[DO NOT MERGE] eval #9842 i:1: [Merge]Extraoral halitosis due to methanethiol oxidase deficiency & Autosomal recessive extra-oral halitosis (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#9842: [Merge]Extraoral halitosis due to methanethiol oxidase deficiency & Autosomal recessive extra-oral halitosis

Original PR (human solution)

#10158: merge autosomal recessive extra-oral halitosis into MONDO:0029144

Agent Commits

• Merge duplicate extraoral halitosis terms

Note: This PR diff shows ONLY the agent's changes. The baseline is eval_base_branch.

Agent Response - PR Comments

Implemented the merge requested in issue #9842.

Summary of changes:

• Obsoleted MONDO:0034186 (autosomal recessive extra-oral halitosis) and marked it as replaced by MONDO:0029144.
• Added property_value: IAO:0000231 MONDO:TermsMerged and retained the issue link on the obsolete term.
• Reduced the obsolete stanza to the expected minimal obsoletion stub.
• Migrated the meaningful content from MONDO:0034186 to MONDO:0029144, including:
  • Orphanet:562538 xref and associated Orphanet subsets
  • GARD:0017996 xref and gard_rare subset
  • nord_rare and rare subsets
  • the more specific parent MONDO:0019222 (inborn disorder of methionine cycle and sulfur amino acid metabolism)
  • has_characteristic HP:0000007 (Autosomal recessive inheritance)
  • synonym autosomal recessive extra-oral halitosis with Orphanet:562538 support

Rationale:

• The issue states that ORDO 562538 exactly matches OMIM:618148, which already exactly matches MONDO:0029144, so MONDO:0034186 should be obsoleted in favor of MONDO:0029144.
• The obsolete term carried useful external mapping and classification metadata not yet present on the surviving term, so those were preserved on MONDO:0029144 rather than dropped.

Checks completed:

• Reviewed the imported issue context from __issue_context__.json.
• Inspected both source stanzas in src/ontology/mondo-edit.obo before editing.
• Confirmed there were no remaining references to MONDO:0034186 outside its own stanza before and after the change.
• Verified the final obsolete stanza contains only: id, obsolete name, IAO:0000231, IAO:0000233, is_obsolete, and replaced_by.
• Compared the pre-change obsolete stanza against the post-change surviving stanza to ensure meaningful content was preserved.
• Reviewed git diff for src/ontology/mondo-edit.obo before commit.

Environment limitation:

• I could not run the requested ODK-backed normalization / robot verify steps because docker is not available in this execution environment, so make NORM and targeted QC could not be executed here.

Commit created:

• c91a222 - Merge duplicate extraoral halitosis terms

---

🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/mondo-agent-config@v3:.
• Iteration: 1
• Run: View workflow run

Agent Response - Issue Comments

Addressed in PR #.

Obsoleted MONDO:0034186 with direct replacement by MONDO:0029144, and migrated the useful Orphanet/GARD-facing metadata and synonym/classification content onto the surviving term.

I also removed the scheduled-obsoletion-only metadata from the obsolete term stub as part of the cleanup.

---

🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/mondo-agent-config@v3:.
• Iteration: 1
• Run: View workflow run

Experiment Config

Parameter	Value
Model	openai/gpt-5.4
Agent config	ai4curation/mondo-agent-config@v3:.
Iteration	1
URL prefix	https://href.li/?
Base branch	eval-base-issue-9842

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977210423