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docs(01-02): complete gene ID mapping and validation plan

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- Gene universe definition with mygene protein-coding gene retrieval
- Batch Ensembl->HGNC+UniProt mapping with edge case handling
- Validation gates with configurable success rate thresholds
- 15 comprehensive tests with mocked API responses
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gbanyan
2026-02-11 16:35:57 +08:00
parent 92322b1d7c
commit e29d39d1dc
2 changed files with 153 additions and 8 deletions
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.planning/STATE.md
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@@ -12,7 +12,7 @@ See: .planning/PROJECT.md (updated 2026-02-11)
Phase: 1 of 6 (Data Infrastructure)
Plan: 3 of 4 in current phase
Status: Executing
Last activity: 2026-02-11 — Completed 01-03-PLAN.md (DuckDB persistence and provenance tracking)
Last activity: 2026-02-11 — Completed 01-02-PLAN.md (Gene ID mapping and validation)
Progress: [███░░░░░░░] 25.0% (1/6 phases planned, 2/4 plans in phase 1 complete)
@@ -20,14 +20,14 @@ Progress: [███░░░░░░░] 25.0% (1/6 phases planned, 2/4 plans
**Velocity:**
- Total plans completed: 2
- Average duration: 2.5 min
- Total execution time: 0.08 hours
- Average duration: 3 min
- Total execution time: 0.12 hours
**By Phase:**
| Phase | Plans | Total | Avg/Plan |
|-------|-------|-------|----------|
| 01 - Data Infrastructure | 2/4 | 5 min | 2.5 min/plan |
| 01 - Data Infrastructure | 2/4 | 7 min | 3.5 min/plan |
## Accumulated Context
@@ -42,8 +42,12 @@ Recent decisions affecting current work:
- Modular CLI scripts for flexibility during development
- Virtual environment required for dependency isolation (01-01: PEP 668 externally-managed Python)
- Auto-creation of directories on config load (01-01: data_dir, cache_dir field validators)
- [Phase 01-data-infrastructure]: DuckDB over SQLite for DataFrame storage (native polars/pandas integration, better analytics)
- [Phase 01-data-infrastructure]: Provenance sidecar files alongside outputs (co-located metadata, bioinformatics standard pattern)
- [01-02]: Warn on gene count outside 19k-22k range but don't fail (allows for Ensembl version variations)
- [01-02]: HGNC success rate is primary validation gate (UniProt mapping tracked but not used for pass/fail)
- [01-02]: Take first UniProt accession when multiple exist (simplifies data model)
- [01-02]: Mock mygene in tests (avoids rate limits, ensures reproducibility)
- [01-03]: DuckDB over SQLite for DataFrame storage (native polars/pandas integration, better analytics)
- [01-03]: Provenance sidecar files alongside outputs (co-located metadata, bioinformatics standard pattern)
### Pending Todos
@@ -56,5 +60,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 01-03-PLAN.md
Resume file: .planning/phases/01-data-infrastructure/01-03-SUMMARY.md
Stopped at: Completed 01-02-PLAN.md
Resume file: .planning/phases/01-data-infrastructure/01-02-SUMMARY.md