Mondo Source Ingest

This repo is dedicated to the integration of various clinical terminologies and ontologies into Mondo. For more details see the documentation.

Work on the Mondo Source Ingest is funded by the NHGRI Phenomics First Grant 1RM1HG010860-01.

Prerequisites

Python is a dev dependency. It's not needed to run the docker containers, but needed for local development situations / debugging.

1. Python 3.9+
2. Docker
3. Docker images
   One or both of the following, depending on if you want to run the stable build latest or dev:
   • a. docker pull obolibrary/odkfull:latest
   • b. docker pull obolibrary/odkfull:dev
4. Optional: odkrunner: Alternative to run.sh. If using this, you would run like odkrun make build-mondo-ingest instead of sh run.sh make build-mondo-ingest. Suggestion: rename the binary to odk; this is the convention of mondo-ingest developers.

Running

Full build

sh run.sh make build-mondo-ingest

Workflows

Reports

A variety of reports are committed as static files in src/ontology/reports/ and are documented in the reports codebook, but some additional reports get rendered into markdown pages as noted below.

Mapping progress report

The mapping progress report consists lists of all unmapped terms fo each ontology, as well as a table of statistics showing total number of terms, excluded terms, deprecated terms, and unmapped terms.

Mapped deprecated terms

The mapped deprecated terms page contains a table of statistics showing total number of deprecated terms that have existing xrefs in Mondo, for each ontology. There is also a link to a page for each ontology which shows the term IDs and their corresponding mapped Mondo ID(s).

Migratable terms

The migrate page contains a table of statistics showing of terms ready for migration / integration into Mondo.