Skip to content

Remove part_of intestinal villus from duodenal/jejunal/ileal epithelium (#3802) - #3806

Open
ai4c-agent[bot] wants to merge 2 commits into
masterfrom
ai4c-agent-issue-3802-run2149
Open

Remove part_of intestinal villus from duodenal/jejunal/ileal epithelium (#3802)#3806
ai4c-agent[bot] wants to merge 2 commits into
masterfrom
ai4c-agent-issue-3802-run2149

Conversation

@ai4c-agent

@ai4c-agent ai4c-agent Bot commented Oct 28, 2026

Copy link
Copy Markdown
Contributor

Closes #3802

Removed these incorrect FMA-sourced axioms, because each epithelium lines the whole organ and not only its villi:

  • duodenal epithelium (UBERON:0008346): removed part_of intestinal villus of duodenum (UBERON:0008342)
  • jejunal epithelium (UBERON:0000400): removed part_of intestinal villus of jejunum (UBERON:0008343)
  • ileal epithelium (UBERON:0008345): removed part_of intestinal villus of ileum (UBERON:0008344)

The existing logical definitions (epithelium ⊓ part_of duodenum/jejunum/ileum) are kept. Nothing else changed.

🤖 Generated by @ai4c-agent

🤖 Generated with Claude Code

@github-actions @claude
Remove part_of intestinal villus axioms from duodenal, jejunal and il…
98f07f5 
…eal epithelium (#3802)

The duodenal (UBERON:0008346), jejunal (UBERON:0000400) and ileal
(UBERON:0008345) epithelia line the whole of their respective organs,
not only the villi, so the FMA-sourced 'part_of intestinal villus of X'
assertions were incorrect (and caused them to be inferred as subclasses
of 'epithelium of intestinal villus'). The existing logical definitions
(epithelium and part_of duodenum/jejunum/ileum) are retained.

Closes #3802

---
🤖 **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/40664405391)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@ai4c-agent ai4c-agent Bot mentioned this pull request Oct 28, 2026
Open
@ai4c-reviewer

ai4c-reviewer Bot commented Oct 28, 2026 •
edited
Loading

Copy link
Copy Markdown

Claude finished @ai4c-agent[bot]'s task in 45s —— View job

PR review: approved

  • Hierarchy and parents are consistent
  • Definitions and supporting references look adequate
  • Obsolete or replacement handling is safe
  • OBO and ODK conventions appear preserved
  • No obvious CI, auth, or workflow regression

The PR removes three incorrect part_of villus axioms (duodenal, jejunal and ileal epithelium). The genus-differentia logical definitions and is_a parents are kept. There are no 🔴 or 🟡 issues, so I submitted an approving review.

ai4c-reviewer[bot]
ai4c-reviewer Bot approved these changes Oct 28, 2026
View reviewed changes

@ai4c-reviewer ai4c-reviewer Bot left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  • Hierarchy and parents are consistent
  • Definitions and supporting references look adequate
  • Obsolete or replacement handling is safe
  • OBO and ODK conventions appear preserved
  • No obvious CI, auth, or workflow regression

The diff removes three FMA-sourced part_of villus axioms (UBERON:0000400, 0008345, 0008346) and nothing else. Each epithelium lines the whole organ, so part_of villus was wrong. The epithelium ⊓ part_of <organ> logical definitions and is_a parents are intact, so classification is unaffected. No obsoletions, no new terms, no workflow files touched. Merge recommended. (@ai4c-agent)

@mkeays

mkeays commented Oct 28, 2026

Copy link
Copy Markdown
Contributor

#gogoeditdiff

@mkeays mkeays self-assigned this Oct 28, 2026
@ubyndr ubyndr mentioned this pull request Oct 28, 2026
Merged
@ubyndr

ubyndr commented Oct 28, 2026

Copy link
Copy Markdown
Contributor

#gogoeditdiff

@ai4c-reviewer

ai4c-reviewer Bot commented Oct 28, 2026 •
edited
Loading

Copy link
Copy Markdown

Claude finished @ubyndr's task in 32s —— View job

PR review: no blocking issues

  • Hierarchy and parents are consistent
  • Definitions and supporting references look adequate
  • Obsolete or replacement handling is safe
  • OBO and ODK conventions appear preserved
  • No obvious CI, auth, or workflow regression

Against origin/master, the diff touches only src/ontology/uberon-edit.obo and removes three lines:

  • UBERON:0000400 (jejunal epithelium) loses part_of UBERON:0008343 (intestinal villus of jejunum).
  • UBERON:0008345 (ileal epithelium) loses part_of UBERON:0008344 (intestinal villus of ileum).
  • UBERON:0008346 (duodenal epithelium) loses part_of UBERON:0008342 (intestinal villus of duodenum).

The removed axioms came from FMA. They were wrong, because each epithelium lines the whole organ and not only its villi. Each term keeps its intersection_of genus-differentia definition (epithelium ⊓ part_of duodenum, jejunum or ileum), and the is_a parents are unchanged. Classification should be unaffected. The change is a pure removal, so it adds no new terms, obsoletions or dangling references.

🔵 SUGGESTION: before merging, confirm that robot convert reserialisation leaves the file unchanged. I saw no sign of drift in the diff.

I did not run the reasoner or the CI build. The review is based on the diff only. I can't submit a formal approving review, so this comment is the review. I found no 🔴 or 🟡 issues and I recommend merging.

The #gogoeditdiff check reported that the branch is 5 commits behind. Update the branch from master and comment #gogoeditdiff again.
· branch ai4c-agent-issue-3802-run2149

@ubyndr

ubyndr commented Oct 28, 2026

Copy link
Copy Markdown
Contributor

#gogoeditdiff

@github-actions

github-actions Bot commented Oct 28, 2026

Copy link
Copy Markdown
Contributor

ROBOT diff report for d71ae99

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/2026-10-28/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/2026-10-28/uberon-base.owl
  • Loaded from: file:/__w/uberon/uberon/pr-base/uberon-base.owl

Ontology imports

Ontology annotations

duodenal epithelium http://purl.obolibrary.org/obo/UBERON_0008346

Removed

Added

ileal epithelium http://purl.obolibrary.org/obo/UBERON_0008345

Removed

Added

jejunal epithelium http://purl.obolibrary.org/obo/UBERON_0000400

Removed

Added

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

duodenal epithelium http://purl.obolibrary.org/obo/UBERON_0008346

Removed

ileal epithelium http://purl.obolibrary.org/obo/UBERON_0008345

Removed

jejunal epithelium http://purl.obolibrary.org/obo/UBERON_0000400

Removed

Generated by workflow run.

@mkeays
mkeays requested a review from ct31-sanger October 29, 2026 08:45

This branch has not been deployed

No deployments
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@ai4c-reviewer ai4c-reviewer[bot] ai4c-reviewer[bot] approved these changes
@ct31-sanger ct31-sanger Awaiting requested review from ct31-sanger

Assignees

@mkeays mkeays

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

duodenal, jejunal, and ileal epithelia should not be part of epithelium of intestinal villus

2 participants

@mkeays @ubyndr