gbanyan
e72c516669
- Created SUMMARY.md with full implementation details - Updated STATE.md: progress 60%, 12/20 plans complete, Phase 3 complete - Documented 4 key decisions (tier priority, bias mitigation, context weights, rate limiting) - All verification criteria met: 17/17 tests pass, CLI functional, bias mitigation validated - Self-check PASSED: all files and commits verified Key accomplishments: - PubMed evidence layer queries per gene across cilia/sensory/cytoskeleton/polarity contexts - Quality tier classification: direct_experimental > hts_hit > functional_mention > incidental - Bias mitigation via log2(total_pubmed_count) prevents well-studied gene dominance - Novel genes with 10 total/5 cilia publications score higher than TP53-like genes with 100K total/5 cilia - Biopython Entrez integration with rate limiting (3/sec default, 10/sec with API key)