usher-exploring

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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)

2026-02-11 19:00:20 +08:00

.planning

docs(03): create phase plan

2026-02-11 18:46:28 +08:00

config

feat(01-01): create Python package scaffold with config system

2026-02-11 16:24:35 +08:00

src/usher_pipeline

feat(03-06): implement literature evidence models, PubMed fetch, and scoring

2026-02-11 19:00:20 +08:00

tests

test(02-02): add comprehensive gnomAD integration tests