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feat: add 6 biomedical domain adapters to verification engine#44

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VibeCodingScientist merged 1 commit intomainfrom
feat/biomedical-domain-adapters
Feb 17, 2026
Merged

feat: add 6 biomedical domain adapters to verification engine#44
VibeCodingScientist merged 1 commit intomainfrom
feat/biomedical-domain-adapters

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Summary

  • Adds 5 new verification adapters: genomics, epidemiology, systems_biology, immunoinformatics, metabolomics (15 new claim types total)
  • Extends existing computational_biology adapter with 2 new API-based claim types: rna_structure, structure_comparison
  • All new adapters are API-based (no Docker) using public APIs: ClinVar, Ensembl VEP, GWAS Catalog, WHO GHO, Reactome, STRING DB, KEGG, IEDB, HMDB, PubChem, MassBank, RCSB PDB, Rfam
  • Optional dependencies (lifelines, networkx) degrade gracefully to score=0.5
  • Supporting changes: dispatcher registration, queue weights, payload models, forum domain constraint (migration 012), skill.md agent docs
  • Verification coverage expands from 7 → 13 domains

Backward compatibility

  • All 7 existing adapters unchanged in behavior and registration order
  • DOCKER_DOMAINS set unchanged — new adapters are all API-based
  • Existing DOMAIN_WEIGHTS values untouched
  • CompBioPayload regex extended (additive only — original 3 types still match)
  • ck_forum_domain is strict superset of old constraint
  • Migration 012 downgrade path tested

Test plan

  • All 12 files pass Python syntax check (verified locally)
  • alembic upgrade head succeeds on server
  • Existing verification flow (trigger → poll → result) still works for original 7 domains
  • New adapters return VerificationResult (not crash) with minimal payloads
  • GET /api/labs/{slug}/discovery/skill.md documents new domains
  • Forum posts with new domains can be inserted after migration

🤖 Generated with Claude Code

Expands verification coverage from 7 to 13 domains with 5 new adapters
(genomics, epidemiology, systems_biology, immunoinformatics, metabolomics)
and 2 new claim types on the existing compbio adapter (rna_structure,
structure_comparison). All new adapters are API-based (no Docker).

New adapters use public APIs: ClinVar, Ensembl VEP, GWAS Catalog,
WHO GHO, Reactome, STRING DB, KEGG, IEDB, HMDB, PubChem, MassBank,
RCSB PDB, Rfam. Optional deps (lifelines, networkx) degrade gracefully.

Supporting changes:
- dispatcher: register 5 new adapters
- verification_queue: add 5 DOMAIN_WEIGHTS entries
- task_payloads: add 5 payload models + extend CompBioPayload
- models.py: expand ck_forum_domain CHECK (6 → 13 domains)
- migration 012: ALTER CHECK constraint
- discovery.py: document new domains + payload fields in skill.md

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@VibeCodingScientist VibeCodingScientist merged commit 51b5803 into main Feb 17, 2026
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