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Compound terms for HubMap (#1722)
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* first draft dos-dp pattern

* update data default

* replace obsolete term

* remove redundant case

* Curate away over compounded

* re-remove obsolete term

* add references

* update definitions.owl

* update data

* update definitions

* update import

* remove duplicate refs

* Update cellPartOfAnatomicalEntity.tsv

Fix redundancy in compound names

* update definitions.owl

* manually merge definitions.owl into edit file

* add readme in archive folder

* remove definitions from catalog

---------

Co-authored-by: Anita Caron <[email protected]>
Co-authored-by: Shawn Tan <[email protected]>
Co-authored-by: Aleix Puig <[email protected]>
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@anitacaron @shawntanzk @aleixpuigb
4 people authored Feb 10, 2023
1 parent 74e05b7 commit dc5cf88
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Showing 9 changed files with 894 additions and 7 deletions.
114 changes: 114 additions & 0 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -2921,6 +2921,19 @@ Declaration(Class(obo:CL_4030041))
Declaration(Class(obo:CL_4030042))
Declaration(Class(obo:CL_4032000))
Declaration(Class(obo:CL_4032001))
Declaration(Class(obo:CL_4033000))
Declaration(Class(obo:CL_4033001))
Declaration(Class(obo:CL_4033002))
Declaration(Class(obo:CL_4033003))
Declaration(Class(obo:CL_4033004))
Declaration(Class(obo:CL_4033005))
Declaration(Class(obo:CL_4033006))
Declaration(Class(obo:CL_4033007))
Declaration(Class(obo:CL_4033008))
Declaration(Class(obo:CL_4033009))
Declaration(Class(obo:CL_4033010))
Declaration(Class(obo:CL_4033011))
Declaration(Class(obo:CL_4033012))
Declaration(Class(obo:CL_4033013))
Declaration(Class(obo:CL_4033014))
Declaration(Class(obo:CP_0000000))
Expand Down Expand Up @@ -2982,7 +2995,9 @@ Declaration(Class(obo:PR_Q96E93))
Declaration(Class(obo:PR_Q9D387))
Declaration(Class(obo:PR_Q9Y5Y4))
Declaration(Class(obo:PR_Q9Z0F7))
Declaration(Class(obo:UBERON_0001004))
Declaration(Class(obo:UBERON_0001335))
Declaration(Class(obo:UBERON_0002339))
Declaration(Class(obo:UBERON_0002548))
Declaration(Class(obo:UBERON_0002707))
Declaration(Class(obo:UBERON_0003209))
Expand All @@ -2996,10 +3011,18 @@ Declaration(Class(obo:UBERON_0009738))
Declaration(Class(obo:UBERON_0009739))
Declaration(Class(obo:UBERON_0009851))
Declaration(Class(obo:UBERON_0009852))
Declaration(Class(obo:UBERON_0010397))
Declaration(Class(obo:UBERON_0011184))
Declaration(Class(obo:UBERON_0011949))
Declaration(Class(obo:UBERON_0012398))
Declaration(Class(obo:UBERON_0012399))
Declaration(Class(obo:UBERON_0012419))
Declaration(Class(obo:UBERON_8400006))
Declaration(Class(obo:UBERON_8400007))
Declaration(Class(obo:UBERON_8400008))
Declaration(Class(obo:UBERON_8410041))
Declaration(Class(obo:UBERON_8410042))
Declaration(Class(obo:UBERON_8410043))
Declaration(ObjectProperty(obo:BFO_0000051))
Declaration(ObjectProperty(obo:RO_0000053))
Declaration(ObjectProperty(obo:RO_0001025))
Expand Down Expand Up @@ -30716,6 +30739,97 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29904965"^^xsd:string) o
AnnotationAssertion(rdfs:label obo:CL_4032001 "reelin GABAergic cortical interneuron")
EquivalentClasses(obo:CL_4032001 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0000956) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534) ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000013879)))

# Class: obo:CL_4033000 (endothelial cell of venule of lymph node)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:28217126"^^xsd:string) obo:IAO_0000115 obo:CL_4033000 "A(n) endothelial cell that is part of a(n) venule of lymph node."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033000 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033000 "endothelial cell of venule of lymph node"^^xsd:string)
EquivalentClasses(obo:CL_4033000 ObjectIntersectionOf(obo:CL_0000115 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410041)))

# Class: obo:CL_4033001 (endothelial cell of arteriole of lymph node)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:28217126"^^xsd:string) obo:IAO_0000115 obo:CL_4033001 "A(n) endothelial cell that is part of a(n) arteriole of lymph node."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033001 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033001 "endothelial cell of arteriole of lymph node"^^xsd:string)
EquivalentClasses(obo:CL_4033001 ObjectIntersectionOf(obo:CL_0000115 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410042)))

# Class: obo:CL_4033002 (neuroendocrine cell of epithelium of crypt of Lieberkuhn)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31390635"^^xsd:string) obo:IAO_0000115 obo:CL_4033002 "A(n) neuroendocrine cell that is part of a(n) epithelium of crypt of Lieberkuhn."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033002 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033002 "neuroendocrine cell of epithelium of crypt of Lieberkuhn"^^xsd:string)
EquivalentClasses(obo:CL_4033002 ObjectIntersectionOf(obo:CL_0000165 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011184)))

# Class: obo:CL_4033003 (myoepithelial cell of bronchus submucosal gland)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19996346"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:5487122"^^xsd:string) obo:IAO_0000115 obo:CL_4033003 "A(n) myoepithelial cell that is part of a(n) bronchus submucosal gland."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033003 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033003 "myoepithelial cell of bronchus submucosal gland"^^xsd:string)
EquivalentClasses(obo:CL_4033003 ObjectIntersectionOf(obo:CL_0000185 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410043)))

# Class: obo:CL_4033004 (smooth muscle cell of taenia coli)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10715339"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:22320805"^^xsd:string) obo:IAO_0000115 obo:CL_4033004 "A(n) smooth muscle cell that is part of a(n) taenia coli."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033004 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033004 "smooth muscle cell of taenia coli"^^xsd:string)
EquivalentClasses(obo:CL_4033004 ObjectIntersectionOf(obo:CL_0000192 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0012419)))

# Class: obo:CL_4033005 (serous secreting cell of bronchus submucosal gland)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:5487122"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:9651178"^^xsd:string) obo:IAO_0000115 obo:CL_4033005 "A(n) serous secreting cell that is part of a(n) bronchus submucosal gland."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033005 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033005 "serous secreting cell of bronchus submucosal gland"^^xsd:string)
EquivalentClasses(obo:CL_4033005 ObjectIntersectionOf(obo:CL_0000313 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410043)))

# Class: obo:CL_4033006 (endothelial cell of efferent lymphatic vessel)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32094869"^^xsd:string) obo:IAO_0000115 obo:CL_4033006 "A(n) endothelial cell that is part of a(n) efferent lymphatic vessel."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033006 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033006 "endothelial cell of efferent lymphatic vessel"^^xsd:string)
EquivalentClasses(obo:CL_4033006 ObjectIntersectionOf(obo:CL_0000115 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0010397)))

# Class: obo:CL_4033007 (brush cell of epithelium of lobar bronchus)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:15817800"^^xsd:string) obo:IAO_0000115 obo:CL_4033007 "A(n) brush cell that is part of a(n) epithelium of lobar bronchus."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033007 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033007 "brush cell of epithelium of lobar bronchus"^^xsd:string)
EquivalentClasses(obo:CL_4033007 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002339)))

# Class: obo:CL_4033008 (vein endothelial cell of respiratory system)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34030460"^^xsd:string) obo:IAO_0000115 obo:CL_4033008 "A(n) vein endothelial cell that is part of a(n) respiratory system."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033008 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033008 "vein endothelial cell of respiratory system"^^xsd:string)
EquivalentClasses(obo:CL_4033008 ObjectIntersectionOf(obo:CL_0002543 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001004)))

# Class: obo:CL_4033009 (goblet cell of epithelium of lobar bronchus)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18757316"^^xsd:string) obo:IAO_0000115 obo:CL_4033009 "A(n) goblet cell that is part of a(n) epithelium of lobar bronchus."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033009 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033009 "goblet cell of epithelium of lobar bronchus"^^xsd:string)
EquivalentClasses(obo:CL_4033009 ObjectIntersectionOf(obo:CL_0000160 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002339)))

# Class: obo:CL_4033010 (neuroendocrine cell of epithelium of lobar bronchus)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26711336"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:33355253"^^xsd:string) obo:IAO_0000115 obo:CL_4033010 "A(n) neuroendocrine cell that is part of a(n) epithelium of lobar bronchus."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033010 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033010 "neuroendocrine cell of epithelium of lobar bronchus"^^xsd:string)
EquivalentClasses(obo:CL_4033010 ObjectIntersectionOf(obo:CL_0000165 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002339)))

# Class: obo:CL_4033011 (smooth muscle cell of large intestine smooth muscle circular layer)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24997029"^^xsd:string) obo:IAO_0000115 obo:CL_4033011 "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle circular layer."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033011 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033011 "smooth muscle cell of large intestine smooth muscle circular layer"^^xsd:string)
EquivalentClasses(obo:CL_4033011 ObjectIntersectionOf(obo:CL_0000192 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0012398)))

# Class: obo:CL_4033012 (smooth muscle cell of large intestine smooth muscle longitudinal layer)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24997029"^^xsd:string) obo:IAO_0000115 obo:CL_4033012 "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle longitudinal layer."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033012 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(rdfs:label obo:CL_4033012 "smooth muscle cell of large intestine smooth muscle longitudinal layer"^^xsd:string)
EquivalentClasses(obo:CL_4033012 ObjectIntersectionOf(obo:CL_0000192 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0012399)))

# Class: obo:CL_4033013 (suprabasal keratinocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35883599"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:9520465"^^xsd:string) Annotation(oboInOwl:hasDbXref "https://www.proteinatlas.org/humanproteome/single+cell+type/squamous+epithelial+cells#suprabasalkeratinocytes"^^xsd:string) obo:IAO_0000115 obo:CL_4033013 "A keratinocyte of the epidermis suprabasal layer. This cell may express the differentiation markers keratin 10 and keratin 1.")
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