[DO NOT MERGE] eval #9930 i:1: Request to add synonyms to: GRIN-related complex neurodevelopmental disorder (MONDO:1060138) (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#9930: Request to add synonyms to: GRIN-related complex neurodevelopmental disorder (MONDO:1060138)

Original PR (human solution)

#10209: added synonyms to MONDO:1060138 GRIN-related complex neurodevelopmental disorder

Agent Commits

• Add GRIN term synonyms

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

Agent Response - PR Comments

Updated MONDO:1060138 (GRIN-related complex neurodevelopmental disorder) by adding three sourced related synonyms:

• GRIN-related encephalopathy [PMID:34884460]
• GRIN-related neurodevelopmental disorder [PMID:40374652]
• GRINpathies [PMID:34884460, PMID:37932875]

I also added a term_tracker_item link back to issue #9930.

Rationale:

• The issue requested several synonyms for this existing term.
• I reviewed the imported issue discussion and checked the current term stanza before editing.
• I validated the cited literature via PubMed/web lookups because aurelian was not available in this environment.
• The published literature I verified supports GRINpathies / grinpathies, not GRINopathies, so I kept the edit conservative and did not introduce the unsupported spelling.
• GRIN-related neurodevelopmental disorder is directly supported by PMID:40374652.
• GRIN-related encephalopathy is compatible with the GRIN-related disorder literature and was added as a related synonym rather than an exact synonym.

Validation performed:

• Checked out and edited the term using the terms/ workflow, then checked it back into src/ontology/mondo-edit.obo.
• Ran robot convert --catalog src/ontology/catalog-v001.xml -i src/ontology/mondo-edit.obo -f obo -o src/ontology/mondo-edit.TMP.obo successfully as a syntax check.
• Could not run the Docker-based ODK normalization workflow in this environment because docker is unavailable.

Completed checklist:

• Read __issue_context__.json
• Reviewed current MONDO:1060138 stanza
• Verified supporting PMIDs for added synonyms
• Applied minimal synonym-only ontology change
• Added issue tracker annotation for #9930
• Ran robot convert syntax validation
• Committed only src/ontology/mondo-edit.obo

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🤖 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 #.

Added sourced synonyms to MONDO:1060138 and linked the term to this issue. I did not add GRINopathies; the literature I verified supports GRINpathies instead.

---

🤖 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-9930

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25977370742