Fixes #2169 relabel lung cell types #2403

aleixpuigb · 2024-06-20T15:07:24Z

Fixes #2169 relabel lung cell types

Addresses #2169 relabel lung cell types

aleixpuigb · 2024-06-20T15:07:44Z

#gogoeditdiff

github-actions · 2024-06-20T15:12:49Z

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-06-20/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-master.owl/cl-simple.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-simple.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-06-20/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

alveolar type 2 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028006`

Removed

alveolar type 2 fibroblast cell label "alveolar type 2 fibroblast cell"

Added

alveolar type 2 fibroblast cell has_related_synonym "AdvF"
- database_cross_reference "PMID:33208946"
- has_synonym_type abbreviation
alveolar type 2 fibroblast cell has exact synonym "alveolar type 2 fibroblast cell"
alveolar type 2 fibroblast cell label "alveolar adventitial fibroblast"

pneumocyte `http://purl.obolibrary.org/obo/CL_0000322`

Removed

pneumocyte label "pneumocyte"
pneumocyte definition "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:20054144"

Added

pneumocyte definition "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:29463737"
- database_cross_reference "PMID:20054144"
pneumocyte label "pulmonary alveolar epithelial cell"
pneumocyte has exact synonym "pneumocyte"
- database_cross_reference "PMID:32491474"

type I pneumocyte `http://purl.obolibrary.org/obo/CL_0002062`

Removed

type I pneumocyte definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:20054144"
- database_cross_reference "http://www.copewithcytokines.de"
type I pneumocyte label "type I pneumocyte"
type I pneumocyte has exact synonym "type 1 pneumocyte"

Added

type I pneumocyte definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:20054144"
- database_cross_reference "http://www.copewithcytokines.de"
- database_cross_reference "PMID:36138472"
type I pneumocyte has exact synonym "type 1 pneumocyte"
- database_cross_reference "PMID:32491474"
type I pneumocyte has exact synonym "type I pneumocyte"
type I pneumocyte label "pulmonary alveolar type 1 cell"

type II pneumocyte `http://purl.obolibrary.org/obo/CL_0002063`

Removed

type II pneumocyte definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:8540632"
- database_cross_reference "ISBN:0412046911"
- database_cross_reference "http://www.copewithcytokines.de"
type II pneumocyte label "type II pneumocyte"

Added

type II pneumocyte label "pulmonary alveolar type 2 cell"
type II pneumocyte has exact synonym "type II pneumocyte"
- database_cross_reference "PMID:32491474"
type II pneumocyte definition "A squamous 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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:8540632"
- database_cross_reference "ISBN:0412046911"
- database_cross_reference "http://www.copewithcytokines.de"
- database_cross_reference "PMID:36138472"

github-actions · 2024-06-20T15:12:51Z

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
Version IRI: None
Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
Version IRI: None
Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

alveolar type 2 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028006`

Removed

alveolar type 2 fibroblast cell label "alveolar type 2 fibroblast cell"

Added

alveolar type 2 fibroblast cell has_related_synonym "AdvF"
- database_cross_reference "PMID:33208946"
- has_synonym_type abbreviation
alveolar type 2 fibroblast cell has_exact_synonym "alveolar type 2 fibroblast cell"
alveolar type 2 fibroblast cell label "alveolar adventitial fibroblast"

pneumocyte `http://purl.obolibrary.org/obo/CL_0000322`

Removed

pneumocyte label "pneumocyte"
pneumocyte definition "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:20054144"

Added

pneumocyte definition "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:29463737"
- database_cross_reference "PMID:20054144"
pneumocyte label "pulmonary alveolar epithelial cell"
pneumocyte has_exact_synonym "pneumocyte"
- database_cross_reference "PMID:32491474"

type I pneumocyte `http://purl.obolibrary.org/obo/CL_0002062`

Removed

type I pneumocyte definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:20054144"
- database_cross_reference "http://www.copewithcytokines.de"
type I pneumocyte label "type I pneumocyte"
type I pneumocyte has_exact_synonym "type 1 pneumocyte"

Added

type I pneumocyte definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:20054144"
- database_cross_reference "http://www.copewithcytokines.de"
- database_cross_reference "PMID:36138472"
type I pneumocyte has_exact_synonym "type 1 pneumocyte"
- database_cross_reference "PMID:32491474"
type I pneumocyte has_exact_synonym "type I pneumocyte"
type I pneumocyte label "pulmonary alveolar type 1 cell"

type II pneumocyte `http://purl.obolibrary.org/obo/CL_0002063`

Removed

type II pneumocyte definition "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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:8540632"
- database_cross_reference "ISBN:0412046911"
- database_cross_reference "http://www.copewithcytokines.de"
type II pneumocyte label "type II pneumocyte"

Added

type II pneumocyte label "pulmonary alveolar type 2 cell"
type II pneumocyte has_exact_synonym "type II pneumocyte"
- database_cross_reference "PMID:32491474"
type II pneumocyte definition "A squamous 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."
- database_cross_reference "GOC:tfm"
- database_cross_reference "PMID:8540632"
- database_cross_reference "ISBN:0412046911"
- database_cross_reference "http://www.copewithcytokines.de"
- database_cross_reference "PMID:36138472"

aleixpuigb · 2024-06-21T10:24:31Z

A new term 'adventitial fibroblast' is needed.

dosumis

See comment on def AT2. (sorry I didn't spot this first time)

src/ontology/cl-edit.owl

aleixpuigb · 2024-06-25T08:52:08Z

Thanks for the review @dosumis. I have done the edits.

AvolaAmg · 2024-06-27T15:08:07Z

src/ontology/cl-edit.owl


-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 "PMID:36138472") Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de") 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.")


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 ?

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!

Reviewer is not available and review comments have been adressed.

aleixpuigb added 3 commits October 11, 2023 12:52

Addresses #2169 relabel lung cell types

8c2c92b

Addresses #2169 relabel lung cell types

Merge branch 'master' into 2169_relabel_lung_cell_types

336e0f6

Merge branch 'master' into 2169_relabel_lung_cell_types

fac872f

aleixpuigb added text definition relabel HuBMAP Needed/useful for HuBMAP labels Jun 20, 2024

aleixpuigb self-assigned this Jun 20, 2024

aleixpuigb marked this pull request as draft June 20, 2024 15:12

Relabel fetal pre-type II pneumocyte

33aa616

aleixpuigb marked this pull request as ready for review June 21, 2024 10:25

aleixpuigb requested a review from JABelfiore June 21, 2024 10:25

dosumis approved these changes Jun 24, 2024

View reviewed changes

dosumis added the Lung_refactor label Jun 24, 2024

dosumis previously requested changes Jun 24, 2024

View reviewed changes

src/ontology/cl-edit.owl Show resolved Hide resolved

Remove squamous from definition

d3c62d7

aleixpuigb requested a review from dosumis June 24, 2024 11:02

aleixpuigb requested review from AvolaAmg and removed request for dosumis and JABelfiore June 25, 2024 12:30

AvolaAmg reviewed Jun 27, 2024

View reviewed changes

Change definition reference and fix acronyms

fde3766

AvolaAmg approved these changes Jun 27, 2024

View reviewed changes

Merge branch 'master' into 2169_relabel_lung_cell_types

4a0d9e6

aleixpuigb merged commit 9b12dff into master Jun 28, 2024
1 check passed

aleixpuigb deleted the 2169_relabel_lung_cell_types branch June 28, 2024 08:42


		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 "PMID:36138472") Annotation(oboInOwl:hasDbXref "http://www.copewithcytokines.de") 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.")

Fixes #2169 relabel lung cell types #2403

Fixes #2169 relabel lung cell types #2403

Conversation

aleixpuigb commented Jun 20, 2024

aleixpuigb commented Jun 20, 2024

github-actions bot commented Jun 20, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

alveolar type 2 fibroblast cell http://purl.obolibrary.org/obo/CL_4028006

Removed

Added

pneumocyte http://purl.obolibrary.org/obo/CL_0000322

Removed

Added

type I pneumocyte http://purl.obolibrary.org/obo/CL_0002062

Removed

Added

type II pneumocyte http://purl.obolibrary.org/obo/CL_0002063

Removed

Added

github-actions bot commented Jun 20, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

alveolar type 2 fibroblast cell http://purl.obolibrary.org/obo/CL_4028006

Removed

Added

pneumocyte http://purl.obolibrary.org/obo/CL_0000322

Removed

Added

type I pneumocyte http://purl.obolibrary.org/obo/CL_0002062

Removed

Added

type II pneumocyte http://purl.obolibrary.org/obo/CL_0002063

Removed

Added

aleixpuigb commented Jun 21, 2024

dosumis left a comment

Choose a reason for hiding this comment

aleixpuigb commented Jun 25, 2024

AvolaAmg Jun 27, 2024

Choose a reason for hiding this comment

aleixpuigb Jun 27, 2024 • edited Loading

Choose a reason for hiding this comment

alveolar type 2 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028006`

pneumocyte `http://purl.obolibrary.org/obo/CL_0000322`

type I pneumocyte `http://purl.obolibrary.org/obo/CL_0002062`

type II pneumocyte `http://purl.obolibrary.org/obo/CL_0002063`

alveolar type 2 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028006`

pneumocyte `http://purl.obolibrary.org/obo/CL_0000322`

type I pneumocyte `http://purl.obolibrary.org/obo/CL_0002062`

type II pneumocyte `http://purl.obolibrary.org/obo/CL_0002063`

aleixpuigb Jun 27, 2024 •

edited

Loading