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190bedaa80
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docs(phase-03): complete phase execution
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2026-02-11 19:18:12 +08:00 |
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e72c516669
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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)
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2026-02-11 19:13:26 +08:00 |
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0e89bf0dd6
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docs(03-02): complete expression evidence layer plan
- Create 03-02-SUMMARY.md with performance metrics, decisions, and deviations
- Update STATE.md: 5 of 6 plans complete in Phase 03 (03-06 remaining)
- Update progress: 55% complete (11/20 plans across all phases)
- Add key decisions: Tau calculation, expression scoring, CellxGene optional
- Record duration: 12 min for 2 tasks (9 files modified)
- Self-check passed: all files and commits verified
Expression layer provides:
- HPA/GTEx tissue expression with Tau specificity index
- Usher-tissue enrichment scoring (retina, inner ear, cilia)
- Optional CellxGene single-cell integration
- CLI command with checkpoint-restart
- 11 passing unit and integration tests
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2026-02-11 19:12:18 +08:00 |
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cfe4b830e6
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docs(03-03): complete protein features plan with SUMMARY and STATE updates
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2026-02-11 19:10:03 +08:00 |
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053f0d926b
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docs(03-05): complete animal model phenotype evidence layer plan
- SUMMARY.md: Ortholog-mapped animal evidence from MGI/ZFIN/IMPC
- Confidence-weighted scoring (mouse +0.4, zebrafish +0.3, IMPC +0.3)
- 14/14 tests passing: ortholog confidence, keyword filtering, NULL preservation
- Deviations: Schema mismatches, NULL handling, polars deprecations auto-fixed
- Duration: 10 minutes, 2 tasks, 8 files, 2 commits
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2026-02-11 19:08:45 +08:00 |
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d8009f1236
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docs(03-04): complete subcellular localization evidence layer
- Created SUMMARY.md with full implementation details
- Updated STATE.md: progress 40%, 8/20 plans complete
- Documented 4 key decisions (evidence terminology, NULL semantics, embedded proteomics, evidence weighting)
- All verification criteria met: 17/17 tests pass, CLI functional, DuckDB integration complete
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2026-02-11 19:08:01 +08:00 |
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99bc975a2c
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docs(03-01): complete annotation completeness plan
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2026-02-11 19:05:56 +08:00 |
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0d252da348
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docs(03): create phase plan
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2026-02-11 18:46:28 +08:00 |
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3354cfe006
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docs(phase-03): research core evidence layers domain
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2026-02-11 18:37:14 +08:00 |
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