Skip to content

Commit

Permalink
Fix duplicated cross-references.
Browse files Browse the repository at this point in the history 
This commit removes all the duplicated cross-references to FMA and MA
terms listed in #2233. The presence of such duplicated cross-references
1) is abnormal since cross-references to FMA and MA are supposed to be
"exact" and 2) interferes with the generation of the CL bridges in
Uberon.

closes #2233
  • Loading branch information
@gouttegd
gouttegd committed Nov 27, 2023
1 parent cc63f5d commit 7c37888
Showing 1 changed file with 0 additions and 16 deletions.
16 changes: 0 additions & 16 deletions src/ontology/cl-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3630,7 +3630,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000025 "BTO:0000369")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000025 "BTO:0003801")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000025 "CALOHA:TS-2191")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000025 "FMA:67343")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000025 "MA:0000388")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000025 "MESH:D010063")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000025 "mature oocyte")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000025 "ovum")
Expand Down Expand Up @@ -3736,7 +3735,6 @@ SubClassOf(obo:CL_0000036 obo:CL_0000035)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl:hasDbXref "GOC:dsd") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:19022770") Annotation(oboInOwl:hasDbXref "http://en.wikipedia.org/wiki/Hematopoietic_stem_cell") obo:IAO_0000115 obo:CL_0000037 "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000037 "BTO:0000725")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000037 "CALOHA:TS-0448")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000037 "FMA:70337")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000037 "FMA:86475")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000037 "MESH:D006412")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000037 "VHOG:0001485")
Expand Down Expand Up @@ -4669,7 +4667,6 @@ AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000129 "brain macrophage")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000129 "BTO:0000078")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000129 "BTO:0000962")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000129 "FMA:54539")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000129 "FMA:54540")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000129 "brain-resident macrophage")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de/") oboInOwl:hasExactSynonym obo:CL_0000129 "hortega cells")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de/") oboInOwl:hasExactSynonym obo:CL_0000129 "microgliocyte")
Expand Down Expand Up @@ -5260,7 +5257,6 @@ EquivalentClasses(obo:CL_0000188 ObjectIntersectionOf(obo:CL_0000000 ObjectSomeV
# Class: obo:CL_0000189 (slow muscle cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0323052908") obo:IAO_0000115 obo:CL_0000189 "A muscle cell that develops tension more slowly than a fast-twitch fiber.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000189 "FMA:84448")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:0815316208") oboInOwl:hasRelatedSynonym obo:CL_0000189 "slow muscle fiber")
AnnotationAssertion(rdfs:label obo:CL_0000189 "slow muscle cell")
SubClassOf(obo:CL_0000189 obo:CL_0008046)
Expand Down Expand Up @@ -5359,7 +5355,6 @@ AnnotationAssertion(owl:deprecated obo:CL_0000201 "true"^^xsd:boolean)
# Class: obo:CL_0000202 (auditory hair cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D006198") Annotation(oboInOwl:hasDbXref "WikipediaVersioned:Hair_cell&oldid=1045345915") obo:IAO_0000115 obo:CL_0000202 "A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000202 "FMA:62364")
AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000202 "auditory receptor cell")
AnnotationAssertion(rdfs:comment obo:CL_0000202 "In mammals these cells are located in the organ of Corti.")
AnnotationAssertion(rdfs:label obo:CL_0000202 "auditory hair cell")
Expand Down Expand Up @@ -7619,7 +7614,6 @@ SubClassOf(obo:CL_0000502 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0070253))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D013799") obo:IAO_0000115 obo:CL_0000503 "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000503 "BTO:0002850")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000503 "FMA:18690")
AnnotationAssertion(rdfs:label obo:CL_0000503 "theca cell")
SubClassOf(obo:CL_0000503 obo:CL_0000499)
SubClassOf(obo:CL_0000503 obo:CL_0000593)
Expand Down Expand Up @@ -9591,7 +9585,6 @@ SubClassOf(obo:CL_0000722 ObjectSomeValuesFrom(obo:RO_0002160 obo:NCBITaxon_6656

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0048103") obo:IAO_0000115 obo:CL_0000723 "A stem cell that can give rise to cell types of the body other than those of the germ-line.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000723 "CALOHA:TS-2086")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000723 "FMA:63368")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000723 "MESH:D053687")
AnnotationAssertion(rdfs:label obo:CL_0000723 "somatic stem cell")
EquivalentClasses(obo:CL_0000723 ObjectIntersectionOf(obo:CL_0000034 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0048103)))
Expand Down Expand Up @@ -10311,7 +10304,6 @@ AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000794 "killer T lymphocyte
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000794 "killer T-cell")
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_0000794 "killer T-lymphocyte")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000794 "CALOHA:TS-0190")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000794 "FMA:70573")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000794 "CD8-positive, alpha-beta cytotoxic T lymphocyte")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000794 "CD8-positive, alpha-beta cytotoxic T-cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000794 "CD8-positive, alpha-beta cytotoxic T-lymphocyte")
Expand Down Expand Up @@ -12819,7 +12811,6 @@ DisjointClasses(obo:CL_0001023 obo:CL_0001026)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl:hasDbXref "GOC:amm") Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:10430905") Annotation(oboInOwl:hasDbXref "PMID:11750107") Annotation(oboInOwl:hasDbXref "PMID:16551251") Annotation(oboInOwl:hasDbXref "PMID:20024907") Annotation(oboInOwl:hasDbXref "PMID:9389721") obo:IAO_0000115 obo:CL_0001024 "CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0001024 "CALOHA:TS-0448")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0001024 "FMA:86475")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16140871") oboInOwl:hasExactSynonym obo:CL_0001024 "CD133-positive hematopoietic stem cell")
AnnotationAssertion(rdfs:comment obo:CL_0001024 "Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617).")
AnnotationAssertion(rdfs:label obo:CL_0001024 "CD34-positive, CD38-negative hematopoietic stem cell")
Expand Down Expand Up @@ -15279,7 +15270,6 @@ SubClassOf(obo:CL_0002162 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000236
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html") obo:IAO_0000115 obo:CL_0002163 "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_0002163 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002163 "2010-08-25T11:05:21Z")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002163 "FMA:75722")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002163 "FMA:75726")
AnnotationAssertion(rdfs:label obo:CL_0002163 "internal pillar cell of cochlea")
SubClassOf(obo:CL_0002163 obo:CL_1000191)
Expand Down Expand Up @@ -16411,7 +16401,6 @@ SubClassOf(obo:CL_0002267 obo:CL_0002659)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "PMID:15153415") obo:IAO_0000115 obo:CL_0002268 "An enteroendocrine cell that stores and secretes Ghrelin.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_0002268 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002268 "2010-09-10T01:47:45Z")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002268 "FMA:63207")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002268 "FMA:63418")
AnnotationAssertion(rdfs:label obo:CL_0002268 "P/D1 enteroendocrine cell")
SubClassOf(obo:CL_0002268 obo:CL_0000164)
Expand Down Expand Up @@ -16825,7 +16814,6 @@ SubClassOf(obo:CL_0002304 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000177
# Class: obo:CL_0002305 (epithelial cell of distal tubule)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") obo:IAO_0000115 obo:CL_0002305 "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002305 "FMA:62125")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002305 "FMA:70981")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002305 "KUPO:0001055")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002305 "kidney distal tubule epithelial cell")
Expand All @@ -16839,7 +16827,6 @@ SubClassOf(obo:CL_0002305 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000413
# Class: obo:CL_0002306 (epithelial cell of proximal tubule)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:1-4160-2328-3") obo:IAO_0000115 obo:CL_0002306 "An epithelial cell of the proximal tubule of the kidney.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002306 "FMA:62125")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002306 "FMA:70973")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002306 "KUPO:0001044")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002306 "kidney proximal tubule epithelial cell")
Expand Down Expand Up @@ -17012,7 +16999,6 @@ AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_0002321 <https
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002321 "2010-09-15T03:39:21Z")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002321 "CALOHA:TS-0263")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002321 "FMA:82840")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002321 "FMA:82841")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002321 "WBbt:0007028")
AnnotationAssertion(rdfs:label obo:CL_0002321 "embryonic cell (metazoa)")
SubClassOf(obo:CL_0002321 obo:CL_0000000)
Expand Down Expand Up @@ -20320,7 +20306,6 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_0002662 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002662 "2011-07-11T01:44:48Z")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002662 "FMA:74504")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002662 "FMA:74505")
AnnotationAssertion(rdfs:label obo:CL_0002662 "luminal cell of lactiferous duct")
SubClassOf(obo:CL_0002662 obo:CL_0002326)

Expand Down Expand Up @@ -26448,7 +26433,6 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000480 obo:CL_0002073

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo:CL_1000481 "A transitional myocyte that is part of the atrioventricular bundle.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000481 "FMA:83388")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000481 "FMA:83885")
AnnotationAssertion(rdfs:label obo:CL_1000481 "transitional myocyte of atrioventricular bundle")
EquivalentClasses(obo:CL_1000481 ObjectIntersectionOf(obo:CL_0002073 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002353)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000481 obo:CL_0002073)
Expand Down

0 comments on commit 7c37888

Please sign in to comment.