doid

Human Disease Ontology (DOID) preprocessed for Mondo disease-ontology ingest.

Setup

1. Install dependencies: uv sync

Run

# OWL pipeline (run inside ODK Docker via odk.sh, or locally with ROBOT installed):
./odk.sh make all          # full pipeline: mirror + build + reports
./odk.sh make MIR=false build   # skip re-downloading

Outputs

File	Description
doid.yaml	Primary artefact for Mondo ingest
doid.owl	Final OWL (LinkML-derived; tmp/transformed-doid.owl is the ROBOT intermediate)
reports/	QC metrics and class counts

Docs

Doc	Contents
docs/plan.md	Pipeline architecture, field mappings, ID scheme
docs/release_notes.md	Ontology stats and verification results per release
docs/pipeline_incidents.md	Pipeline incidents: errors, deviations, resolutions