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

docs(03-01): complete annotation completeness plan

Browse Source
This commit is contained in:
gbanyan
2026-02-11 19:05:56 +08:00
parent 942aaf2ec3
commit 99bc975a2c
2 changed files with 305 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files

24
.planning/STATE.md
View File

@@ -9,19 +9,19 @@ See: .planning/PROJECT.md (updated 2026-02-11)
## Current Position
Phase: 2 of 6 (Prototype Evidence Layer)
Plan: 2 of 2 in current phase (phase complete)
Status: Phase 2 complete — verified (9/9 must-haves, 3/3 requirements)
Last activity: 2026-02-11 — Phase 2 verified and complete
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)
Progress: [█████░░░░░] 33.3% (2/6 phases complete)
Progress: [█████░░░░░] 35.0% (7/20 plans complete across all phases)
## Performance Metrics
**Velocity:**
- Total plans completed: 6
- Average duration: 3.7 min
- Total execution time: 0.37 hours
- Total plans completed: 7
- Average duration: 4.1 min
- Total execution time: 0.48 hours
**By Phase:**
@@ -29,6 +29,7 @@ Progress: [█████░░░░░] 33.3% (2/6 phases complete)
|-------|-------|-------|----------|
| 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 |
## Accumulated Context
@@ -62,6 +63,9 @@ Recent decisions affecting current work:
- [02-02]: CLI evidence command group for extensibility (future evidence sources follow same pattern)
- [02-02]: Checkpoint at table level (has_checkpoint checks DuckDB table existence)
- [02-02]: Integration tests with synthetic fixtures (no external downloads, fast, reproducible)
- [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)
### Pending Todos
@@ -74,5 +78,5 @@ None yet.
## Session Continuity
Last session: 2026-02-11 - Plan execution
Stopped at: Completed 02-02-PLAN.md (gnomAD evidence layer integration) - Phase 2 complete
Resume file: .planning/phases/02-prototype-evidence-layer/02-02-SUMMARY.md
Stopped at: Completed 03-01-PLAN.md (annotation completeness evidence layer)
Resume file: .planning/phases/03-core-evidence-layers/03-01-SUMMARY.md