MOD-mappings

This project provides mappings between the MOD ontology and a number other ontologies

Repository Structure

config/ - configuration files
- project-cruft.json -- edit this if you need to change any of the project template values in .cruft.json
mappings/ - SSSOM mapping files (do not edit these)
sources/ - source files (edit these)

To update the mapping registry from OLS:

sh odk.sh make update_registry -B

To update the mappings:

sh odk.sh make mappings

If the run requires a recently published SSSOM or OAK feature, first update ODK:

docker pull obolibrary/odkfull:dev

and then run the dependencies goal together with the mappings goal:

IMAGE=odkfull:dev sh odk.sh make mappings

For Windows, append :dev to obolibrary/odkfull in the odk.bat file.

Note: If running on a Windows machine, replace sh odk.sh with odk.bat in the above commands.

Only mappings of base entities are extracted. This ensures that we do not import the same UBERON mapping for every species specific anatomy ontology (XAO). This is realised as a filtering step that relies on the crude assumption that the ontology ID is somehow reflected in the subject_id.

This project was made with the mapping-commons-cookiecutter.