Revise endometrial ciliated epithelial cells classification and add links to GO terms #2440

Caroline-99 · 2024-07-18T08:39:32Z

Revise endometrial ciliated epithelial cells classification and add links to GO terms

…s to GO terms An ongoing PR for cleaning up ciliated epithelial cells hierarchy and links to GO terms - Imported GO terms into CL: - GO:0097730 (non-motile cilium) - GO:0036126 (sperm flagellum)

…lial cell - Updated logical and textual definition of endometrial ciliated epithelial cell. -Included links to GO terms - Added references to support that endometrial ciliated epithelial cell are multi-ciliated cells

Caroline-99 · 2024-07-22T10:47:19Z

#gogoeditdiff

github-actions · 2024-07-22T10:48:23Z

Your branch is 3 commit/s behind, please update your branch.

…and-villi

…ttps://github.com/obophenotype/cell-ontology into 2305-links-to-GO-terms-for-types-of-cilia-and-villi

dosumis · 2024-07-23T08:21:42Z

#gogoeditdiff

github-actions · 2024-07-23T08:26:22Z

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/2024-07-23/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/2024-07-23/cl-simple.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-simple-pr.owl/cl-simple.owl

Ontology imports

Ontology annotations

endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030040`

Removed

endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"
- database_cross_reference "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells"
endometrial ciliated epithelial cell SubClassOf ciliated epithelial cell

Added

endometrial ciliated epithelial cell definition "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface."
- database_cross_reference "PMID:37999981"
- database_cross_reference "doi:10.1038/s41591-020-1040-z"
- database_cross_reference "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells"
- database_cross_reference "PMID:31290979"
endometrial ciliated epithelial cell SubClassOf multi-ciliated epithelial cell

glandular endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030042`

Removed

glandular endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial glandular epithelium."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

Added

glandular endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

luminal endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030041`

Removed

luminal endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial luminal epithelium."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

Added

luminal endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

github-actions · 2024-07-23T08:26:24Z

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

endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030040`

Removed

endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"
- database_cross_reference "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells"
endometrial ciliated epithelial cell EquivalentTo ciliated cell and epithelial cell and (part of some endometrium epithelium)

Added

endometrial ciliated epithelial cell definition "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of motile cilia on its apical surface, which facilitates the movement of mucous across the endometrial surface."
- database_cross_reference "PMID:37999981"
- database_cross_reference "doi:10.1038/s41591-020-1040-z"
- database_cross_reference "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells"
- database_cross_reference "PMID:31290979"
endometrial ciliated epithelial cell EquivalentTo multi-ciliated epithelial cell and (part of some endometrium epithelium) and (has part some motile cilium)

glandular endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030042`

Removed

glandular endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial glandular epithelium."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

Added

glandular endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

luminal endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030041`

Removed

luminal endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial luminal epithelium."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

Added

luminal endometrial ciliated epithelial cell definition "A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface."
- database_cross_reference "doi:10.1038/s41591-020-1040-z"

…and links to GO terms" This reverts commit f946491. Reason, GO terms to be imported were not added.

aleixpuigb

It looks good.

dosumis · 2024-07-23T14:08:07Z

Related #2460

- Imported GO:0097729 - 9+2 motile cilium - Updated logical definition - Updated textual definition and added reference to support 9+2 motile cilia

aleixpuigb

Please, see inline comments.

src/ontology/cl-edit.owl

An ongoing PR - Clean up ciliated epithelial cells hierarchy and link…

f946491

…s to GO terms An ongoing PR for cleaning up ciliated epithelial cells hierarchy and links to GO terms - Imported GO terms into CL: - GO:0097730 (non-motile cilium) - GO:0036126 (sperm flagellum)

Caroline-99 linked an issue Jul 18, 2024 that may be closed by this pull request

Links to GO terms for types of cilia and villi #2305

Closed

Caroline-99 self-assigned this Jul 18, 2024

Caroline-99 marked this pull request as draft July 18, 2024 08:43

Caroline-99 added 2 commits July 22, 2024 11:37

Update cl-edit.owl

7e9dff3

Merge branch 'master' into 2305-links-to-GO-terms-for-types-of-cilia-…

3c3206b

…and-villi

Caroline-99 marked this pull request as ready for review July 22, 2024 10:58

Caroline-99 added 2 commits July 22, 2024 12:12

Updated textual defs

c7d8985

Merge branch '2305-links-to-GO-terms-for-types-of-cilia-and-villi' of h…

f12b2fd

…ttps://github.com/obophenotype/cell-ontology into 2305-links-to-GO-terms-for-types-of-cilia-and-villi

Caroline-99 changed the title ~~Clean up ciliated epithelial cells hierarchy and links to GO terms~~ Clean up endometrial ciliated epithelial cells classification and add links to GO terms Jul 22, 2024

Caroline-99 changed the title ~~Clean up endometrial ciliated epithelial cells classification and add links to GO terms~~ Revise endometrial ciliated epithelial cells classification and add links to GO terms Jul 22, 2024

Caroline-99 mentioned this pull request Jul 22, 2024

Links to GO terms for types of cilia and villi #2305

Closed

Caroline-99 requested a review from aleixpuigb July 23, 2024 10:26

Revert "An ongoing PR - Clean up ciliated epithelial cells hierarchy …

36a451a

…and links to GO terms" This reverts commit f946491. Reason, GO terms to be imported were not added.

aleixpuigb previously approved these changes Jul 23, 2024

View reviewed changes

dosumis added this to the Sprint 22/07/24 milestone Jul 23, 2024

Updated logical and textual defs

dd1fbe8

- Imported GO:0097729 - 9+2 motile cilium - Updated logical definition - Updated textual definition and added reference to support 9+2 motile cilia

Caroline-99 dismissed aleixpuigb’s stale review via dd1fbe8 July 24, 2024 08:41

aleixpuigb requested changes Jul 24, 2024

View reviewed changes

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Caroline-99 added 2 commits July 24, 2024 11:45

DOI updated

fc37ef9

Update cl-edit.owl

e1d5866

aleixpuigb approved these changes Jul 24, 2024

View reviewed changes

Caroline-99 merged commit 2f18f6a into master Jul 24, 2024
1 check passed

Revise endometrial ciliated epithelial cells classification and add links to GO terms #2440

Revise endometrial ciliated epithelial cells classification and add links to GO terms #2440

Conversation

Caroline-99 commented Jul 18, 2024 • edited Loading

Caroline-99 commented Jul 22, 2024

github-actions bot commented Jul 22, 2024

dosumis commented Jul 23, 2024

github-actions bot commented Jul 23, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

endometrial ciliated epithelial cell http://purl.obolibrary.org/obo/CL_4030040

Removed

Added

glandular endometrial ciliated epithelial cell http://purl.obolibrary.org/obo/CL_4030042

Removed

Added

luminal endometrial ciliated epithelial cell http://purl.obolibrary.org/obo/CL_4030041

Removed

Added

github-actions bot commented Jul 23, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

endometrial ciliated epithelial cell http://purl.obolibrary.org/obo/CL_4030040

Removed

Added

glandular endometrial ciliated epithelial cell http://purl.obolibrary.org/obo/CL_4030042

Removed

Added

luminal endometrial ciliated epithelial cell http://purl.obolibrary.org/obo/CL_4030041

Removed

Added

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dosumis commented Jul 23, 2024

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Caroline-99 commented Jul 18, 2024 •

edited

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endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030040`

glandular endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030042`

luminal endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030041`

endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030040`

glandular endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030042`

luminal endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030041`