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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
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gbanyan
2026-02-11 19:08:45 +08:00
parent d8009f1236
commit 053f0d926b
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.planning/STATE.md
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@@ -30,6 +30,7 @@ Progress: [█████░░░░░] 40.0% (8/20 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 | 2/6 | 16 min | 8.0 min/plan |
| Phase 03 P05 | 10 | 2 tasks | 8 files |
## Accumulated Context
@@ -70,6 +71,8 @@ Recent decisions affecting current work:
- [03-04]: Proteomics absence stored as False (informative negative) vs HPA absence as NULL (unknown/not tested)
- [03-04]: Curated proteomics reference gene sets (CiliaCarta, Centrosome-DB) embedded as Python constants for simpler deployment
- [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)
### Pending Todos