83 lines
4.0 KiB
Markdown
83 lines
4.0 KiB
Markdown
# Project State
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## Project Reference
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See: .planning/PROJECT.md (updated 2026-02-11)
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**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.
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**Current focus:** Phase 2 complete — ready for Phase 3
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## Current Position
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Phase: 3 of 6 (Core Evidence Layers)
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Plan: 1 of 6 in current phase
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Status: In progress — 03-01 complete (annotation completeness)
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Last activity: 2026-02-11 — Completed 03-01-PLAN.md (annotation completeness evidence layer)
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Progress: [█████░░░░░] 35.0% (7/20 plans complete across all phases)
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## Performance Metrics
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**Velocity:**
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- Total plans completed: 7
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- Average duration: 4.1 min
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- Total execution time: 0.48 hours
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**By Phase:**
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| Phase | Plans | Total | Avg/Plan |
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|-------|-------|-------|----------|
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| 01 - Data Infrastructure | 4/4 | 14 min | 3.5 min/plan |
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| 02 - Prototype Evidence Layer | 2/2 | 8 min | 4.0 min/plan |
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| 03 - Core Evidence Layers | 1/6 | 7 min | 7.2 min/plan |
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## Accumulated Context
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### Decisions
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Decisions are logged in PROJECT.md Key Decisions table.
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Recent decisions affecting current work:
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- Python over R/Bioconductor for rich data integration ecosystem
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- Weighted rule-based scoring over ML for explainability
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- Public data only for reproducibility
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- Modular CLI scripts for flexibility during development
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- Virtual environment required for dependency isolation (01-01: PEP 668 externally-managed Python)
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- Auto-creation of directories on config load (01-01: data_dir, cache_dir field validators)
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- [01-02]: Warn on gene count outside 19k-22k range but don't fail (allows for Ensembl version variations)
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- [01-02]: HGNC success rate is primary validation gate (UniProt mapping tracked but not used for pass/fail)
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- [01-02]: Take first UniProt accession when multiple exist (simplifies data model)
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- [01-02]: Mock mygene in tests (avoids rate limits, ensures reproducibility)
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- [01-03]: DuckDB over SQLite for DataFrame storage (native polars/pandas integration, better analytics)
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- [01-03]: Provenance sidecar files alongside outputs (co-located metadata, bioinformatics standard pattern)
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- [01-04]: Click for CLI framework (standard Python CLI library with excellent UX)
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- [01-04]: Setup command uses checkpoint-restart pattern (gene universe fetch can take minutes)
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- [01-04]: Mock mygene in integration tests (avoids external API dependency, reproducible)
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- [02-01]: httpx over requests for streaming downloads (async-native, cleaner API)
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- [02-01]: structlog for structured logging (JSON-formatted, context-aware)
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- [02-01]: LOEUF normalization with inversion (lower LOEUF = more constrained = higher 0-1 score)
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- [02-01]: Quality flags instead of filtering (preserve all genes with measured/incomplete_coverage/no_data categorization)
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- [02-01]: NULL preservation pattern (unknown constraint != zero constraint, must not be conflated)
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- [02-01]: Lazy polars evaluation (LazyFrame until final collect() for query optimization)
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- [02-02]: load_to_duckdb uses CREATE OR REPLACE for idempotency (safe to re-run)
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- [02-02]: CLI evidence command group for extensibility (future evidence sources follow same pattern)
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- [02-02]: Checkpoint at table level (has_checkpoint checks DuckDB table existence)
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- [02-02]: Integration tests with synthetic fixtures (no external downloads, fast, reproducible)
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- [03-01]: Annotation tier thresholds: Well >= (20 GO AND 4 UniProt), Partial >= (5 GO OR 3 UniProt)
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- [03-01]: Composite annotation score weighting: GO 50%, UniProt 30%, Pathway 20%
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- [03-01]: NULL GO counts treated as zero for tier classification but preserved as NULL in data (conservative assumption)
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### Pending Todos
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None yet.
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### Blockers/Concerns
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None yet.
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## Session Continuity
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Last session: 2026-02-11 - Plan execution
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Stopped at: Completed 03-01-PLAN.md (annotation completeness evidence layer)
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Resume file: .planning/phases/03-core-evidence-layers/03-01-SUMMARY.md
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