gbanyan/usher-exploring
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

docs(03-04): complete subcellular localization evidence layer

Browse Source 
- 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
This commit is contained in:
gbanyan
2026-02-11 19:08:01 +08:00
parent 46059874f2
commit d8009f1236
7 changed files with 927 additions and 29 deletions
Download Patch File Download Diff File Expand all files Collapse all files

24
.planning/STATE.md
View File

@@ -10,18 +10,18 @@ See: .planning/PROJECT.md (updated 2026-02-11)
## Current Position
Phase: 3 of 6 (Core Evidence Layers)
Plan: 1 of 6 in current phase
Status: In progress — 03-01 complete (annotation completeness)
Last activity: 2026-02-11 — Completed 03-01-PLAN.md (annotation completeness evidence layer)
Plan: 4 of 6 in current phase
Status: In progress — 03-04 complete (subcellular localization)
Last activity: 2026-02-11 — Completed 03-04-PLAN.md (Subcellular Localization evidence layer)
Progress: [█████░░░░░] 35.0% (7/20 plans complete across all phases)
Progress: [█████░░░░░] 40.0% (8/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 7
- Average duration: 4.1 min
- Total execution time: 0.48 hours
- Total plans completed: 8
- Average duration: 4.7 min
- Total execution time: 0.63 hours
**By Phase:**
@@ -29,7 +29,7 @@ Progress: [█████░░░░░] 35.0% (7/20 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 | 1/6 | 7 min | 7.2 min/plan |
| 03 - Core Evidence Layers | 2/6 | 16 min | 8.0 min/plan |
## Accumulated Context
@@ -66,6 +66,10 @@ Recent decisions affecting current work:
- [03-01]: Annotation tier thresholds: Well >= (20 GO AND 4 UniProt), Partial >= (5 GO OR 3 UniProt)
- [03-01]: Composite annotation score weighting: GO 50%, UniProt 30%, Pathway 20%
- [03-01]: NULL GO counts treated as zero for tier classification but preserved as NULL in data (conservative assumption)
- [03-04]: Evidence type terminology standardized to computational (not predicted) for consistency with bioinformatics convention
- [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
### Pending Todos
@@ -78,5 +82,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 03-01-PLAN.md (annotation completeness evidence layer)
Resume file: .planning/phases/03-core-evidence-layers/03-01-SUMMARY.md
Stopped at: Completed 03-04-PLAN.md (Subcellular Localization evidence layer)
Resume file: .planning/phases/03-core-evidence-layers/03-04-SUMMARY.md