Fix swapped definitions of basal/functional layers of endometrium (#3803) by ai4c-agent[bot] · Pull Request #3807 · obophenotype/uberon

ai4c-agent · 2026-10-28T11:46:33Z

Changes

UBERON:0022355 basal layer of endometrium

Definition replaced (it previously described the luminal layer) with the expanded definition proposed in the issue [PMID:26552890, PMID:37288662].
Logical definition: 'organ component layer' and (part_of some endometrium) and (adjacent_to some myometrium) (was 'endometrium epithelium' and (adjacent_to some 'uterine lumen')).

UBERON:0022356 outer layer of endometrium → functional layer of endometrium

Relabelled to "functional layer of endometrium" (this was already an EXACT synonym from FMA:86493). The old label "outer layer of endometrium" is kept as a RELATED synonym, not EXACT, because "outer" is misleading for the layer next to the lumen.
Definition replaced with the expanded definition proposed in the issue [PMID:25141152, PMID:26552890, PMID:37288662].
Logical definition: 'organ component layer' and (part_of some endometrium) and (adjacent_to some 'uterine lumen') (was 'endometrium epithelium' and (adjacent_to some myometrium)).

Rationale for genus change: both layers contain stroma, glands and blood vessels as well as epithelium, so endometrium epithelium was too narrow a genus.

Both terms also get a term_tracker_item pointing to the issue. I checked that the cited PMIDs exist and are on topic: endometrial stem/progenitor cells, uterine vasculature in the cycle, and cyclic decidualization. Locally, ELK reasoning with --equivalent-classes-allowed asserted-only passed. No other terms reference these two IDs.

🤖 Generated by @ai4c-agent

Model: claude-opus-5-5
Agent harness: claude-code
Triggered by: @mkeays
Run: View workflow run

🤖 Generated with Claude Code

@mkeays

- UBERON:0022355 'basal layer of endometrium': definition and logical definition previously described the luminal (functional) layer. Now defined as an organ component layer, part of endometrium, adjacent to myometrium, with expanded definition [PMID:26552890, PMID:37288662]. - UBERON:0022356: relabelled from 'outer layer of endometrium' to 'functional layer of endometrium' (old label kept as RELATED synonym). Now defined as an organ component layer, part of endometrium, adjacent to uterine lumen, with expanded definition [PMID:25141152, PMID:26552890, PMID:37288662]. - Genus changed from 'endometrium epithelium' to 'organ component layer', since both layers contain stroma, glands and vasculature, not just epithelium. - Added term_tracker_item links to the issue. Requested by @mkeays in #3803. --- 🤖 **Generated by @ai4c-agent** - Model: `claude-opus-5-5` - Agent harness: claude-code - Triggered by: @mkeays - Run: [View workflow run](https://github.com/obophenotype/uberon/actions/runs/40682033176) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

github-actions · 2026-10-28T11:49:04Z

This PR modifies some logical definitions. See details below:

Number of classes with modified logical definitions: 2

functional layer of endometrium

No changes in inferred subclasses.

basal layer of endometrium

No changes in inferred subclasses.

@mkeays

As requested by @mkeays on #3803: - UBERON:0022355 basal layer of endometrium: added EXACT synonyms 'basalis layer', 'endometrial basal layer', and Latin 'stratum basale endometrii' (OMO:0003011 latin term). - UBERON:0022356 functional layer of endometrium: added EXACT synonyms 'functionalis layer', 'endometrial functional layer', and Latin 'stratum functionale endometrii' (OMO:0003011 latin term). --- 🤖 **Generated by @ai4c-agent** - Model: `claude-opus-5-5` - Agent harness: claude-code - Triggered by: @mkeays - Run: [View workflow run](https://github.com/obophenotype/uberon/actions/runs/40684942829) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

ai4c-agent · 2026-10-28T12:08:12Z

Added the requested synonyms (all EXACT; the two Latin forms are tagged with the OMO:0003011 latin term synonym type):

UBERON:0022355 basal layer of endometrium: "basalis layer", "endometrial basal layer", "stratum basale endometrii"
UBERON:0022356 functional layer of endometrium: "functionalis layer", "endometrial functional layer", "stratum functionale endometrii"

🤖 Generated by @ai4c-agent

Model: claude-opus-5-5
Agent harness: claude-code
Triggered by: @mkeays
Run: View workflow run

@mkeays

…trium (#3803) Add a foaf:depiction to UBERON:0022355 (basal layer of endometrium) and UBERON:0022356 (functional layer of endometrium), as @mkeays requested. The image is https://upload.wikimedia.org/wikipedia/commons/8/87/Cells_of_the_uterus_in_different_menstrual_cycle_stages.png (Figure 6 of Ong et al. 2026, Sci Adv, PMID:42853913). Each depiction axiom carries three annotations: - xref PMID:42853913 - rdfs:comment citing the figure source - dcterms:license https://creativecommons.org/licenses/by/4.0/ I confirmed the PMID matches the paper and that Wikimedia Commons lists the file as CC BY 4.0. --- 🤖 **Generated by @ai4c-agent** - Model: `claude-opus-5-5` - Agent harness: claude-code - Triggered by: @mkeays - Run: [View workflow run](https://github.com/obophenotype/uberon/actions/runs/40716323564) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

ai4c-reviewer · 2026-10-29T09:55:00Z

Claude finished @mkeays's task in 39s —— View job

PR review

Hierarchy and parents are consistent
Definitions and supporting references look adequate
Obsolete or replacement handling is safe (no obsoletions)
OBO and ODK conventions appear preserved
No obvious CI, auth, or workflow regression (only uberon-edit.obo changed)

Summary

The swapped definitions and logical definitions are corrected. Basal is now organ component layer and part_of endometrium and adjacent_to myometrium. Functional is now organ component layer and part_of endometrium and adjacent_to uterine lumen. Both match the anatomy, and the genus change away from "endometrium epithelium" is justified because both layers also contain stroma, glands and vessels.
The definitions are mirrored by the logical axioms and cite PMIDs. I did not re-fetch the PMIDs myself. The PR description says they were checked.
The relabel keeps the old "outer layer of endometrium" as a RELATED synonym, which is sensible because it is misleading. The Latin synonyms use the OMO:0003011 type, which is declared in the file header.
term_tracker_item links to definitions of endometrium layers are the wrong way round #3803.
The bot's #gogoeditdiff run reports no changes in inferred subclasses.

🔵 SUGGESTION: The branch is 1 commit behind master. Update it and comment #gogoeditdiff again before merging.

I submitted an APPROVE review.

ai4c-reviewer

Checklist: all five items checked (see details in the Claude comment). Only suggestion: update branch from master and re-run #gogoeditdiff.

ct31-sanger · 2026-10-29T10:52:20Z

#gogoeditdiff

github-actions · 2026-10-29T10:58:27Z

ROBOT diff report for `e5d6ffa`

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/uberon/uberon-base.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2026-10-29/uberon-base.owl
Loaded from: file:/__w/uberon/uberon/master-base/uberon-base.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2026-10-29/uberon-base.owl
Loaded from: file:/__w/uberon/uberon/pr-base/uberon-base.owl

Ontology imports

Ontology annotations

basal layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022355`

Removed

basal layer of endometrium IAO_0000115 "The layer of endometrial epithelium adjacent to the uterine cavity."
- hasDbXref "Wikipedia:Endometrium#Histology"
basal layer of endometrium EquivalentTo endometrium epithelium and (RO_0002220 some uterine lumen)
basal layer of endometrium SubClassOf endometrium epithelium
basal layer of endometrium SubClassOf RO_0002220 some uterine lumen

Added

basal layer of endometrium IAO_0000233 "https://github.com/obophenotype/uberon/issues/3803"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
basal layer of endometrium hasExactSynonym "basalis layer"
basal layer of endometrium hasExactSynonym "endometrial basal layer"
basal layer of endometrium depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/Cells_of_the_uterus_in_different_menstrual_cycle_stages.png"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
- hasDbXref "PMID:42853913"
- comment "Figure 6 from "Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract" (Ong et al (2026) Science Advances 12(41): eaef2358)."
- license "https://creativecommons.org/licenses/by/4.0/"
basal layer of endometrium IAO_0000115 "The layer of the endometrium adjacent to the myometrium, comprising the basal portions of the uterine glands and the surrounding vascularized stroma, and supplied by the basal arteries. In menstruating species it is retained at menstruation and serves as the regenerative source from which the functional layer is restored; it harbours the epithelial and mesenchymal progenitor cell populations responsible for that regeneration."
- hasDbXref "PMID:37288662"
- hasDbXref "PMID:26552890"
basal layer of endometrium hasExactSynonym "stratum basale endometrii"
- hasSynonymType OMO_0003011
basal layer of endometrium EquivalentTo organ component layer and (BFO_0000050 some endometrium) and (RO_0002220 some myometrium)
basal layer of endometrium SubClassOf organ component layer
basal layer of endometrium SubClassOf reproductive structure
basal layer of endometrium SubClassOf BFO_0000050 some endometrium
basal layer of endometrium SubClassOf RO_0002220 some myometrium

functional layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022356`

Removed

functional layer of endometrium hasExactSynonym "functional layer of endometrium"
- hasDbXref "FMA:86493"
functional layer of endometrium IAO_0000115 "The layer of endometrial epithelium adjacent to the myometrium."
- hasDbXref "Wikipedia:Endometrium#Histology"
functional layer of endometrium label "outer layer of endometrium"
functional layer of endometrium EquivalentTo endometrium epithelium and (RO_0002220 some myometrium)
functional layer of endometrium SubClassOf endometrium epithelium
functional layer of endometrium SubClassOf RO_0002220 some myometrium

Added

functional layer of endometrium IAO_0000233 "https://github.com/obophenotype/uberon/issues/3803"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
functional layer of endometrium hasExactSynonym "endometrial functional layer"
functional layer of endometrium hasExactSynonym "functionalis layer"
functional layer of endometrium hasRelatedSynonym "outer layer of endometrium"
functional layer of endometrium depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/Cells_of_the_uterus_in_different_menstrual_cycle_stages.png"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
- hasDbXref "PMID:42853913"
- comment "Figure 6 from "Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract" (Ong et al (2026) Science Advances 12(41): eaef2358)."
- license "https://creativecommons.org/licenses/by/4.0/"
functional layer of endometrium IAO_0000115 "The layer of the endometrium adjacent to the uterine lumen, comprising the luminal epithelium, the superficial portions of the uterine glands, and the surrounding vascularized stroma, and supplied by the spiral arterioles. It proliferates and differentiates across the ovarian cycle under the influence of oestrogen and progesterone, and is the site of embryo implantation and decidualization. In menstruating species it is shed at menstruation and regenerated from the basal layer in the following cycle."
- hasDbXref "PMID:37288662"
- hasDbXref "PMID:26552890"
- hasDbXref "PMID:25141152"
functional layer of endometrium hasExactSynonym "stratum functionale endometrii"
- hasSynonymType OMO_0003011
functional layer of endometrium label "functional layer of endometrium"
functional layer of endometrium EquivalentTo organ component layer and (BFO_0000050 some endometrium) and (RO_0002220 some uterine lumen)
functional layer of endometrium SubClassOf organ component layer
functional layer of endometrium SubClassOf reproductive structure
functional layer of endometrium SubClassOf BFO_0000050 some endometrium
functional layer of endometrium SubClassOf RO_0002220 some uterine lumen

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

Ontology comparison

Left

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

Right

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

Ontology imports

Ontology annotations

basal layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022355`

Removed

basal layer of endometrium definition "The layer of endometrial epithelium adjacent to the uterine cavity."^^string
- database_cross_reference "Wikipedia:Endometrium#Histology"^^string
basal layer of endometrium EquivalentTo endometrium epithelium and (adjacent to some uterine lumen)

Added

basal layer of endometrium term tracker item "https://github.com/obophenotype/uberon/issues/3803"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
basal layer of endometrium has exact synonym "basalis layer"^^string
basal layer of endometrium has exact synonym "endometrial basal layer"^^string
basal layer of endometrium depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/Cells_of_the_uterus_in_different_menstrual_cycle_stages.png"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
- license "https://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string)
- comment "Figure 6 from "Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract" (Ong et al (2026) Science Advances 12(41): eaef2358)."^^string
- database_cross_reference "PMID:42853913"^^string
basal layer of endometrium definition "The layer of the endometrium adjacent to the myometrium, comprising the basal portions of the uterine glands and the surrounding vascularized stroma, and supplied by the basal arteries. In menstruating species it is retained at menstruation and serves as the regenerative source from which the functional layer is restored; it harbours the epithelial and mesenchymal progenitor cell populations responsible for that regeneration."^^string
- database_cross_reference "PMID:26552890"^^string
- database_cross_reference "PMID:37288662"^^string
basal layer of endometrium has exact synonym "stratum basale endometrii"^^string
- has_synonym_type latin term
basal layer of endometrium EquivalentTo organ component layer and (part of some endometrium) and (adjacent to some myometrium)

functional layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022356`

Removed

functional layer of endometrium has exact synonym "functional layer of endometrium"^^string
- database_cross_reference "FMA:86493"^^string
functional layer of endometrium definition "The layer of endometrial epithelium adjacent to the myometrium."^^string
- database_cross_reference "Wikipedia:Endometrium#Histology"^^string
functional layer of endometrium label "outer layer of endometrium"^^string
functional layer of endometrium EquivalentTo endometrium epithelium and (adjacent to some myometrium)

Added

functional layer of endometrium term tracker item "https://github.com/obophenotype/uberon/issues/3803"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
functional layer of endometrium has exact synonym "endometrial functional layer"^^string
functional layer of endometrium has exact synonym "functionalis layer"^^string
functional layer of endometrium has_related_synonym "outer layer of endometrium"^^string
functional layer of endometrium depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/Cells_of_the_uterus_in_different_menstrual_cycle_stages.png"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)
- license "https://creativecommons.org/licenses/by/4.0/"^^[string](http://www.w3.org/2001/XMLSchema#string)
- comment "Figure 6 from "Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract" (Ong et al (2026) Science Advances 12(41): eaef2358)."^^string
- database_cross_reference "PMID:42853913"^^string
functional layer of endometrium definition "The layer of the endometrium adjacent to the uterine lumen, comprising the luminal epithelium, the superficial portions of the uterine glands, and the surrounding vascularized stroma, and supplied by the spiral arterioles. It proliferates and differentiates across the ovarian cycle under the influence of oestrogen and progesterone, and is the site of embryo implantation and decidualization. In menstruating species it is shed at menstruation and regenerated from the basal layer in the following cycle."^^string
- database_cross_reference "PMID:26552890"^^string
- database_cross_reference "PMID:25141152"^^string
- database_cross_reference "PMID:37288662"^^string
functional layer of endometrium has exact synonym "stratum functionale endometrii"^^string
- has_synonym_type latin term
functional layer of endometrium label "functional layer of endometrium"^^string
functional layer of endometrium EquivalentTo organ component layer and (part of some endometrium) and (adjacent to some uterine lumen)

Generated by workflow run.

ct31-sanger

Looks good to me!

dosumis · 2026-10-29T15:25:21Z

Looks great. Please go ahead and merge.

ai4c-agent Bot mentioned this pull request Oct 28, 2026

definitions of endometrium layers are the wrong way round #3803

Closed

mkeays self-assigned this Oct 28, 2026

mkeays and others added 3 commits October 28, 2026 13:04

Merge branch 'master' into ai4c-agent-issue-3803-run2160

f61ce63

Merge branch 'master' into ai4c-agent-issue-3803-run2160

e5d6ffa

mkeays marked this pull request as ready for review October 29, 2026 09:54

mkeays requested a review from ct31-sanger October 29, 2026 09:54

ai4c-reviewer Bot approved these changes Oct 29, 2026

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ct31-sanger approved these changes Oct 29, 2026

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dosumis approved these changes Oct 29, 2026

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dosumis merged commit c1116ac into master Oct 29, 2026
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dosumis deleted the ai4c-agent-issue-3803-run2160 branch October 29, 2026 15:27

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ai4c-agent Bot commented Oct 28, 2026

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github-actions Bot commented Oct 28, 2026

functional layer of endometrium

basal layer of endometrium

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ROBOT diff report for e5d6ffa

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

basal layer of endometrium http://purl.obolibrary.org/obo/UBERON_0022355

Removed

Added

functional layer of endometrium http://purl.obolibrary.org/obo/UBERON_0022356

Removed

Added

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

basal layer of endometrium http://purl.obolibrary.org/obo/UBERON_0022355

Removed

Added

functional layer of endometrium http://purl.obolibrary.org/obo/UBERON_0022356

Removed

Added

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dosumis commented Oct 29, 2026

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ai4c-reviewer Bot commented Oct 29, 2026 •

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ROBOT diff report for `e5d6ffa`

basal layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022355`

functional layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022356`

basal layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022355`

functional layer of endometrium `http://purl.obolibrary.org/obo/UBERON_0022356`