[DO NOT MERGE] eval #31873 i:1: Obsoletion request: GO:0061817 endoplasmic reticulum-plasma membrane tethering (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#31873: Obsoletion request: GO:0061817 endoplasmic reticulum-plasma membrane tethering

Original PR (human solution)

#32022: Obsolete GO:0061817 endoplasmic reticulum-plasma membrane tethering

Agent Commits

• Obsolete GO:0061817 MF term

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

Agent Response - PR Comments

Obsoleted GO:0061817 endoplasmic reticulum-plasma membrane tethering because the issue correctly identified it as representing a molecular function rather than a biological process.

Changes made:

• Converted GO:0061817 to an obsolete term in src/ontology/go-edit.obo
• Updated the label to obsolete endoplasmic reticulum-plasma membrane tethering
• Preserved the original definition provenance and converted the definition to the required OBSOLETE. form
• Removed the synonym and biological process parentage from the obsolete stanza
• Added an obsoletion comment explaining the reason
• Added property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31873" xsd:anyURI
• Added is_obsolete: true
• Added replaced_by: GO:0160214 (endoplasmic reticulum-plasma membrane adaptor activity)

Rationale:

• The original BP term described membrane tethering accomplished by a tether/adaptor molecule, which is better modeled as the MF term GO:0160214.
• The issue discussion explicitly requested obsoletion and identified GO:0160214 as the annotation target to use.
• GO:0051643 endoplasmic reticulum localization remains broader, but the direct replacement used here is the more specific MF requested in the issue comments.

Validation and checks:

• Checked the imported issue context and local repo guidance
• Used the term obsoletion workflow and edited the term through obo-checkout.pl / obo-checkin.pl
• Confirmed there were no internal GO ontology references to GO:0061817 outside its own stanza
• Ran make travis_build in src/ontology; build passed
• Queried direct annotation usage with runoak -i amigo: associations GO:0061817

Annotation impact note:

• Direct annotations to GO:0061817 are still present in AmiGO, including many IBA annotations, so annotation migration remains necessary after the ontology obsoletion.
• This matches the issue history noting that annotation review/migration is part of the follow-up work.

Checklist:

• PLAN: analyzed issue context and intent
• PRE-VALIDATION: validated ontology state as part of local make travis_build
• TERM-SEARCH: reviewed GO:0061817, GO:0160214, and GO:0051643
• DESIGN-PATTERNS: not applicable beyond standard obsoletion pattern
• EDITS: used checkout/checkin workflow via terms/
• RELATIONSHIPS: removed obsolete-term logical/structural axioms
• SPECIALIZED-EDITS: used obsoletion workflow
• METADATA: added correct obsoletion metadata and issue tracker link
• AUTOMATED-VALIDATION: make travis_build passed
• REFERENCE-VALIDATION: preserved existing definition provenance only; no new references introduced
• CHANGES-COMMITTED: committed local ontology change

---

🤖 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

Obsoleted GO:0061817 as requested and mapped it to GO:0160214 endoplasmic reticulum-plasma membrane adaptor activity.

Validation passed locally.

One follow-up point: direct annotations to GO:0061817 are still present in AmiGO, with many remaining IBA annotations, so annotation migration/review should still be completed on the annotation side.

Changes committed locally and ready for 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-31873

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25978840224