docs(03-06): complete literature evidence layer
- 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)
gbanyan
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