[DO NOT MERGE] eval #31114 i:1: NTR: Terreic acid biosynthetic process (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#31114: NTR: Terreic acid biosynthetic process

Original PR (human solution)

#32032: Fix created_by GOC:vw -> vw on three terms (issue #31114)

Agent Commits

• Fix terreic acid term labels and metadata
• Merge pull request #32028 from geneontology/dragon-ai-agent-issue-31114-run8107

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

Agent Response - PR Comments

Implemented the remaining fixes requested in issue #31114 and committed them locally.

What changed:

• GO:0180067
  • Renamed primary label from terreate biosynthetic process to terreic acid biosynthetic process
  • Swapped the related synonym so terreate biosynthetic process is retained as RELATED
  • Updated the text definition to use terreic acid
  • Corrected created_by: GOC:vw to created_by: vw
• GO:0180069
  • Renamed primary label from positive regulation of terreate biosynthetic process to positive regulation of terreic acid biosynthetic process
  • Updated the definition to standard GO positive-regulation phrasing: Any process that activates or increases the frequency, rate or extent of terreic acid biosynthetic process.
  • Updated the logical definition text label on the regulated target to match the renamed parent term
  • Corrected created_by: GOC:vw to created_by: vw

Rationale:

• This follows the issue-thread decision to use the biologist-friendly terreic acid labels as the primary term names while retaining the pH 7.3 ChEBI form CHEBI:233617 ! terreate in the logical definition.
• The created_by value was corrected to match GO convention and local precedent for curator initials.

Validation performed:

• Full ontology validation with cd src/ontology && make travis_build
• Result: passed cleanly

Checklist:

• PLAN: issue history reviewed and requested scope identified
• PRE-VALIDATION: current ontology validated before concluding changes via full build run
• TERM-SEARCH: inspected existing GO:0180067, GO:0180069, related GO:0140880, and nearby creator-metadata precedent
• DESIGN-PATTERNS: checked chemical-entity and design-pattern guidance; no new over-specifying axioms added
• EDITS: used obo-checkout.pl/obo-checkin.pl workflow with local terms/
• RELATIONSHIPS: retained existing logical pattern and pH 7.3 CHEBI reference
• SPECIALIZED-EDITS: chemical-entity guidance applied
• METADATA: corrected created_by on the affected existing terms only; left creation dates unchanged
• AUTOMATED-VALIDATION: make travis_build passed
• REFERENCE-VALIDATION: reused existing PMID 25265334; no new references introduced
• CHANGES-COMMITTED: local commit created for src/ontology/go-edit.obo only

---

🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/go-ontology-agent-config@v9:.
• Iteration: 1
• Run: View workflow run

Agent Response - Issue Comments

Implemented locally and committed.

Summary:

• Swapped the primary labels back to the originally requested terreic acid forms for:
  • GO:0180067 terreic acid biosynthetic process
  • GO:0180069 positive regulation of terreic acid biosynthetic process
• Kept the pH 7.3 CHEBI logical definition chemical as CHEBI:233617 ! terreate, which matches GO chemical-entity practice.
• Corrected created_by from GOC:vw to vw on both issue terms.

Validation:

• make travis_build passes cleanly.

Changes committed in PR #.

---

🤖 Generated by opencode agent

• Runtime: opencode
• Model: openai/gpt-5.4
• Agent config: ai4curation/go-ontology-agent-config@v9:.
• Iteration: 1
• Run: View workflow run

Experiment Config

Parameter	Value
Model	openai/gpt-5.4
Agent config	ai4curation/go-ontology-agent-config@v9:.
Iteration	1
URL prefix	https://href.li/?
Base branch	eval-base-issue-31114

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25979191823