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docs(03-06): complete literature evidence layer

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- 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)
This commit is contained in:
gbanyan
2026-02-11 19:13:26 +08:00
parent 0e89bf0dd6
commit e72c516669
2 changed files with 241 additions and 10 deletions
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25
.planning/STATE.md
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@@ -10,18 +10,18 @@ See: .planning/PROJECT.md (updated 2026-02-11)
## Current Position
Phase: 3 of 6 (Core Evidence Layers)
Plan: 5 of 6 in current phase (03-02 complete, 03-06 remaining)
Status: In progress — 03-02 complete (expression evidence)
Last activity: 2026-02-11 — Completed 03-02-PLAN.md (Tissue Expression evidence layer)
Plan: 6 of 6 in current phase (phase complete)
Status: Phase 3 complete — ready for Phase 4
Last activity: 2026-02-11 — Completed 03-06-PLAN.md (Literature Evidence layer)
Progress: [██████░░░░] 55.0% (11/20 plans complete across all phases)
Progress: [██████░░░░] 60.0% (12/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 11
- Average duration: 5.4 min
- Total execution time: 1.0 hours
- Total plans completed: 12
- Average duration: 5.6 min
- Total execution time: 1.1 hours
**By Phase:**
@@ -29,11 +29,12 @@ Progress: [██████░░░░] 55.0% (11/20 plans complete across al
|-------|-------|-------|----------|
| 01 - Data Infrastructure | 4/4 | 14 min | 3.5 min/plan |
| 02 - Prototype Evidence Layer | 2/2 | 8 min | 4.0 min/plan |
| 03 - Core Evidence Layers | 5/6 | 39 min | 7.8 min/plan |
| 03 - Core Evidence Layers | 6/6 | 52 min | 8.7 min/plan |
| Phase 03 P02 | 12 min | 2 tasks | 9 files |
| Phase 03 P03 | 11 min | 2 tasks | 7 files |
| Phase 03 P04 | 8 min | 2 tasks | 8 files |
| Phase 03 P05 | 10 min | 2 tasks | 8 files |
| Phase 03 P06 | 13 min | 2 tasks | 10 files |
## Accumulated Context
@@ -87,6 +88,10 @@ Recent decisions affecting current work:
- [03-02]: Tau specificity requires complete tissue data (any NULL -> NULL Tau)
- [03-02]: Expression score composite: 40% enrichment + 30% Tau + 30% target rank
- [03-02]: Inner ear data primarily from CellxGene scRNA-seq (not HPA/GTEx bulk)
- [03-06]: HTS hits prioritized over functional mentions in evidence tier hierarchy (direct > HTS > functional > incidental)
- [03-06]: Quality-weighted scoring uses log2 normalization to mitigate well-studied gene bias (prevents TP53-like dominance)
- [03-06]: Context weights cilia/sensory=2.0, cytoskeleton/polarity=1.0 for primary target prioritization
- [03-06]: Rate limiting via decorator pattern (3 req/sec default, 10 req/sec with NCBI API key)
### Pending Todos
@@ -99,5 +104,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 03-02-PLAN.md (Tissue Expression evidence layer)
Resume file: .planning/phases/03-core-evidence-layers/03-02-SUMMARY.md
Stopped at: Completed 03-06-PLAN.md (Literature Evidence layer) - Phase 3 complete
Resume file: .planning/phases/03-core-evidence-layers/03-06-SUMMARY.md