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Summary

  • Remove 'located in' thoracic cavity relationship from esophagus (UBERON:0001043) since esophagus has cervical and abdominal parts
  • Replace 'branching part of' with 'connecting branch of' for esophageal artery (UBERON:0035539) relationship to thoracic aorta

Changes Made

  1. Esophagus (UBERON:0001043): Removed located_in UBERON:0002224 \! thoracic cavity axiom because the esophagus has cervical and abdominal parts in addition to its thoracic part
  2. Esophageal artery (UBERON:0035539): Changed branching_part_of UBERON:0001515 \! thoracic aorta to connecting_branch_of UBERON:0001515 \! thoracic aorta

Fixes #3572

🤖 Generated with Claude Code
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- Remove 'located in' thoracic cavity relationship from esophagus (UBERON:0001043) since esophagus has cervical and abdominal parts
- Replace 'branching part of' with 'connecting branch of' for esophageal artery (UBERON:0035539) relationship to thoracic aorta

Fixes #3572

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
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@aleixpuigb
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#gogoeditdiff

@aleixpuigb aleixpuigb requested a review from Caroline-99 June 30, 2025 14:57
@aleixpuigb aleixpuigb mentioned this pull request Jun 30, 2025
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#gogoeditdiff

@aleixpuigb
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#gogoeditdiff

This PR #3576 needs to be merged for gogoeditdiff to work

@gouttegd
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gouttegd commented Jul 1, 2025

This PR #3576 needs to be merged for gogoeditdiff to work

Done now. :)

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#gogoeditdiff

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github-actions bot commented Jul 1, 2025

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/2025-07-01/uberon-base.owl
  • Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-main.owl/uberon-base.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
  • Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2025-07-01/uberon-base.owl
  • Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-pr.owl/uberon-base.owl

Ontology imports

Ontology annotations

Leydig's organ http://purl.obolibrary.org/obo/UBERON_0000040

Removed

crop http://purl.obolibrary.org/obo/UBERON_0007356

Removed

esophageal artery http://purl.obolibrary.org/obo/UBERON_0035539

Removed

Added

esophageal taste bud http://purl.obolibrary.org/obo/UBERON_0034724

Removed

esophagus http://purl.obolibrary.org/obo/UBERON_0001043

Removed

esophagus muscle http://purl.obolibrary.org/obo/UBERON_0003832

Removed

esophagus skeletal muscle http://purl.obolibrary.org/obo/UBERON_0004831

Removed

Added

peptonephridium http://purl.obolibrary.org/obo/UBERON_0006976

Removed

submucosal esophageal gland http://purl.obolibrary.org/obo/UBERON_0008989

Removed

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github-actions bot commented Jul 1, 2025

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

esophageal artery http://purl.obolibrary.org/obo/UBERON_0035539

Removed

Added

esophagus http://purl.obolibrary.org/obo/UBERON_0001043

Removed

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@Caroline-99 Caroline-99 left a comment

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Everything looks good to me.

@aleixpuigb aleixpuigb merged commit 5e3ce08 into master Jul 2, 2025
6 checks passed
@aleixpuigb aleixpuigb deleted the issue-3572 branch July 2, 2025 14:47
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Revise esophagus and esophageal artery partonomy

5 participants