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Fixes #2169 relabel lung cell types #2403

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merged 7 commits into from
Jun 28, 2024
Merged

Fixes #2169 relabel lung cell types #2403

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8c2c92b
Addresses #2169 relabel lung cell types
aleixpuigb Oct 11, 2023
336e0f6
Merge branch 'master' into 2169_relabel_lung_cell_types
aleixpuigb Jan 9, 2024
fac872f
Merge branch 'master' into 2169_relabel_lung_cell_types
aleixpuigb Jun 20, 2024
33aa616
Relabel fetal pre-type II pneumocyte
aleixpuigb Jun 20, 2024
d3c62d7
Remove squamous from definition
aleixpuigb Jun 24, 2024
fde3766
Change definition reference and fix acronyms
aleixpuigb Jun 27, 2024
4a0d9e6
Merge branch 'master' into 2169_relabel_lung_cell_types
aleixpuigb Jun 28, 2024
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44 changes: 25 additions & 19 deletions src/ontology/cl-edit.owl
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Expand Up @@ -6311,15 +6311,16 @@ AnnotationAssertion(oboInOwl:consider obo:CL_0000321 obo:CL_1001597)
AnnotationAssertion(rdfs:label obo:CL_0000321 "obsolete seminal fluid secreting cell")
AnnotationAssertion(owl:deprecated obo:CL_0000321 "true"^^xsd:boolean)

# Class: obo:CL_0000322 (pneumocyte)
# Class: obo:CL_0000322 (pulmonary alveolar epithelial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:20054144") obo:IAO_0000115 obo:CL_0000322 "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:20054144") Annotation(oboInOwl:hasDbXref "PMID:29463737") obo:IAO_0000115 obo:CL_0000322 "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates.")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000322 "BTO:0000395")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000322 "CALOHA:TS-2168")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000322 "FMA:62499")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000322 "alveolar epithelial cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32491474") oboInOwl:hasExactSynonym obo:CL_0000322 "pneumocyte")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000322 "pneumonocyte")
AnnotationAssertion(rdfs:label obo:CL_0000322 "pneumocyte")
AnnotationAssertion(rdfs:label obo:CL_0000322 "pulmonary alveolar epithelial cell")
SubClassOf(obo:CL_0000322 obo:CL_0000066)
SubClassOf(obo:CL_0000322 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004821))

Expand Down Expand Up @@ -14199,38 +14200,36 @@ AnnotationAssertion(rdfs:label obo:CL_0002061 "T-helper 9 cell")
EquivalentClasses(obo:CL_0002061 ObjectIntersectionOf(obo:CL_0000492 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000008982) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002215) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032638)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002061 obo:CL_0000492)

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Hi there, this paper PMID:36138472 refers to it as pulmonary alveolar type 2 cell rather than pulmonary alveolar type1 cell. Could you use a different reference maybe this one PMID: 29463737 ?

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@aleixpuigb aleixpuigb Jun 27, 2024 •
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Hi @AvolaAmg , I will update the reference, thank you. It is true that while mentioning that pulmonary alveolar type 1 are squamous cells, it is not the main focus on the paper and your proposed is more adequate. Cheers!

# Class: obo:CL_0002062 (type I pneumocyte)
# Class: obo:CL_0002062 (pulmonary alveolar type 1 cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:20054144") Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de") obo:IAO_0000115 obo:CL_0002062 "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:20054144") Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de") Annotation(oboInOwl:hasDbXref "PMID:29463737") obo:IAO_0000115 obo:CL_0002062 "A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange.")
AnnotationAssertion(terms:contributor obo:CL_0002062 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002062 "2010-06-23T04:37:54Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002062 "BTO:0000780")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002062 "FMA:62500")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "AT1")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "ATI")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "lung type 1 cells")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "membranous pneumocytes")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "pulmonary alveolar type I cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "small alveolar cells")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "squamous alveolar cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "squamous alveolar lining cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "type 1 alveolar epithelial cells")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "type 1 pneumocyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32491474") oboInOwl:hasExactSynonym obo:CL_0002062 "type 1 pneumocyte")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "type I alveolar cells")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "type I alveolar epithelial cells")
AnnotationAssertion(rdfs:label obo:CL_0002062 "type I pneumocyte")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002062 "type I pneumocyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29463737") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0002062 "AT1")
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0002062 "ATI")
AnnotationAssertion(rdfs:label obo:CL_0002062 "pulmonary alveolar type 1 cell")
EquivalentClasses(obo:CL_0002062 ObjectIntersectionOf(obo:CL_0000322 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0007585)))

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# Class: obo:CL_0002063 (type II pneumocyte)
# Class: obo:CL_0002063 (pulmonary alveolar type 2 cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0412046911") Annotation(oboInOwl:hasDbXref "PMID:8540632") Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de") obo:IAO_0000115 obo:CL_0002063 "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0412046911") Annotation(oboInOwl:hasDbXref "PMID:36138472") Annotation(oboInOwl:hasDbXref "PMID:8540632") Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de") obo:IAO_0000115 obo:CL_0002063 "A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli.")
AnnotationAssertion(terms:contributor obo:CL_0002063 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_0002063 "2010-06-24T12:04:13Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002063 "BTO:0000538")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002063 "FMA:62501")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "AT2")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "ATII")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "TII")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "cuboidal type II cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "granular pneumocyte")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "great alveolar cell")
Expand All @@ -14241,8 +14240,12 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "type 2 pneumocyte")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "type II alveolar cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "type II alveolar epithelial cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002063 "type II alveolocyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32491474") oboInOwl:hasExactSynonym obo:CL_0002063 "type II pneumocyte")
AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0002063 "lung type II cell")
AnnotationAssertion(rdfs:label obo:CL_0002063 "type II pneumocyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36138472") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0002063 "AT2")
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_0002063 "ATII")
AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0002063 "TII")
AnnotationAssertion(rdfs:label obo:CL_0002063 "pulmonary alveolar type 2 cell")
EquivalentClasses(obo:CL_0002063 ObjectIntersectionOf(obo:CL_0000322 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0032940) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0043129)))
SubClassOf(obo:CL_0002063 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4040003))

Expand Down Expand Up @@ -30540,7 +30543,7 @@ AnnotationAssertion(rdfs:label obo:CL_4028004 "alveolar type 1 fibroblast cell")
SubClassOf(obo:CL_4028004 obo:CL_0002241)
SubClassOf(obo:CL_4028004 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002299))

# Class: obo:CL_4028006 (alveolar type 2 fibroblast cell)
# Class: obo:CL_4028006 (alveolar adventitial fibroblast)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26706109") Annotation(oboInOwl:hasDbXref "PMID:28886382") Annotation(oboInOwl:hasDbXref "PMID:29752282") Annotation(oboInOwl:hasDbXref "PMID:30675802") Annotation(oboInOwl:hasDbXref "PMID:33208946") Annotation(oboInOwl:hasDbXref "PMID:33624948") obo:IAO_0000115 obo:CL_4028006 "A pulmonary interstitial fibroblast that is part of the alveolus and localizes to vascular adventitia.")
AnnotationAssertion(terms:contributor obo:CL_4028006 <https://orcid.org/0000-0002-3293-5463>)
Expand All @@ -30550,9 +30553,11 @@ AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4028006 "alveolar fibroblast
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4028006 "matrix fibroblast 2")
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4028006 "mesenchymal alveolar niche cell")
AnnotationAssertion(oboInOwl:hasBroadSynonym obo:CL_4028006 "type-2 associated stromal cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4028006 "alveolar type 2 fibroblast cell")
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4028006 "AF2")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33208946") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4028006 "AdvF")
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4028006 "MANC")
AnnotationAssertion(rdfs:label obo:CL_4028006 "alveolar type 2 fibroblast cell")
AnnotationAssertion(rdfs:label obo:CL_4028006 "alveolar adventitial fibroblast")
SubClassOf(obo:CL_4028006 obo:CL_0002241)
SubClassOf(obo:CL_4028006 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002299))

Expand Down Expand Up @@ -32016,16 +32021,17 @@ AnnotationAssertion(rdfs:label obo:CL_4040002 "enteroglial cell")
EquivalentClasses(obo:CL_4040002 ObjectIntersectionOf(obo:CL_0000125 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002005)))
SubClassOf(obo:CL_4040002 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007939))

# Class: obo:CL_4040003 (fetal pre-type II pneumocyte)
# Class: obo:CL_4040003 (fetal pre-type II pulmonary alveolar epithelial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1316350") obo:IAO_0000115 obo:CL_4040003 "Precursor of type II pneumocyte. These cells do not have lamellar bodies, which are a marker of type II pneumocyte maturity.")
AnnotationAssertion(terms:contributor obo:CL_4040003 <https://orcid.org/0000-0002-0819-0473>)
AnnotationAssertion(terms:date obo:CL_4040003 "2023-06-02T09:19:31Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9624168") oboInOwl:hasExactSynonym obo:CL_4040003 "fetal alveolar pre-type II epithelial cell")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-0819-0473") oboInOwl:hasExactSynonym obo:CL_4040003 "fetal pre-type 2 pneumocyte")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12114192") oboInOwl:hasExactSynonym obo:CL_4040003 "fetal pre-type II alveolar epithelial cell")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4040003 "fetal pre-type II pneumocyte")
AnnotationAssertion(oboInOwl:note obo:CL_4040003 "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350).")
AnnotationAssertion(rdfs:label obo:CL_4040003 "fetal pre-type II pneumocyte")
AnnotationAssertion(rdfs:label obo:CL_4040003 "fetal pre-type II pulmonary alveolar epithelial cell")
SubClassOf(obo:CL_4040003 obo:CL_0000322)

# Class: obo:CL_4040004 (mesenchymal stem cell of orbital adipose tissue)
Expand Down
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