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Addresses #1892 NTR for respiratory new terms #1896

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merged 8 commits into from
Mar 20, 2023
Merged

Addresses #1892 NTR for respiratory new terms #1896

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6d3ba8e
Addresses #1892 NTR for respiratory new terms
aleixpuigb Mar 16, 2023
89b6107
Update cl-edit.owl
aleixpuigb Mar 16, 2023
f7f6ca3
import_Uberon
aleixpuigb Mar 16, 2023
8bde66a
Update cl-edit.owl
aleixpuigb Mar 17, 2023
96e2461
Merge branch 'master' into 1892_NTR_lung
aleixpuigb Mar 17, 2023
5405527
Update cl-edit.owl
aleixpuigb Mar 20, 2023
dbee4e7
Update cl-edit.owl
aleixpuigb Mar 20, 2023
c1bcb50
Update cl-edit.owl
aleixpuigb Mar 20, 2023
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116 changes: 116 additions & 0 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -2938,6 +2938,16 @@ Declaration(Class(obo:CL_4033012))
Declaration(Class(obo:CL_4033013))
Declaration(Class(obo:CL_4033014))
Declaration(Class(obo:CL_4033015))
Declaration(Class(obo:CL_4033016))
Declaration(Class(obo:CL_4033017))
Declaration(Class(obo:CL_4033018))
Declaration(Class(obo:CL_4033020))
Declaration(Class(obo:CL_4033021))
Declaration(Class(obo:CL_4033022))
Declaration(Class(obo:CL_4033023))
Declaration(Class(obo:CL_4033024))
Declaration(Class(obo:CL_4033025))
Declaration(Class(obo:CL_4033026))
Declaration(Class(obo:CP_0000000))
Declaration(Class(obo:CP_0000025))
Declaration(Class(obo:CP_0000027))
Expand Down Expand Up @@ -2999,6 +3009,7 @@ Declaration(Class(obo:PR_Q9Y5Y4))
Declaration(Class(obo:PR_Q9Z0F7))
Declaration(Class(obo:UBERON_0001004))
Declaration(Class(obo:UBERON_0001335))
Declaration(Class(obo:UBERON_0002222))
Declaration(Class(obo:UBERON_0002339))
Declaration(Class(obo:UBERON_0002548))
Declaration(Class(obo:UBERON_0002707))
Expand All @@ -3009,6 +3020,8 @@ Declaration(Class(obo:UBERON_0004026))
Declaration(Class(obo:UBERON_0005101))
Declaration(Class(obo:UBERON_0005102))
Declaration(Class(obo:UBERON_0006841))
Declaration(Class(obo:UBERON_0008304))
Declaration(Class(obo:UBERON_0008305))
Declaration(Class(obo:UBERON_0009738))
Declaration(Class(obo:UBERON_0009739))
Declaration(Class(obo:UBERON_0009851))
Expand Down Expand Up @@ -30820,6 +30833,108 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32555229") Annotation(ob
AnnotationAssertion(rdfs:label obo:CL_4033015 "retinal astrocyte")
EquivalentClasses(obo:CL_4033015 ObjectIntersectionOf(obo:CL_0000127 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000966)))

# Class: obo:CL_4033016 (secondary crest myofibroblast)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31331942") Annotation(oboInOwl:hasDbXref "PMID:33624948") obo:IAO_0000115 obo:CL_4033016 "A myofibroblast that is part of an alveoli during alveolarization. The contractile force of this cell elongates the secondary crest, while producing a framework of elastin and tenascin. During the maturation of the septa, secondary crest myofibroblasts, together with matrix fibroblasts, secrete metalloproteinases and other ECM‐remodeling proteins to thin the septal tip ECM. The secondary crest myofibroblast continues producing elastin, eventually undergoing apoptosis during adulthood.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033016 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033016 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033016 "2023-03-16T09:17:47Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31331942") oboInOwl:hasExactSynonym obo:CL_4033016 "secondary-crest myofibroblast")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33624948") Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/cl#abbreviation>) oboInOwl:hasRelatedSynonym obo:CL_4033016 "SCMF")
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AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25448080") Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/cl#abbreviation>) Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/uberon#PLURAL>) oboInOwl:hasRelatedSynonym obo:CL_4033016 "SCMFs")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31331942") oboInOwl:hasRelatedSynonym obo:CL_4033016 "alveolar myofibroblast")
AnnotationAssertion(rdfs:label obo:CL_4033016 "secondary crest myofibroblast")
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SubClassOf(obo:CL_4033016 obo:CL_0000186)
SubClassOf(obo:CL_4033016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000114))
SubClassOf(obo:CL_4033016 ObjectSomeValuesFrom(obo:RO_0000056 obo:GO_0048286))
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# Class: obo:CL_4033017 (bronchiolar smooth muscle cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "ISBN:9781260462982") Annotation(oboInOwl:hasDbXref "PMID:15347627") obo:IAO_0000115 obo:CL_4033017 "A smooth muscle cell that is part of a bronchiole.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033017 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033017 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033017 "2023-03-16T09:38:17Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4033017 "bronchiolar smooth muscle cell")
EquivalentClasses(obo:CL_4033017 ObjectIntersectionOf(obo:CL_0000192 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002186)))

# Class: obo:CL_4033018 (lung megakaryocyte)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33351116") obo:IAO_0000115 obo:CL_4033018 "A megakaryocyte that is resident in the lung connective tissue.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033018 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033018 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033018 "2023-03-16T11:31:23Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33351116") Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/cl#abbreviation>) Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/uberon/core#PLURAL>) oboInOwl:hasRelatedSynonym obo:CL_4033018 "lung MKs")
AnnotationAssertion(rdfs:label obo:CL_4033018 "lung megakaryocyte")
SubClassOf(obo:CL_4033018 obo:CL_0000556)

# Class: obo:CL_4033020 (mucus secreting cell of trachea gland)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18931053") Annotation(oboInOwl:hasDbXref "PMID:29656943") obo:IAO_0000115 obo:CL_4033020 "A mucus secreting cell that is part of a submucosal gland of the trachea.")
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AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033020 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033020 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033020 "2023-03-16T13:03:13Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:18931053") oboInOwl:hasExactSynonym obo:CL_4033020 "tracheal submucosal gland mucous cell")
AnnotationAssertion(rdfs:label obo:CL_4033020 "mucus secreting cell of trachea gland")
EquivalentClasses(obo:CL_4033020 ObjectIntersectionOf(obo:CL_0000319 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005203)))
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# Class: obo:CL_4033021 (myoepithelial cell of trachea gland)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29656943") obo:IAO_0000115 obo:CL_4033021 "A myoepithelial cell that is part of a submucosal gland of the trachea.")
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AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033021 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033021 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033021 "2023-03-16T13:36:43Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4033021 "myoepithelial cell of trachea gland")
EquivalentClasses(obo:CL_4033021 ObjectIntersectionOf(obo:CL_0000185 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005203)))

# Class: obo:CL_4033022 (mucus secreting cell of bronchus submucosal gland)
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AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19965983") obo:IAO_0000115 obo:CL_4033022 "A mucus secreting cell of a submucosal gland of the bronchus.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033022 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033022 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033022 "2023-03-16T15:12:52Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:5487122") oboInOwl:hasExactSynonym obo:CL_4033022 "bronchial gland mucous cell")
AnnotationAssertion(rdfs:label obo:CL_4033022 "mucus secreting cell of bronchus submucosal gland")
EquivalentClasses(obo:CL_4033022 ObjectIntersectionOf(obo:CL_0000319 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410043)))

# Class: obo:CL_4033023 (airway submucosal gland collecting duct epithelial cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25648514") Annotation(oboInOwl:hasDbXref "PMID:29656943") obo:IAO_0000115 obo:CL_4033023 "An epithelial cell that is part of a collecting duct of an airway submucosal gland.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033023 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033023 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033023 "2023-03-16T15:20:28Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4033023 "airway submucosal gland collecting duct epithelial cell")
SubClassOf(obo:CL_4033023 obo:CL_0000066)
SubClassOf(obo:CL_4033023 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410077))

# Class: obo:CL_4033024 (airway submucosal gland duct basal cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29656943") Annotation(oboInOwl:hasDbXref "PMID:35046051") obo:IAO_0000115 obo:CL_4033024 "A basal cell that is part of a duct of an airway submucosal gland.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033024 <https://orcid.org/0000-0001-6677-8489>)
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AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033024 "https://orcid.org/0000-0002-9185-3994")
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033024 "2023-03-16T15:51:39Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4033024 "airway submucosal gland duct basal cell")
SubClassOf(obo:CL_4033024 obo:CL_0000646)
SubClassOf(obo:CL_4033024 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8410077))

# Class: obo:CL_4033025 (perichondrial fibroblast)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "wikipedia:Perichondrium") obo:IAO_0000115 obo:CL_4033025 "A fibroblast that is part of the fibrous layer of the perichondrium. This cell is responsible for collagen fiber production.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033025 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033025 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033025 "2023-03-16T16:12:50Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:CL_4033025 "perichondrial fibroblast")
EquivalentClasses(obo:CL_4033025 ObjectIntersectionOf(obo:CL_0000057 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008305)))

# Class: obo:CL_4033026 (lung perichondrial fibroblast)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36543915") obo:IAO_0000115 obo:CL_4033026 "A perichondrial fibroblast that is part of the lung")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033026 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4033026 <https://orcid.org/0000-0002-9185-3994>)
AnnotationAssertion(<http://purl.org/dc/terms/date> obo:CL_4033026 "2023-03-16T16:15:39Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36543915") Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/cl#abbreviation>) oboInOwl:hasRelatedSynonym obo:CL_4033026 "PC-fibro")
AnnotationAssertion(rdfs:label obo:CL_4033026 "lung perichondrial fibroblast")
EquivalentClasses(obo:CL_4033026 ObjectIntersectionOf(obo:CL_4033025 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002048)))

# Class: obo:CP_0000000 (obsolete CP:0000000)

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Unsure if there is a specific reason "lung" is used here and "airway" used in other terms. Ref describes "PC-fibro around the airway cartilage".

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Thank you for your comment, @bvarner-ebi. Initially I was considering airway for this same reason, however in the text you are quoting it is describing the localisation of PC-fibro in an image showing an airway. That doesn't exclude that it is also present in other pulmonary parts, as this cell is "enriched in the airways", but that doesn't mean it is exclusive, as cartilage it is not exclusive around the airways: "Cartilage (hyaline type) has the function of maintaining airway patency and it also serves for the attachment of local muscle and connective tissue."

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If this cell type does exist in lung tissue, would you please add that reference to the term. The quote mentioned above refers to the airways as well.

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@aleixpuigb aleixpuigb Mar 20, 2023 •
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Looking at the scRNA-seq data, the majority of cells identified as PC-fibro came from airway tissue, but a small proportion (~0'4%) was found in parenchymal tissue:
image
Of course the number of cells is very small and they can be false positives (in the umap they don't map with the PC-fibro cluster) or a different kind of perichondrial cells. In the later case, it makes more sense to use 'lung perichondrial fibroblast' to encompass all PC-fibro found in the lung.

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If that is from the dbxref, and if Par stands for parenchyma, it seems reasonable.

AnnotationAssertion(obo:IAO_0100001 obo:CP_0000000 obo:CL_0017500)
Expand Down Expand Up @@ -30895,4 +31010,5 @@ SubClassOf(ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000
SubClassOf(ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000945)) obo:CL_0000164)
SubClassOf(ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001264)) obo:CL_0000164)
SubClassOf(Annotation(oboInOwl:hasDbXref <https://github.com/obophenotype/cell-ontology/issues/757>) ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_7742)) ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000031))
SubClassOf(ObjectIntersectionOf(obo:CL_0000556 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000114)) obo:CL_4033018)
)
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