2d29f43848
docs(06-02): complete sensitivity analysis plan
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- Create SUMMARY.md with implementation details and verification results
- Update STATE.md: progress 100% (20/20 plans), plan 06-02 complete
- Record decisions: perturbation deltas, stability threshold, renormalization
- All tasks completed with 2 commits in 3 minutes
2026-02-12 04:44:13 +08:00
a2d6e97acf
docs(06-01): complete negative controls and recall@k validation plan
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Summary:
- Created negative_controls.py with 13 housekeeping genes
- Added recall@k metrics (absolute and percentage thresholds)
- Added per-source breakdown for OMIM vs SYSCILIA
- Updated STATE.md with Phase 6 progress and decisions
Plan Summary: .planning/phases/06-validation/06-01-SUMMARY.md
2026-02-12 04:43:59 +08:00
964c1cebe8
docs(phase-05): complete phase execution
2026-02-12 04:15:50 +08:00
00e2836eb9
docs(05-03): complete CLI report command plan
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- Create 05-03-SUMMARY.md with comprehensive execution report
- Update STATE.md: Phase 5 complete (3/3 plans), progress 90% (18/20)
- Record decisions: CLI pattern, configurable thresholds, skip flags, graceful degradation
- Document deviations: 2 auto-fixed bugs (tier threshold format, parameter name)
- Update metrics: Phase 05 total 12 min (4.0 min/plan avg)
- All tests pass (9/9 CliRunner integration tests)
2026-02-12 04:09:26 +08:00
5f14dc2e64
docs(05-02): complete visualization and reproducibility report plan
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- Plan 05-02 executed successfully
- 2 tasks completed with 2 commits
- 13 tests passing (6 visualization + 7 reproducibility)
- 4 files created, 2 files modified
- Duration: 5 minutes
- Updated STATE.md with progress (17/20 plans complete, 85%)
2026-02-12 04:03:08 +08:00
434c79c0a8
docs(05-01): complete output generation core plan
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- Add 05-01-SUMMARY.md with performance metrics and decisions
- Update STATE.md to Phase 5, Plan 1 of 3 (80% overall progress)
- Record key decisions: configurable tiers, dual-format output, YAML provenance
- Document deviation: pl.count() -> pl.len() deprecation fix
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com >
2026-02-12 04:01:24 +08:00
de678858cd
docs(phase-04): complete phase execution
2026-02-11 21:01:50 +08:00
386fbf51b2
docs(04-03): complete CLI score command and tests plan
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- SUMMARY.md: CLI orchestration with checkpoint-restart + 10 comprehensive tests
- STATE.md: Updated position (Phase 4 complete), progress (75%), velocity, decisions
- Duration: 3 minutes, 2 tasks, 4 files (3 created, 1 modified)
2026-02-11 20:56:31 +08:00
c501951b0f
docs(04-02): complete QC and validation plan
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- Add SUMMARY for quality control and positive control validation
- Update STATE.md: Plan 2 of 3 in Phase 04 complete
- Progress: 70% (14/20 plans complete)
- Decisions: scipy MAD outlier detection, PERCENT_RANK validation
2026-02-11 20:50:00 +08:00
71c4e8f736
docs(04-01): complete known gene compilation and weighted scoring plan
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- Known genes: 38 (10 OMIM Usher + 28 SYSCILIA SCGS v2 core)
- ScoringWeights.validate_sum() enforcing weight sum = 1.0
- NULL-preserving weighted average (weighted_sum / available_weight)
- Quality flags based on evidence_count thresholds
- Per-layer contributions for explainability
- 2 tasks, 4 files, 4 min duration
2026-02-11 20:44:09 +08:00
190bedaa80
docs(phase-03): complete phase execution
2026-02-11 19:18:12 +08:00
e72c516669
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)
2026-02-11 19:13:26 +08:00
0e89bf0dd6
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
2026-02-11 19:12:18 +08:00
cfe4b830e6
docs(03-03): complete protein features plan with SUMMARY and STATE updates
2026-02-11 19:10:03 +08:00
053f0d926b
docs(03-05): complete animal model phenotype evidence layer plan
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- SUMMARY.md: Ortholog-mapped animal evidence from MGI/ZFIN/IMPC
- Confidence-weighted scoring (mouse +0.4, zebrafish +0.3, IMPC +0.3)
- 14/14 tests passing: ortholog confidence, keyword filtering, NULL preservation
- Deviations: Schema mismatches, NULL handling, polars deprecations auto-fixed
- Duration: 10 minutes, 2 tasks, 8 files, 2 commits
2026-02-11 19:08:45 +08:00
d8009f1236
docs(03-04): complete subcellular localization evidence layer
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- Created SUMMARY.md with full implementation details
- Updated STATE.md: progress 40%, 8/20 plans complete
- Documented 4 key decisions (evidence terminology, NULL semantics, embedded proteomics, evidence weighting)
- All verification criteria met: 17/17 tests pass, CLI functional, DuckDB integration complete
2026-02-11 19:08:01 +08:00
99bc975a2c
docs(03-01): complete annotation completeness plan
2026-02-11 19:05:56 +08:00
ffb4963d2b
docs(phase-02): complete phase execution
2026-02-11 18:28:13 +08:00
a0388cf4e1
docs(02-02): complete gnomAD evidence layer integration plan
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- DuckDB persistence: gnomad_constraint table with CREATE OR REPLACE (idempotent)
- CLI evidence command: usher-pipeline evidence gnomad with checkpoint-restart
- Provenance tracking: records processing steps, saves sidecar JSON
- Query helpers: query_constrained_genes validates GCON-03 interpretation
- 12 integration tests: end-to-end pipeline, checkpoint, provenance, CLI
- Phase 2 complete: Evidence layer pattern established for future sources
- Duration: 4 min, 2 tasks, 5 files, 70 tests passing
Phase 2 (Prototype Evidence Layer) complete.
2026-02-11 18:23:32 +08:00
c6198122ac
docs(02-01): complete gnomAD constraint data pipeline plan
2026-02-11 18:16:35 +08:00
34437fdf0a
docs(phase-01): complete phase execution
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Phase 1 (Data Infrastructure) verified: 5/5 must-haves, 12/12 artifacts,
9/9 key links, 7/7 requirements satisfied. All 4 plans executed across
3 waves with 49 tests passing.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com >
2026-02-11 16:50:30 +08:00
102dcdbe84
docs(01-04): complete CLI integration and end-to-end testing plan
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- CLI entry point with setup and info commands
- Full infrastructure integration verified
- 6 integration tests with mocked APIs
- Phase 01 Data Infrastructure complete
2026-02-11 16:45:12 +08:00
e29d39d1dc
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
2026-02-11 16:35:57 +08:00
92322b1d7c
docs(01-03): complete DuckDB persistence and provenance tracking plan
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Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com >
2026-02-11 16:34:00 +08:00
9ee3ec2e84
docs(01-01): complete project scaffold and config system plan
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- Created comprehensive SUMMARY.md with all execution details
- Updated STATE.md: 1/4 plans in phase 1 complete, 16.7% overall progress
- Documented deviation (venv creation) and decisions
- Verified all files and commits exist (self-check passed)
2026-02-11 16:28:03 +08:00
f80f384a61
docs: create roadmap (6 phases)
2026-02-11 15:47:36 +08:00
