP_0000556>)
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000573> <http://purl.obolibrary.org/obo/MP_0020242>)

# Class: <http://purl.obolibrary.org/obo/MP_0000574> (abnormal foot pad morphology)

Expand Down Expand Up @@ -19817,7 +19819,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/MP_0000575> <http://purl.obolibrary.o

# Class: <http://purl.obolibrary.org/obo/MP_0000576> (clubfoot)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ISBN:0-683-40008-8") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:10709991") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0000576> "congenital deformation of the feet; foot is plantarflexed, inverted and adducted")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ISBN:0-683-40008-8") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:10709991") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0000576> "congenital deformation of the autopods; hind or forelimb foot is plantarflexed, inverted and adducted")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/MP_0000576> "Fyler:4171")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000576> "club foot")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000576> "clubbed feet")
Expand All @@ -19827,7 +19829,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespac
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0000576> "MP:0000576")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/MP_0000576> <http://purl.obolibrary.org/obo/mp-edit#CvDC_Terms>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000576> "clubfoot")
EquivalentClasses(<http://purl.obolibrary.org/obo/MP_0000576> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001883> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002387>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000460>))))
EquivalentClasses(<http://purl.obolibrary.org/obo/MP_0000576> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0001883> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0002470>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000460>))))
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000576> <http://purl.obolibrary.org/obo/MP_0000572>)

# Class: <http://purl.obolibrary.org/obo/MP_0000577> (absent eccrine glands)
Expand All @@ -19844,12 +19846,13 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000577> "abse
EquivalentClasses(<http://purl.obolibrary.org/obo/MP_0000577> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000462> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0000423>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000460>))))
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000577> <http://purl.obolibrary.org/obo/MP_0013458>)

# Class: <http://purl.obolibrary.org/obo/MP_0000578> (ulcerated paws)
# Class: <http://purl.obolibrary.org/obo/MP_0000578> (ulcerated autopod)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "J:17194") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0000578> "inflammatory, often suppurating lesions on the paws; often become necrotic")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000578> "ulcerated paws")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0000578> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0000578> "MP:0000578")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000578> "ulcerated paws")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000578> "ulcerated autopod")
EquivalentClasses(<http://purl.obolibrary.org/obo/MP_0000578> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000470> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/MPATH_579> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/UBERON_0002470>))) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000460>))))
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000578> <http://purl.obolibrary.org/obo/MP_0000572>)

Expand Down Expand Up @@ -19907,6 +19910,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/MP_0000583> <http://purl.obolibrary.org/obo/mp-edit#IMPC>)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000583> "long toenails")
EquivalentClasses(<http://purl.obolibrary.org/obo/MP_0000583> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000573> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/UBERON_0001705>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002314> <http://purl.obolibrary.org/obo/UBERON_0002387>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002573> <http://purl.obolibrary.org/obo/PATO_0000460>))))
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000583> <http://purl.obolibrary.org/obo/MP_0000556>)
SubClassOf(<http://purl.obolibrary.org/obo/MP_0000583> <http://purl.obolibrary.org/obo/MP_0012401>)

# Class: <http://purl.obolibrary.org/obo/MP_0000585> (kinked tail)
Expand Down Expand Up @@ -23423,9 +23427,9 @@ SubClassOf(<http://purl.obolibrary.org/obo/MP_0000961> <http://purl.obolibrary.o
# Class: <http://purl.obolibrary.org/obo/MP_0000962> (disorganized dorsal root ganglion)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:10804168") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:10804169") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0000962> "loss of segmentation pattern of dorsal root ganglia or loss of regular spacing between the ganglia")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000962> "disorganised dorsal root ganglia")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000962> "disorganized DRG")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000962> "disorganized spinal ganglia")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0000962> "disorganised dorsal root ganglia")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0000962> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0000962> "MP:0000962")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0000962> "disorganized dorsal root ganglion")
Expand Down Expand Up @@ -40302,7 +40306,9 @@ SubClassOf(<http://purl.obolibrary.org/obo/MP_0002771> <http://purl.obolibrary.o

# Class: <http://purl.obolibrary.org/obo/MP_0002772> (brachypodia)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "J:31930") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MGI:il") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0002772> "abnormally short feet")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "J:31930") Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MGI:il") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0002772> "decreased length of the autopod")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0002772> "decreased autopod length")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0002772> "short feet")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0002772> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0002772> "MP:0002772")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0002772> "brachypodia")
Expand Down Expand Up @@ -80744,8 +80750,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/MP_0008511> <http://purl.obolibrary.o
# Class: <http://purl.obolibrary.org/obo/MP_0008512> (disorganized retina inner nuclear layer)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MGI:monikat") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0008512> "derangement of the normal pattern of the retinal layer that contains the cell bodies of bipolar, horizontal, and amacrine cells")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008512> "disorganized retinal inner nuclear layer")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008512> "disorganised retinal INL")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008512> "disorganized retinal inner nuclear layer")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0008512> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0008512> "MP:0008512")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0008512> "disorganized retina inner nuclear layer")
Expand Down Expand Up @@ -80801,9 +80807,9 @@ SubClassOf(<http://purl.obolibrary.org/obo/MP_0008515> <http://purl.obolibrary.o
# Class: <http://purl.obolibrary.org/obo/MP_0008516> (disorganized retina outer nuclear layer)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MGI:monikat") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0008516> "derangement of the normal pattern of the retinal layer that contains the nuclei and cell bodies of rods and cones")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008516> "disorganised retina ONL")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008516> "disorganized retinal ONL")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008516> "disorganized retinal outer nuclear layer")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008516> "disorganised retina ONL")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0008516> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0008516> "MP:0008516")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0008516> "disorganized retina outer nuclear layer")
Expand Down Expand Up @@ -80855,9 +80861,9 @@ SubClassOf(<http://purl.obolibrary.org/obo/MP_0008519> <http://purl.obolibrary.o
# Class: <http://purl.obolibrary.org/obo/MP_0008520> (disorganized retina outer plexiform layer)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MGI:monikat") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0008520> "a derangement of the normal pattern of the retinal layer that is the site of synapses between the rods and cones (axons) and the horizontal and bipolar cells (dendrites)")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008520> "disorganised retina OPL")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008520> "disorganized retinal OPL")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008520> "disorganized retinal outer plexiform layer")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0008520> "disorganised retina OPL")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0008520> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0008520> "MP:0008520")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0008520> "disorganized retina outer plexiform layer")
Expand Down Expand Up @@ -153623,12 +153629,13 @@ EquivalentClasses(<http://purl.obolibrary.org/obo/MP_0020241> ObjectSomeValuesFr
SubClassOf(<http://purl.obolibrary.org/obo/MP_0020241> <http://purl.obolibrary.org/obo/MP_0006043>)
SubClassOf(<http://purl.obolibrary.org/obo/MP_0020241> <http://purl.obolibrary.org/obo/MP_0020239>)

# Class: <http://purl.obolibrary.org/obo/MP_0020242> (enlarged paws)
# Class: <http://purl.obolibrary.org/obo/MP_0020242> (increased autopod size)

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://orcid.org/0000-0001-5208-3432>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0020242> "larger than average size of the feet")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://orcid.org/0000-0001-5208-3432>) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MP_0020242> "larger than average size of the autopod")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0020242> "increased paw size")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MP_0020242> "enlarged paws")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0020242> "MP:0020242")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0020242> "enlarged paws")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0020242> "increased autopod size")
SubClassOf(<http://purl.obolibrary.org/obo/MP_0020242> <http://purl.obolibrary.org/obo/MP_0000572>)

# Class: <http://purl.obolibrary.org/obo/MP_0020243> (abnormal pyruvate kinase activity)
Expand Down Expand Up @@ -181883,6 +181890,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/MP_0031291> "MPheno.ontology")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/MP_0031291> "MP:0031291")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MP_0031291> "pes valgus")
SubClassOf(<http://purl.obolibrary.org/obo/MP_0031291> <http://purl.obolibrary.org/obo/MP_0000556>)
SubClassOf(<http://purl.obolibrary.org/obo/MP_0031291> <http://purl.obolibrary.org/obo/MP_0000572>)

# Class: <http://purl.obolibrary.org/obo/MP_0031292> (increased facial hemangioma incidence)
Expand Down
2 changes: 1 addition & 1 deletion src/patterns/data/default/abnormallyDecreasedLengthOfAnatomicalEntity.tsv
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
defined_class defined_class_label anatomical_entity anatomical_entity_label
http://purl.obolibrary.org/obo/MP_0002772 brachypodia http://purl.obolibrary.org/obo/UBERON_0002387 pes
http://purl.obolibrary.org/obo/MP_0002772 brachypodia http://purl.obolibrary.org/obo/UBERON_0002470 autopod region
http://purl.obolibrary.org/obo/MP_0004708 short lumbar vertebrae http://purl.obolibrary.org/obo/UBERON_0002414 lumbar vertebra
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