Disease registry¶
The registry is three surfaces, not one number:
| Surface | What it is |
|---|---|
| Discoverable modules | Disease.list_all() — runnable on-disk packages |
| On-disk directories | Same tree including blocked GO-like slugs |
| Harvest catalog | disease_registry.json — Open Targets harvest/scaffold catalog |
Listing is not validation. Registry breadth is not curation depth. Use nosograph disease corpus-status, coverage, and public-status.yaml.
Why CI-validated modules used to be missing from harvest JSON¶
Harvest merge and batch_scaffold skip directories that already exist. The eight CI-validated packages (sle, ra, ms, ss, ssc, t1d, ibd, ad) and several reference/playbook short slugs were created as first-class modules before the OT harvest, so they never entered the JSON catalog. Identifier Mondo/EFO indexes are built from that JSON.
The process fix is python scripts/reconcile_harvest_registry.py, gated by python scripts/check_registry_harvest.py. Do not hand-append rows.
Intentional exclusions¶
Blocked slugs (positive_regulation_of_ovulation, sensory_perception_of_sound, zz_scaffold_test) and GO-like / response_to_* / trait_in_response_to_* directories that remain on disk are not harvest diseases. Discovery already excludes the blocklist; the GO-like dirs can still appear in list_all() until separately purged.
Phase 2 classified the 13 discoverable on-disk harvest exclusions (A–E). None are category C (delete with strong evidence): every directory is an AUTO-GENERATED disease add scaffold with populated genes.json. New GO-like scaffolds are refused. Do not bulk-delete these modules.
| Class | Meaning | Slugs |
|---|---|---|
| A | Disease-like; admit to harvest | none of the 13 |
| B | OT/EFO measurement or treatment-response trait; keep | heart_rate_response_to_exercise, heart_rate_response_to_recovery_post_exercise, response_to_bronchodilator, response_to_covid_19_vaccine, response_to_paracetamol, response_to_selective_serotonin_reuptake_inhibitor, response_to_statin, response_to_surgery, response_to_vaccine |
| C | Delete with strong evidence (empty / duplicate / test-only) | none |
| D | GO biological-process slug; keep | response_to_stimulus, response_to_xenobiotic_stimulus |
| E | PGx-adjacent trait_in_response_to_*; keep pending owner relocation |
trait_in_response_to_apixaban, trait_in_response_to_triamcinolone_acetonide |
Authoritative table: ON_DISK_GO_RESPONSE_EXCLUSIONS in src/med_research/diseases/harvest_registry.py. Unclassified new GO-like dirs fail python scripts/reconcile_harvest_registry.py --check.