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docs(03-02): complete expression evidence layer plan

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- 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
This commit is contained in:
gbanyan
2026-02-11 19:12:18 +08:00
parent cfe4b830e6
commit 0e89bf0dd6
2 changed files with 215 additions and 10 deletions
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.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: 3 of 6 in current phase (03-03 complete)
Status: In progress — 03-03 complete (protein features)
Last activity: 2026-02-11 — Completed 03-03-PLAN.md (Protein Features evidence layer)
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)
Progress: [█████░░░░░] 45.0% (9/20 plans complete across all phases)
Progress: [██████░░░░] 55.0% (11/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 9
- Average duration: 5.2 min
- Total execution time: 0.78 hours
- Total plans completed: 11
- Average duration: 5.4 min
- Total execution time: 1.0 hours
**By Phase:**
@@ -29,7 +29,8 @@ Progress: [█████░░░░░] 45.0% (9/20 plans complete across all
|-------|-------|-------|----------|
| 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 | 3/6 | 27 min | 9.0 min/plan |
| 03 - Core Evidence Layers | 5/6 | 39 min | 7.8 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 |
@@ -80,6 +81,12 @@ Recent decisions affecting current work:
- [03-04]: Computational evidence (HPA Uncertain/Approved) downweighted to 0.6x vs experimental (Enhanced/Supported, proteomics) at 1.0x
- [Phase 03-05]: Ortholog confidence based on HCOP support count (HIGH: 8+, MEDIUM: 4-7, LOW: 1-3)
- [Phase 03-05]: NULL score for genes without orthologs (preserves NULL pattern)
- [03-02]: HPA bulk TSV download over per-gene API (efficient for 20K genes)
- [03-02]: GTEx retina/fallopian tube may be NULL (not in all versions)
- [03-02]: CellxGene optional dependency with --skip-cellxgene flag (large install)
- [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)
### Pending Todos
@@ -92,5 +99,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 03-03-PLAN.md (Protein Features evidence layer)
Resume file: .planning/phases/03-core-evidence-layers/03-03-SUMMARY.md
Stopped at: Completed 03-02-PLAN.md (Tissue Expression evidence layer)
Resume file: .planning/phases/03-core-evidence-layers/03-02-SUMMARY.md