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Merge pull request #1256 from obophenotype/for_todays_release
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New terms and edits for SCA
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@paolaroncaglia
paolaroncaglia authored Sep 9, 2021
2 parents a956036 + dd9597e commit 12f2802
Showing 1 changed file with 55 additions and 16 deletions.
71 changes: 55 additions & 16 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -1924,8 +1924,11 @@ Declaration(Class(obo:CL_0009056))
Declaration(Class(obo:CL_0009057))
Declaration(Class(obo:CL_0009058))
Declaration(Class(obo:CL_0009059))
Declaration(Class(obo:CL_0009060))
Declaration(Class(obo:CL_0009061))
Declaration(Class(obo:CL_0009062))
Declaration(Class(obo:CL_0009063))
Declaration(Class(obo:CL_0009064))
Declaration(Class(obo:CL_0009065))
Declaration(Class(obo:CL_0009066))
Declaration(Class(obo:CL_0010000))
Expand Down Expand Up @@ -4124,7 +4127,7 @@ EquivalentClasses(obo:CL_0000118 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeV

# Class: obo:CL_0000119 (cerebellar Golgi cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "NIFSTD:sao1415726815"^^xsd:string) obo:IAO_0000115 obo:CL_0000119 "Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell enters ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "NIFSTD:sao1415726815"^^xsd:string) obo:IAO_0000115 obo:CL_0000119 "Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004.")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000119 "Golgi cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000119 "Golgi neuron")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000119 "cerebellar Golgi neuron")
Expand Down Expand Up @@ -11002,16 +11005,19 @@ SubClassOf(obo:CL_0000844 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000843))
# Class: obo:CL_0000845 (marginal zone B cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:dsd"^^xsd:string) Annotation(oboInOwl:hasDbXref "ISBN:0781735149"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:10933592"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:20933013"^^xsd:string) Annotation(oboInOwl:hasDbXref "http://en.wikipedia.org/wiki/Marginal-zone_B_cell"^^xsd:string) obo:IAO_0000115 obo:CL_0000845 "A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high."^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "MZ B cell"^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "MZ B lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "MZ B-cell"^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "MZ B-lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "marginal zone B lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "marginal zone B-cell"^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "marginal zone B-lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "MZ B cell"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "MZ B lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "MZ B-cell"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "MZ B-lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "marginal zone B cell"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "marginal zone B lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "marginal zone B-cell"^^xsd:string)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000845 "marginal zone B-lymphocyte"^^xsd:string)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "B cell of marginal zone of spleen")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000845 "marginal zone of spleen B cell")
AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0000845 "cell"^^xsd:string)
AnnotationAssertion(rdfs:comment obo:CL_0000845 "MZ B cells are reportedly CD1-positive (mice), CD20-positive, CD48-positive, CD84-positive, CD150-positive, CD229-positive, and CD352-positive."^^xsd:string)
AnnotationAssertion(rdfs:label obo:CL_0000845 "marginal zone B cell"^^xsd:string)
AnnotationAssertion(rdfs:label obo:CL_0000845 "marginal zone B cell of spleen")
EquivalentClasses(obo:CL_0000845 ObjectIntersectionOf(obo:CL_0000785 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001251) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001289) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001338) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0042742) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount> obo:GO_0071753) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/cl#lacks_plasma_membrane_part> obo:PR_000001880) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/cl#lacks_plasma_membrane_part> obo:PR_000002037)))
SubClassOf(Annotation(oboInOwl:is_inferred "true"^^xsd:string) obo:CL_0000845 obo:CL_0000785)

Expand Down Expand Up @@ -14170,7 +14176,7 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true"^^xsd:string) obo:CL_0002037 ob

# Class: obo:CL_0002038 (T follicular helper cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:19855402"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:20107805"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:22043829"^^xsd:string) obo:IAO_0000115 obo:CL_0002038 "A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that expresses is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production."^^xsd:string)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:19855402"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:20107805"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:22043829"^^xsd:string) obo:IAO_0000115 obo:CL_0002038 "A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production."^^xsd:string)
AnnotationAssertion(oboInOwl:created_by obo:CL_0002038 "tmeehan"^^xsd:string)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002038 "2009-10-29T04:01:27Z"^^xsd:string)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20207847"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_0002038 "T(FH)"^^xsd:string)
Expand Down Expand Up @@ -22572,7 +22578,7 @@ EquivalentClasses(obo:CL_0009036 ObjectIntersectionOf(obo:CL_0000235 ObjectSomeV

# Class: obo:CL_0009037 (lymph node mantle zone B cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:8011279"^^xsd:string) Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865/"^^xsd:string) Annotation(oboInOwl:hasDbXref "https://www.arppress.org/v/vspfiles/assets/images/Chapter1T25LymphNodes.pdf") obo:IAO_0000115 obo:CL_0009037 "A B lymphocyte that resides in the mantle zone of the lymph node germinal center. These are generally IgM and IgD positive activated B cells that form a 'corona' around the germinal center and are part of the establishment of a secondary lymphatic follicule.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:8011279"^^xsd:string) Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865/"^^xsd:string) Annotation(oboInOwl:hasDbXref "https://www.arppress.org/v/vspfiles/assets/images/Chapter1T25LymphNodes.pdf"^^xsd:string) obo:IAO_0000115 obo:CL_0009037 "A B lymphocyte that resides in the mantle zone of the lymph node germinal center. These are generally IgM and IgD positive activated B cells that form a 'corona' around the germinal center and are part of the establishment of a secondary lymphatic follicule.")
AnnotationAssertion(oboInOwl:created_by obo:CL_0009037 <http://orcid.org/0000-0002-2825-0621>)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0009037 "mantle zone B cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009037 "mantle zone B cell of lymph node")
Expand Down Expand Up @@ -22679,13 +22685,14 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_0009048 <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label obo:CL_0009048 "anorectum macrophage")
EquivalentClasses(obo:CL_0009048 ObjectIntersectionOf(obo:CL_0000235 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410050)))

# Class: obo:CL_0009049 (smooth muscle cell of high endothelial venule)
# Class: obo:CL_0009049 (smooth muscle cell of high endothelial venule of lymph node)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27881983"^^xsd:string) Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865"^^xsd:string) obo:IAO_0000115 obo:CL_0009049 "A layer of smooth muscle cells that forms the outer layer of the high endothelial venule and pumps to allow flow of lymph fluid carrying lymphocytes.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27881983"^^xsd:string) Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865"^^xsd:string) obo:IAO_0000115 obo:CL_0009049 "A layer of smooth muscle cells that forms the outer layer of the high endothelial venule of lymph node and pumps to allow flow of lymph fluid carrying lymphocytes.")
AnnotationAssertion(oboInOwl:created_by obo:CL_0009049 <http://orcid.org/0000-0002-2825-0621>)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009049 "high endothelial venule smooth muscle cell")
AnnotationAssertion(rdfs:label obo:CL_0009049 "smooth muscle cell of high endothelial venule")
EquivalentClasses(obo:CL_0009049 ObjectIntersectionOf(obo:CL_0000192 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410037)))
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0009049 "high endothelial venule smooth muscle cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009049 "high endothelial venule of lymph node smooth muscle cell")
AnnotationAssertion(rdfs:label obo:CL_0009049 "smooth muscle cell of high endothelial venule of lymph node")
EquivalentClasses(obo:CL_0009049 ObjectIntersectionOf(obo:CL_0000192 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410038)))

# Class: obo:CL_0009050 (B cell of anorectum)

Expand Down Expand Up @@ -22776,6 +22783,16 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_0009059 <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label obo:CL_0009059 "plasma cell of medullary sinus of lymph node")
EquivalentClasses(obo:CL_0009059 ObjectIntersectionOf(obo:CL_0000786 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0009744)))

# Class: obo:CL_0009060 (marginal zone B cell of lymph node)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "WikipediaVersioned:Marginal_zone_B-cell&oldid=1032071222"^^xsd:string) Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865") obo:IAO_0000115 obo:CL_0009060 "A mature B cell located in the marginal zone of the lymph node.")
AnnotationAssertion(oboInOwl:created_by obo:CL_0009060 <http://orcid.org/0000-0002-2825-0621>)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0009060 "marginal zone B cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009060 "lymph node marginal zone B cell")
AnnotationAssertion(oboInOwl:inSubset obo:CL_0009060 <http://purl.obolibrary.org/obo/pato#location_grouping>)
AnnotationAssertion(rdfs:label obo:CL_0009060 "marginal zone B cell of lymph node")
EquivalentClasses(obo:CL_0009060 ObjectIntersectionOf(obo:CL_0000785 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410065)))

# Class: obo:CL_0009061 (intestinal crypt stem cell of anorectum)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-3440-1876"^^xsd:string) obo:IAO_0000115 obo:CL_0009061 "An intestinal crypt stem cell that is located in the anorectum.")
Expand All @@ -22785,6 +22802,17 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_0009061 <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label obo:CL_0009061 "intestinal crypt stem cell of anorectum")
EquivalentClasses(obo:CL_0009061 ObjectIntersectionOf(obo:CL_0002250 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410050)))

# Class: obo:CL_0009062 (germinal center T cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:21739669"^^xsd:string) Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865") obo:IAO_0000115 obo:CL_0009062 "A specialized type of CD4 positive T cell, the follicular helper T cell (TFH cell), that upregulates CXCR5 expression to enable its follicular localization. These specialised T cells reside in the germinal center of the lymph node.")
AnnotationAssertion(oboInOwl:created_by obo:CL_0009062 <http://orcid.org/0000-0002-2825-0621>)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009062 "T follicular helper cell of germinal center of lymph node")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009062 "T follicular helper cell of lymph node germinal center")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009062 "lymph node germinal center T follicular helper cell")
AnnotationAssertion(oboInOwl:inSubset obo:CL_0009062 <http://purl.obolibrary.org/obo/pato#location_grouping>)
AnnotationAssertion(rdfs:label obo:CL_0009062 "germinal center T cell")
EquivalentClasses(obo:CL_0009062 ObjectIntersectionOf(obo:CL_0002038 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0009039)))

# Class: obo:CL_0009063 (enteroendocrine cell of anorectum)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-3440-1876"^^xsd:string) obo:IAO_0000115 obo:CL_0009063 "An enteroendocrine cell that is located in the anorectum.")
Expand All @@ -22794,6 +22822,17 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_0009063 <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label obo:CL_0009063 "enteroendocrine cell of anorectum")
EquivalentClasses(obo:CL_0009063 ObjectIntersectionOf(obo:CL_0000164 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410050)))

# Class: obo:CL_0009064 (lymph node paracortex T cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-4183-8865"^^xsd:string) obo:IAO_0000115 obo:CL_0009064 "A T cell located in the lymph node paracortex, where macrophages and dendritic cells present antigenic peptides to these naïve T cells, stimulating them to become activated helper T cells or cytotoxic T lymphocytes.")
AnnotationAssertion(oboInOwl:created_by obo:CL_0009064 <http://orcid.org/0000-0002-2825-0621>)
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0009064 "paracortex T cell")
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0009064 "paracortical T cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0009064 "T cell of lymph node paracortex")
AnnotationAssertion(oboInOwl:inSubset obo:CL_0009064 <http://purl.obolibrary.org/obo/pato#location_grouping>)
AnnotationAssertion(rdfs:label obo:CL_0009064 "lymph node paracortex T cell")
EquivalentClasses(obo:CL_0009064 ObjectIntersectionOf(obo:CL_0000084 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410066)))

# Class: obo:CL_0009065 (tuft cell of anorectum)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://orcid.org/0000-0003-3440-1876"^^xsd:string) obo:IAO_0000115 obo:CL_0009065 "An intestinal tuft cell that is located in the anorectum.")
Expand Down

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