gbanyan
8aa66987f8
feat(03-06): implement literature evidence models, PubMed fetch, and scoring
- Create LiteratureRecord pydantic model with context-specific counts
- Implement PubMed query via Biopython Entrez with rate limiting (3/sec default, 10/sec with API key)
- Define SEARCH_CONTEXTS for cilia, sensory, cytoskeleton, cell_polarity queries
- Implement evidence tier classification: direct_experimental > functional_mention > hts_hit > incidental > none
- Implement quality-weighted scoring with bias mitigation via log2(total_pubmed_count) normalization
- Add biopython>=1.84 dependency to pyproject.toml
- Support checkpoint-restart for long-running PubMed queries (estimated 3-11 hours for 20K genes)