[DO NOT MERGE] eval #31902 i:1: NTR: [venom-mediated inflammatory response+... leukocyte infiltration+... release of inflammatory mediator] (opencode/openai/gpt-5.4, .)

[cmungall]

⚠️ EVALUATION ONLY - DO NOT MERGE ⚠️

Original Issue

#31902: NTR: [venom-mediated inflammatory response+... leukocyte infiltration+... release of inflammatory mediator]

Original PR (human solution)

#32041: Add GO:7770071 venom-mediated activation of inflammatory response (#31902)

Agent Commits

• Add venom-mediated inflammatory response terms

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

Agent Response - PR Comments

Implemented issue #31902 by adding a small venom-related inflammation term set and one relationship update batch in src/ontology/go-edit.obo.

Changes made:

• Added GO:7770071 venom-mediated inflammatory response
  • is_a: GO:0035738 ! venom-mediated perturbation of biological process
  • synonym: venom-mediated inflammation BROAD
  • definition provenance: PMID:32024243, PMID:19000915
• Added GO:7770072 venom-mediated leukocyte infiltration
  • is_a: GO:7770071 ! venom-mediated inflammatory response
  • relationship: part_of GO:0006954 ! inflammatory response
  • exact synonym for the leucocyte spelling variant
  • definition provenance: PMID:32024243, PMID:19000915, PMID:26072684
• Added GO:7770073 venom-mediated release of inflammatory mediator
  • is_a: GO:7770071 ! venom-mediated inflammatory response
  • related synonym: venom-mediated production of proinflammatory mediator
  • definition provenance: PMID:32024243, PMID:26072684
• Updated GO:0044480 venom-mediated mast cell degranulation
  • added relationship: part_of GO:7770071 ! venom-mediated inflammatory response
• Updated GO:0044398 venom-mediated edema
  • added relationship: part_of GO:7770071 ! venom-mediated inflammatory response

Rationale:

• The issue requested a new parent inflammatory-response term with children covering leukocyte infiltration and inflammatory mediator release, plus a link from venom-mediated mast cell degranulation.
• Literature support from the cited papers directly covers venom metalloproteinase-induced edema, leukocyte infiltrates/accumulation, and inflammatory mediator release.
• I modeled these as conservative asserted subclasses and part_of links rather than new logical definitions, following local precedent for venom-mediated outcome terms.
• venom-mediated edema remained under venom-mediated perturbation of biological process and was additionally linked by part_of to the new inflammatory-response parent so the requested child relationship is represented without changing its established asserted parentage.

Validation and checks completed:

• PLAN: issue context reviewed and request was clear
• PRE-VALIDATION: ontology syntax conversion succeeded before edits
• RESEARCH: created RESEARCH.md with validated PMID-backed support statements
• TERM-SEARCH: reviewed existing venom-mediated and inflammation-related GO terms
• DESIGN-PATTERNS: reviewed local ontology precedent and documented in DESIGN_PATTERNS.md
• EDITS: used obo-checkout.pl / obo-checkin.pl with local terms/ files
• RELATIONSHIPS: added only minimal asserted is_a and part_of relations appropriate to precedent
• METADATA: added created_by, creation_date, and term_tracker_item on new terms only
• REFERENCE-VALIDATION: validated quoted support text with linkml-reference-validator
• AUTOMATED-VALIDATION: cd src/ontology && make travis_build passed

Commit created locally:

• 6e04188 Add venom-mediated inflammatory response terms

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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

Added the requested venom inflammation term set and committed the ontology changes locally for PR #.

Summary:

• added venom-mediated inflammatory response
• added venom-mediated leukocyte infiltration
• added venom-mediated release of inflammatory mediator
• linked venom-mediated mast cell degranulation as part of the new inflammatory-response term
• linked venom-mediated edema as part of the new inflammatory-response term

The cited PMIDs support edema, leukocyte infiltrates, and inflammatory mediator release caused by snake venom metalloproteinases, and the ontology build validated after the edits.

---

🤖 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-31902

See workflow artifacts for full agent trace.

[cmungall]

📋 Traces: traces/25979826219