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)

Developer Documentation

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.

Design decisions:

1. 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.

Credits

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