Enterocyte refactor renaming by JABelfiore · Pull Request #2944 · obophenotype/cell-ontology

JABelfiore · 2025-02-10T16:47:49Z

No description provided.

enterocyte of epithelium of small intestine --> small intestine enterocyte early enterocyte --> early small intestine enterocyte.

dosumis · 2025-02-14T10:36:33Z

#gogoeditdiff

github-actions · 2025-02-14T10:42:26Z

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/2025-03-12/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/2025-03-12/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

enterocyte `http://purl.obolibrary.org/obo/CL_0000584`

Removed

enterocyte IAO_0000115 "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen."
- hasDbXref "SANBI:mhl"
enterocyte hasNarrowSynonym "differentiated enterocyte"
- hasDbXref "https://orcid.org/0000-0001-9610-7627"
- hasDbXref "PMID:33290721"

Added

enterocyte IAO_0000115 "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. This covers both the large and small intestine."
- hasDbXref "SANBI:mhl"

enterocyte of epithelium of intestinal villus `http://purl.obolibrary.org/obo/CL_1000335`

Added

enterocyte of epithelium of intestinal villus hasExactSynonym "late small intestine enterocyte"
enterocyte of epithelium of intestinal villus hasExactSynonym "mature small intestine enterocyte"

immature colonocyte `http://purl.obolibrary.org/obo/CL_4047018`

Removed

immature colonocyte label "early colonocyte"@en
immature colonocyte EquivalentTo immature small intestine enterocyte and (BFO_0000050 some UBERON_0000397)
immature colonocyte SubClassOf immature small intestine enterocyte

Added

immature colonocyte label "immature colonocyte"@en
immature colonocyte hasExactSynonym "early colonocyte"

immature small intestine enterocyte `http://purl.obolibrary.org/obo/CL_4047019`

Removed

immature small intestine enterocyte label "early enterocyte"@en

Added

immature small intestine enterocyte label "immature small intestine enterocyte"@en
immature small intestine enterocyte hasExactSynonym "early enterocyte"

immature small intestine entrocyte `http://purl.obolibrary.org/obo/CL_0008050`

Added

immature small intestine entrocyte label "immature small intestine entrocyte"
immature small intestine entrocyte date "2025-03-11T18:54:02Z"^^dateTime
immature small intestine entrocyte contributor 0000-0002-7073-9172
Class: immature small intestine entrocyte
immature small intestine entrocyte SubClassOf small intestine enterocyte

mature colonocyte `http://purl.obolibrary.org/obo/CL_0008052`

Added

mature colonocyte date "2025-03-11T18:55:58Z"^^dateTime
mature colonocyte label "mature colonocyte"
mature colonocyte contributor 0000-0002-7073-9172
Class: mature colonocyte
mature colonocyte SubClassOf colonocyte
mature colonocyte SubClassOf RO_0002207 some immature colonocyte

mature small intestince enterocyte `http://purl.obolibrary.org/obo/CL_0008051`

Added

mature small intestince enterocyte date "2025-03-11T18:54:17Z"^^dateTime
mature small intestince enterocyte label "mature small intestince enterocyte"
mature small intestince enterocyte contributor 0000-0002-7073-9172
Class: mature small intestince enterocyte
mature small intestince enterocyte SubClassOf RO_0002207 some immature small intestine enterocyte
mature small intestince enterocyte SubClassOf small intestine enterocyte

small intestine enterocyte `http://purl.obolibrary.org/obo/CL_1000334`

Removed

small intestine enterocyte label "enterocyte of epithelium of small intestine"

Added

small intestine enterocyte hasExactSynonym "enterocyte of epithelium of small intestine"
small intestine enterocyte label "small intestine enterocyte"

github-actions · 2025-02-14T10:42:28Z

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

Ontology comparison

Left

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

Ontology imports

Ontology annotations

early colonocyte `http://purl.obolibrary.org/obo/CL_4047018`

Removed

early colonocyte label "early colonocyte"@en
early colonocyte EquivalentTo early enterocyte and (part of some colonic epithelium)

Added

early colonocyte label "immature colonocyte"@en
early colonocyte has_exact_synonym "early colonocyte"
early colonocyte SubClassOf colonocyte

early enterocyte `http://purl.obolibrary.org/obo/CL_4047019`

Removed

early enterocyte label "early enterocyte"@en

Added

early enterocyte label "immature small intestine enterocyte"@en
early enterocyte has_exact_synonym "early enterocyte"

enterocyte `http://purl.obolibrary.org/obo/CL_0000584`

Removed

enterocyte definition "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen."
- database_cross_reference "SANBI:mhl"
enterocyte has_narrow_synonym "differentiated enterocyte"
- database_cross_reference "https://orcid.org/0000-0001-9610-7627"
- database_cross_reference "PMID:33290721"

Added

enterocyte definition "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen. This covers both the large and small intestine."
- database_cross_reference "SANBI:mhl"

enterocyte of epithelium of intestinal villus `http://purl.obolibrary.org/obo/CL_1000335`

Added

enterocyte of epithelium of intestinal villus has_exact_synonym "late small intestine enterocyte"
enterocyte of epithelium of intestinal villus has_exact_synonym "mature small intestine enterocyte"

enterocyte of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000334`

Removed

enterocyte of epithelium of small intestine label "enterocyte of epithelium of small intestine"

Added

enterocyte of epithelium of small intestine has_exact_synonym "enterocyte of epithelium of small intestine"
enterocyte of epithelium of small intestine label "small intestine enterocyte"

immature small intestine entrocyte `http://purl.obolibrary.org/obo/CL_0008050`

Added

immature small intestine entrocyte label "immature small intestine entrocyte"
immature small intestine entrocyte date "2025-03-11T18:54:02Z"^^dateTime
immature small intestine entrocyte contributor 0000-0002-7073-9172
Class: immature small intestine entrocyte
immature small intestine entrocyte SubClassOf enterocyte of epithelium of small intestine

mature colonocyte `http://purl.obolibrary.org/obo/CL_0008052`

Added

mature colonocyte date "2025-03-11T18:55:58Z"^^dateTime
mature colonocyte label "mature colonocyte"
mature colonocyte contributor 0000-0002-7073-9172
Class: mature colonocyte
mature colonocyte SubClassOf colonocyte
mature colonocyte SubClassOf directly develops from some early colonocyte

mature small intestince enterocyte `http://purl.obolibrary.org/obo/CL_0008051`

Added

mature small intestince enterocyte date "2025-03-11T18:54:17Z"^^dateTime
mature small intestince enterocyte label "mature small intestince enterocyte"
mature small intestince enterocyte contributor 0000-0002-7073-9172
Class: mature small intestince enterocyte
mature small intestince enterocyte SubClassOf directly develops from some early enterocyte
mature small intestince enterocyte SubClassOf enterocyte of epithelium of small intestine

- [x] Make sure early is not part of standard/mature - [x] Get rid of differentiated enterocyte from synonyms - [x] Mature and immature to be used instead of early and late

QUick attempt at fix. Needs review to see if any more earlier changes need reverting.

dosumis · 2025-03-12T11:50:00Z

#gogoeditdiff

github-actions · 2025-03-12T11:51:22Z

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

dosumis · 2025-03-12T12:05:32Z

#gogoeditdiff

dosumis · 2025-04-02T10:31:12Z

Remaining issues:

General definition of enterocyte refers to mature state. Ditto colonocyte.
Defs needed for mature colonocyte + immature and mature small intestine enterocyte
EC def of immature small intestine enterocyte is dubious
Species neutral terminology: Can we make enterocyte neutral, or should we aim to use 'gut absorptive cell'? A: making either species neutral requires deleting taxon restriction on mucosa to chordata (in Uberon). Suggest push to second ticket.

mkeays · 2026-10-13T11:26:31Z

Proposed updates:

Rather than making a lot of mature-specific definitions of existing terms more general to encompass mature and immature states, rename "enterocyte" (CL:0000584) to "mature enterocyte", and add a sibling term "immature enterocyte" as a subclass of "gut absorptive cell" (CL:0000677). Definition of "gut absorptive cell" needs to be made more general as it specifies microvilli -- looks like it came from ZFA as the definition is the same. If we broaden it to be any absorptive cell in the gut it would be applicable to more taxa as well. Then "immature colonocyte" and "immature small intestine enterocyte" can be children of "immature enterocyte".
Rename CL:1000347 "colonocyte" to "mature colonocyte" and keep the relationships in the description of CL:0008052, but remove CL:0008052.
Rename CL:1000334 "small intestine enterocyte" to "mature small intestine enterocyte" and keep the relationships in the description of CL:0008051 but remove CL:0008051.
There are two terms here called "immature small intestine enterocyte" -- CL:4047019 and CL:0008050. We should replace CL:0008050 with CL:4047019.
On CL:4047019 we should remove the Equivalent To relationship and add a 'part of' some 'epithelium of crypt of Lieberkuhn of small intestine' (UBERON:0022280).

mkeays · 2026-10-13T13:17:18Z

Proposed new definition for CL:0000677: "An epithelial cell of the gut epithelium that is committed to the absorptive lineage."
This is broad enough to cover gut in any taxon that has a gut and any stage of differentiation following transit amplifying stage.

mkeays · 2026-10-13T14:01:35Z

Also add general "enterocyte" and "colonocyte" term to cover either immature or mature states, as these are often referred to together (e.g. the enterocyte cluster includes both mature and immature enterocytes).

…3782, #3778)

…2882)

mkeays · 2026-10-15T10:45:59Z

Fixed a couple of definitions to broaden them as they were too small-intestine-specific.

Used rdfs:comment to clarify usage of the words "early" and "immature" in lysosome-rich enterocyte and vacuolated fetal-type enterocyte. These terms both have "early enterocyte" and "immature enterocyte" as related synonyms, but they mean "early" and "immature" in an organism development context rather than a cell maturation context as we've used in above commits. I think it makes sense to keep them despite the conflict because they are words that are used in both contexts to refer to different things.

…#2882)

…ocyte (#2882)

… for obsolete one (#3785)

…ocytes (#3785)

mkeays · 2026-10-20T11:12:54Z

replacing CL:1000339 (enterocyte of epithelium proper of small intestine) with CL:0019035 (small intestine enterocyte) -- the former was in cellxgene_subset so may need to update them?

…es (#2882, #3785)

)

…#3785)

…2785)

)

JABelfiore added 2 commits January 20, 2025 15:29

enterocyte renaming

16086a5

enterocyte of epithelium of small intestine --> small intestine enterocyte early enterocyte --> early small intestine enterocyte.

Merge branch 'master' into 2882-enterocyte-refactor-renaming

ec6871d

JABelfiore requested a review from dosumis February 10, 2025 16:47

JABelfiore self-assigned this Feb 10, 2025

JABelfiore linked an issue Feb 10, 2025 that may be closed by this pull request

Enterocyte refactor & renaming #2882

Open

JABelfiore changed the title ~~2882 enterocyte refactor renaming~~ Enterocyte refactor renaming Feb 10, 2025

JABelfiore and others added 3 commits February 11, 2025 12:18

Merge branch 'master' into 2882-enterocyte-refactor-renaming

030472a

Merge branch 'master' into 2882-enterocyte-refactor-renaming

d4b3b38

Merge branch 'master' into 2882-enterocyte-refactor-renaming

019b253

JABelfiore and others added 8 commits February 18, 2025 10:52

Merge branch 'master' into 2882-enterocyte-refactor-renaming

6c9a471

Merge branch 'master' into 2882-enterocyte-refactor-renaming

f2da425

Merge branch 'master' into 2882-enterocyte-refactor-renaming

bc13dd8

Merge branch 'master' into 2882-enterocyte-refactor-renaming

0e33aa4

Merge branch 'master' into 2882-enterocyte-refactor-renaming

a4ef85e

Update cl-edit.owl

017dd70

- [x] Make sure early is not part of standard/mature - [x] Get rid of differentiated enterocyte from synonyms - [x] Mature and immature to be used instead of early and late

refactoring

8ad3ddd

Update cl-edit.owl

5d3aa57

QUick attempt at fix. Needs review to see if any more earlier changes need reverting.

Merge branch 'master' into 2882-enterocyte-refactor-renaming

30f5b46

dosumis marked this pull request as draft March 12, 2025 12:21

updating gut absorptive cell to make it broader (#2882)

9fae906

mkeays self-assigned this Oct 14, 2026

adding intermediate enterocyte and children with synonyms from CAP (#…

8ac28c0

…3782, #3778)

This was referenced Oct 15, 2026

CL new term request: mid villus enterocyte #3782

Open

CL new term request: mid crypt colonocyte #3778

Open

[NTR] gut progenitors and descendants along the crypt-villus/surface axis #3785

Open

Merge branch 'master' into 2882-enterocyte-refactor-renaming

8b0e0c8

mkeays mentioned this pull request Oct 15, 2026

NTR: enterocyte progenitor cell (CL:9900001) — fixes #3758 #3760

Closed

mkeays added 2 commits October 15, 2026 11:33

adding comments to clarify different usage of 'early' and 'immature' (#…

7ec6130

…2882)

updating definitions to make them more general (#2882)

9c03cf4

mkeays added 8 commits October 15, 2026 13:19

adding synonyms suggested by CAP to enterocyte progenitor

67df98c

adding locations for progenitors, and subclass of gut absorptive cell (…

88fd9e3

…#2882)

renaming enterocytes/colonocytes in line with HGCA (#2882, #3785)

ea79d06

reparenting some terms to general enterocyte rather than mature enter…

d4f6b8d

…ocyte (#2882)

making CL:1000337 obsolete (#2882, #3785)

1431c11

Merge branch 'master' into 2882-enterocyte-refactor-renaming

a1a0b4b

some restructuring for small intestine enterocytes, updating consider…

53638fb

… for obsolete one (#3785)

removing 'proper', adding equivalent classes to small intestine enter…

0df2402

…ocytes (#3785)

mkeays added 7 commits October 20, 2026 12:13

replacing CL:1000339 with CL:0019035 (#3785, #2882)

8c0fc9e

adding part of intestinal villus to new maturation stage SI enterocyt…

45fa55c

…es (#2882, #3785)

restructuring large intestine and making one term obsolete (#2882, #3785

658ada1

)

updating Equivalent To relationship for BEST4+ colonocyte (#2882, #3785)

766c0ab

fixing data type for date (#2882, #3785)

7b3d45d

updating part of relationships for large intestine enterocytes (#2882, …

9050893

…#3785)

making gut absorptive cell broader to cover non-vertebrates (#2882, #…

a21b345

…2785)

mkeays marked this pull request as ready for review October 20, 2026 14:58

mkeays added 3 commits October 21, 2026 15:12

Merge branch 'master' into 2882-enterocyte-refactor-renaming

474e8d9

Merge branch 'master' into 2882-enterocyte-refactor-renaming

b439eee

updating directly develops from relation for TA cell of SI (#2882, #3785

e795a46

)

Conversation

JABelfiore commented Feb 10, 2025

Uh oh!

dosumis commented Feb 14, 2025

Uh oh!

github-actions Bot commented Feb 14, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

enterocyte http://purl.obolibrary.org/obo/CL_0000584

Removed

Added

enterocyte of epithelium of intestinal villus http://purl.obolibrary.org/obo/CL_1000335

Added

immature colonocyte http://purl.obolibrary.org/obo/CL_4047018

Removed

Added

immature small intestine enterocyte http://purl.obolibrary.org/obo/CL_4047019

Removed

Added

immature small intestine entrocyte http://purl.obolibrary.org/obo/CL_0008050

Added

mature colonocyte http://purl.obolibrary.org/obo/CL_0008052

Added

mature small intestince enterocyte http://purl.obolibrary.org/obo/CL_0008051

Added

small intestine enterocyte http://purl.obolibrary.org/obo/CL_1000334

Removed

Added

Uh oh!

github-actions Bot commented Feb 14, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

early colonocyte http://purl.obolibrary.org/obo/CL_4047018

Removed

Added

early enterocyte http://purl.obolibrary.org/obo/CL_4047019

Removed

Added

enterocyte http://purl.obolibrary.org/obo/CL_0000584

Removed

Added

enterocyte of epithelium of intestinal villus http://purl.obolibrary.org/obo/CL_1000335

Added

enterocyte of epithelium of small intestine http://purl.obolibrary.org/obo/CL_1000334

Removed

Added

immature small intestine entrocyte http://purl.obolibrary.org/obo/CL_0008050

Added

mature colonocyte http://purl.obolibrary.org/obo/CL_0008052

Added

mature small intestince enterocyte http://purl.obolibrary.org/obo/CL_0008051

Added

Uh oh!

dosumis commented Mar 12, 2025

Uh oh!

github-actions Bot commented Mar 12, 2025

Uh oh!

dosumis commented Mar 12, 2025

Uh oh!

dosumis commented Apr 2, 2025

Uh oh!

mkeays commented Oct 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

mkeays commented Oct 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

mkeays commented Oct 13, 2026

Uh oh!

mkeays commented Oct 15, 2026

Uh oh!

mkeays commented Oct 20, 2026

github-actions Bot commented Feb 14, 2025 •

edited

Loading

enterocyte `http://purl.obolibrary.org/obo/CL_0000584`

enterocyte of epithelium of intestinal villus `http://purl.obolibrary.org/obo/CL_1000335`

immature colonocyte `http://purl.obolibrary.org/obo/CL_4047018`

immature small intestine enterocyte `http://purl.obolibrary.org/obo/CL_4047019`

immature small intestine entrocyte `http://purl.obolibrary.org/obo/CL_0008050`

mature colonocyte `http://purl.obolibrary.org/obo/CL_0008052`

mature small intestince enterocyte `http://purl.obolibrary.org/obo/CL_0008051`

small intestine enterocyte `http://purl.obolibrary.org/obo/CL_1000334`

github-actions Bot commented Feb 14, 2025 •

edited

Loading

early colonocyte `http://purl.obolibrary.org/obo/CL_4047018`

early enterocyte `http://purl.obolibrary.org/obo/CL_4047019`

enterocyte `http://purl.obolibrary.org/obo/CL_0000584`

enterocyte of epithelium of intestinal villus `http://purl.obolibrary.org/obo/CL_1000335`

enterocyte of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000334`

immature small intestine entrocyte `http://purl.obolibrary.org/obo/CL_0008050`

mature colonocyte `http://purl.obolibrary.org/obo/CL_0008052`

mature small intestince enterocyte `http://purl.obolibrary.org/obo/CL_0008051`

mkeays commented Oct 13, 2026 •

edited

Loading

mkeays commented Oct 13, 2026 •

edited

Loading