[DO NOT MERGE] eval #31051 i:1: Taxon constraint: GO:0046544 development of secondary male sexual characteristics (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#31051: Taxon constraint: GO:0046544 development of secondary male sexual characteristics

Original PR (human solution)

#32037: Issue #31051: rename secondary sexual characteristic terms with 'animal' prefix

Agent Commits

• Revise animal secondary sex characteristic labels

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

Agent Response - PR Comments

Implemented the issue #31051 follow-up requested in the thread: replace the interim sensu Metazoa labels with animal ... labels while preserving the metazoan taxon restriction on the parent term.

Changes made:

• Updated GO:0045136 label from development of secondary sexual characteristics, sensu Metazoa to development of animal secondary sexual characteristics
• Updated GO:0046543 label from development of secondary female sexual characteristics, sensu Metazoa to development of animal secondary female sexual characteristics
• Updated GO:0046544 label from development of secondary male sexual characteristics, sensu Metazoa to development of animal secondary male sexual characteristics
• Updated child is_a comments to reflect the renamed parent label
• Updated the label column for GO:0045136 in src/taxon_constraints/only_in_taxon.tsv

Rationale:

• This follows the curator request in the issue thread and is more consistent with existing GO lexical precedent such as animal organ development versus plant organ development.
• The only_in_taxon Metazoa restriction remains on GO:0045136, so the biological scope established in the previous change is preserved.
• The existing EXACT synonyms with the unsuffixed names were retained for discoverability and backward-friendly search behavior.

Validation:

• Pre-validation: make travis_build passed before edits
• Post-edit validation: make travis_build passed after edits

Checklist:

• PLAN: issue and comment thread reviewed; final requested action was clear
• PRE-VALIDATION: ontology validated before edits
• RESEARCH: not needed beyond curator discussion already captured in the issue
• TERM-SEARCH: affected GO terms and taxon constraint entry reviewed
• DESIGN-PATTERNS: checked naming precedent; no logical-definition changes needed
• EDITS: used obo-checkout.pl / obo-checkin.pl workflow for edited terms
• RELATIONSHIPS: no relationship changes required beyond preserving existing scope
• SPECIALIZED-EDITS: taxon-constraint guidance consulted; no new TC logic introduced
• METADATA: existing metadata retained; no new term metadata required
• AUTOMATED-VALIDATION: make travis_build passed
• REFERENCE-VALIDATION: no new references introduced
• ISSUE-ALIGNMENT: change matches the latest curator direction in the issue thread

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🤖 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 the requested follow-up in PR #.

Summary:

• renamed the three affected terms to use animal ... wording for consistency with existing GO naming precedent:
  • GO:0045136 development of animal secondary sexual characteristics
  • GO:0046543 development of animal secondary female sexual characteristics
  • GO:0046544 development of animal secondary male sexual characteristics
• retained the existing EXACT synonyms with the older generic wording for searchability
• kept the parent-level only_in_taxon Metazoa constraint on GO:0045136

make travis_build passes after the update.

---

🤖 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-31051

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25979822693