Fixes #2855 NTR limbal epithelial stem cell #2857

aleixpuigb · 2024-12-11T16:07:14Z

Fixes #2855 NTR limbal epithelial stem cell

- Mesothelial cells of gut now part of serosa - tidying up partonomy for intestinal lining - Fixed brush border on enteroycte

partial fix to missing classifications under intestinal epithelial cell

moved colon goblet cell to po colonic epithlium

Changing the partonomy from colon to colonic epithelium.

Fixes #2855 NTR limbal epithelial stem cell

aleixpuigb · 2024-12-11T16:08:14Z

Unfortunately the branch was not created from master.

aleixpuigb · 2024-12-11T16:08:30Z

#gogoeditdiff

github-actions · 2024-12-11T16:14:31Z

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

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-12-11/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
Version IRI: http://purl.obolibrary.org/obo/cl/releases/2024-12-11/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

UBERON_0000482 `http://purl.obolibrary.org/obo/UBERON_0000482`

Added

Class: UBERON_0000482

UBERON_0006761 `http://purl.obolibrary.org/obo/UBERON_0006761`

Added

Class: UBERON_0006761

limbal epithelial stem cell of cornea `http://purl.obolibrary.org/obo/CL_4033093`

Added

limbal epithelial stem cell of cornea hasExactSynonym "limbal stem cell"
- hasDbXref "PMID:17562792"
limbal epithelial stem cell of cornea hasExactSynonym "limbal epithelial stem cell"
- hasDbXref "PMID:20614614"
limbal epithelial stem cell of cornea label "limbal epithelial stem cell of cornea"
limbal epithelial stem cell of cornea contributor 0000-0001-7655-4833
limbal epithelial stem cell of cornea date "2024-12-11T13:59:19Z"^^dateTime
limbal epithelial stem cell of cornea hasRelatedSynonym "LSC"
- hasDbXref "PMID:36983561"
- hasSynonymType OMO_0003000
limbal epithelial stem cell of cornea hasRelatedSynonym "LESC"
- hasDbXref "PMID:20614614"
- hasSynonymType OMO_0003000
limbal epithelial stem cell of cornea contributor 0000-0001-6677-8489
limbal epithelial stem cell of cornea IAO_0000115 "A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023)."
- hasDbXref "PMID:29105366"
- hasDbXref "PMID:37768272"
- hasDbXref "PMID:20614614"
- hasDbXref "PMID:36983561"
Class: limbal epithelial stem cell of cornea
limbal epithelial stem cell of cornea EquivalentTo stem cell and (BFO_0000050 some UBERON_0006761)
limbal epithelial stem cell of cornea SubClassOf stem cell
limbal epithelial stem cell of cornea SubClassOf BFO_0000050 some UBERON_0000482
limbal epithelial stem cell of cornea SubClassOf BFO_0000050 some UBERON_0006761
limbal epithelial stem cell of cornea SubClassOf RO_0002203 some corneal epithelial cell

github-actions · 2024-12-11T16:14:35Z

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

UBERON_0000482 `http://purl.obolibrary.org/obo/UBERON_0000482`

Added

Class: UBERON_0000482

limbal epithelial stem cell of cornea `http://purl.obolibrary.org/obo/CL_4033093`

Added

limbal epithelial stem cell of cornea has exact synonym "limbal stem cell"
- database_cross_reference "PMID:17562792"
limbal epithelial stem cell of cornea has exact synonym "limbal epithelial stem cell"
- database_cross_reference "PMID:20614614"
limbal epithelial stem cell of cornea label "limbal epithelial stem cell of cornea"
limbal epithelial stem cell of cornea contributor 0000-0001-7655-4833
limbal epithelial stem cell of cornea date "2024-12-11T13:59:19Z"^^dateTime
limbal epithelial stem cell of cornea has_related_synonym "LSC"
- has_synonym_type abbreviation
- database_cross_reference "PMID:36983561"
limbal epithelial stem cell of cornea has_related_synonym "LESC"
- has_synonym_type abbreviation
- database_cross_reference "PMID:20614614"
limbal epithelial stem cell of cornea contributor 0000-0001-6677-8489
limbal epithelial stem cell of cornea definition "A stem cell that is part of the corneo-scleral limbus. This cell type resides at the basal layer of the epithelium and has a small size and high nuclear to cytoplasmatic ratio (Secker and Daniels, 2009). A limbal stem cell is responsible for corneal epithelial renewal and repair (Li et al., 2023), and to help maintain a clear corneal surface by preventing conjunctival epithelial cells from migrating onto the cornea (Wang et al., 2023)."
- database_cross_reference "PMID:37768272"
- database_cross_reference "PMID:29105366"
- database_cross_reference "PMID:36983561"
- database_cross_reference "PMID:20614614"
Class: limbal epithelial stem cell of cornea
limbal epithelial stem cell of cornea EquivalentTo stem cell and (part of some corneo-scleral junction)
limbal epithelial stem cell of cornea SubClassOf part of some UBERON_0000482
limbal epithelial stem cell of cornea SubClassOf develops into some corneal epithelial cell

src/ontology/cl-edit.owl

Comment has been addressed

dosumis and others added 26 commits October 17, 2024 22:27

Update cl-edit.owl

1323caf

- Mesothelial cells of gut now part of serosa - tidying up partonomy for intestinal lining - Fixed brush border on enteroycte

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

0712a44

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

2b8fc50

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

40126ea

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

2b63cac

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

7bc48d3

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

6660de1

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

7cc1c84

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

5164f0a

Update cl-edit.owl

e7d5723

partial fix to missing classifications under intestinal epithelial cell

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

5822d1d

Update cl-edit.owl

8623c27

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

ba26df9

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

97f9175

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

67c2740

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

e1648c3

Update cl-edit.owl

6fe231c

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

1069960

Fixes #2674 #2825

f0e72d3

Update cl-edit.owl

fb1f929

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

507df8d

Update cl-edit.owl

06e7532

moved colon goblet cell to po colonic epithlium

Merge branch 'master' into separating_gut_meosthelial_from_gut_lining

cb91a60

Fixed 'early colonocyte'

562ed34

Changing the partonomy from colon to colonic epithelium.

Fixes #2855 NTR limbal epithelial stem cell

920bf8a

Fixes #2855 NTR limbal epithelial stem cell

Merge branch 'master' into 2855_NTR_limbal_epithelial_cell_cornea

19862a1

aleixpuigb added new term request HuBMAP Needed/useful for HuBMAP labels Dec 11, 2024

aleixpuigb self-assigned this Dec 11, 2024

aleixpuigb requested review from AvolaAmg and removed request for AvolaAmg December 11, 2024 17:08

aleixpuigb assigned Caroline-99 Dec 16, 2024

Merge branch 'master' into 2855_NTR_limbal_epithelial_cell_cornea

16a39b6

aleixpuigb unassigned Caroline-99 Dec 16, 2024

aleixpuigb requested a review from Caroline-99 December 16, 2024 09:03

dosumis previously requested changes Dec 16, 2024

View reviewed changes

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

Caroline-99 and others added 2 commits December 17, 2024 09:31

Merge branch 'master' into 2855_NTR_limbal_epithelial_cell_cornea

fc18777

Add SubclassOf 'epithelial fate stem cell'

6734351

Caroline-99 approved these changes Dec 17, 2024

View reviewed changes

Merge branch 'master' into 2855_NTR_limbal_epithelial_cell_cornea

5cc368c

aleixpuigb merged commit e9bf7bd into master Dec 17, 2024
1 check passed

aleixpuigb deleted the 2855_NTR_limbal_epithelial_cell_cornea branch December 17, 2024 12:07

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fixes #2855 NTR limbal epithelial stem cell #2857

Fixes #2855 NTR limbal epithelial stem cell #2857

aleixpuigb commented Dec 11, 2024

aleixpuigb commented Dec 11, 2024

aleixpuigb commented Dec 11, 2024

github-actions bot commented Dec 11, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

UBERON_0000482 `http://purl.obolibrary.org/obo/UBERON_0000482`

Added

UBERON_0006761 `http://purl.obolibrary.org/obo/UBERON_0006761`

Added

limbal epithelial stem cell of cornea `http://purl.obolibrary.org/obo/CL_4033093`

Added

github-actions bot commented Dec 11, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

UBERON_0000482 `http://purl.obolibrary.org/obo/UBERON_0000482`

Added

limbal epithelial stem cell of cornea `http://purl.obolibrary.org/obo/CL_4033093`

Added

Fixes #2855 NTR limbal epithelial stem cell #2857

Fixes #2855 NTR limbal epithelial stem cell #2857

Conversation

aleixpuigb commented Dec 11, 2024

aleixpuigb commented Dec 11, 2024

aleixpuigb commented Dec 11, 2024

github-actions bot commented Dec 11, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

UBERON_0000482 http://purl.obolibrary.org/obo/UBERON_0000482

Added

UBERON_0006761 http://purl.obolibrary.org/obo/UBERON_0006761

Added

limbal epithelial stem cell of cornea http://purl.obolibrary.org/obo/CL_4033093

Added

github-actions bot commented Dec 11, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

UBERON_0000482 http://purl.obolibrary.org/obo/UBERON_0000482

Added

limbal epithelial stem cell of cornea http://purl.obolibrary.org/obo/CL_4033093

Added

UBERON_0000482 `http://purl.obolibrary.org/obo/UBERON_0000482`

UBERON_0006761 `http://purl.obolibrary.org/obo/UBERON_0006761`

limbal epithelial stem cell of cornea `http://purl.obolibrary.org/obo/CL_4033093`

UBERON_0000482 `http://purl.obolibrary.org/obo/UBERON_0000482`

limbal epithelial stem cell of cornea `http://purl.obolibrary.org/obo/CL_4033093`