[DO NOT MERGE] eval #31935 i:1: Missing parent: GO:0061852 retrograde transporter complex, Golgi to ER (plus term label and definition) (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#31935: Missing parent: GO:0061852 retrograde transporter complex, Golgi to ER (plus term label and definition)

Original PR (human solution)

#31946: Reclassify GO:0061852 as retrograde cargo receptor complex, Golgi to ER (#31935)

Agent Commits

• Refine GO:0061852 cargo receptor complex

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

Agent Response - PR Comments

Updated GO:0061852 to align its label, definition, and classification with the biology described in the issue.

Summary of changes

• Renamed GO:0061852 from retrograde transporter complex, Golgi to ER to retrograde cargo receptor complex, Golgi to ER.
• Refined the definition from a generic transporter-complex description to a cargo receptor complex description.
• Changed the asserted parent from GO:1990351 transporter complex to GO:0062137 cargo receptor complex.
• Preserved the older transporter wording as BROAD synonyms:
  • retrograde transporter complex, Golgi to endoplasmic reticulum
  • retrograde transporter complex, Golgi to ER
• Left the existing capable_of_part_of relationship to retrograde Golgi-to-ER transport unchanged.

Rationale

• The issue requested that this term be treated as a cargo receptor complex rather than a generic transporter complex.
• The new primary label now matches the requested biological scope more precisely.
• The older transporter wording is broader than the revised concept, so keeping it as BROAD synonymy is safer than leaving it as exact synonymy.
• No new logical definition was added; a minimal parent/label/definition update was sufficient and lower risk.

Validation and workflow

• Read the issue context from __issue_context__.json.
• Consulted existing ontology precedent for GO:0062137 cargo receptor complex and the current GO:0061852 stanza.
• Followed the GO edit workflow using obo-checkout.pl and obo-checkin.pl with a local terms/ checkout file.
• Pre-validated by running robot convert -i go-edit.obo -f obo.
• Ran full ontology validation with cd src/ontology && make travis_build and it passed.

Checklist

• PLAN: issue analyzed and requested change was clear
• PRE-VALIDATION: syntax conversion succeeded before edits
• TERM-SEARCH: inspected GO:0061852 and GO:0062137
• DESIGN-PATTERNS: confirmed no new logical pattern was needed; minimal structural edit only
• EDITS: used checkout/checkin workflow rather than direct editing of go-edit.obo
• RELATIONSHIPS: retained the existing transport relationship; updated only the parent needed by scope
• METADATA: no new term metadata added because this was an edit to an existing term
• AUTOMATED-VALIDATION: make travis_build passed
• REFERENCE-VALIDATION: reused existing PMID-backed definition provenance; no new references introduced
• ISSUE-ALIGNMENT: changes match the request for parent, label, and definition refinement

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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

Updated GO:0061852 as requested.

• renamed the term to retrograde cargo receptor complex, Golgi to ER
• refined the definition to describe it as a cargo receptor complex
• reparented it under GO:0062137 cargo receptor complex
• kept the broader transporter wording as BROAD synonyms rather than primary labels

Validation passed locally with make travis_build.

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-31935

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25980862588