gbanyan
e29d39d1dc
- 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
2.3 KiB
Project State
Project Reference
See: .planning/PROJECT.md (updated 2026-02-11)
Core value: Produce a high-confidence, multi-evidence-backed ranked list of under-studied cilia/Usher candidate genes that is fully traceable — every gene's inclusion is explainable by specific evidence, and every gap is documented. Current focus: Phase 1 - Data Infrastructure
Current Position
Phase: 1 of 6 (Data Infrastructure) Plan: 3 of 4 in current phase Status: Executing 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)
Performance Metrics
Velocity:
- Total plans completed: 2
- Average duration: 3 min
- Total execution time: 0.12 hours
By Phase:
| Phase | Plans | Total | Avg/Plan |
|---|---|---|---|
| 01 - Data Infrastructure | 2/4 | 7 min | 3.5 min/plan |
Accumulated Context
Decisions
Decisions are logged in PROJECT.md Key Decisions table. Recent decisions affecting current work:
- Python over R/Bioconductor for rich data integration ecosystem
- Weighted rule-based scoring over ML for explainability
- Public data only for reproducibility
- 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)
- [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
None yet.
Blockers/Concerns
None yet.
Session Continuity
Last session: 2026-02-11 - Plan execution Stopped at: Completed 01-02-PLAN.md Resume file: .planning/phases/01-data-infrastructure/01-02-SUMMARY.md