CHEBI OBO Slim

A slimmed down version of CHEBI sufficient to cover 99% of the term needs across OBO ontologies.

Maintainers

• @matentzn
• @shawntanzk

How to add additional terms?

1. Make a Pull request on https://github.com/obophenotype/chebi_obo_slim/blob/main/seed.txt. In the PR, indicate which terms you are adding (at least the ids) and for which ontology.
2. If you are a member of obophenotype organisation:
   • You should make sure seed.txt is sorted alphanumerically
   • Merge the changes without review at your own discretion
3. If you are not a member of obophenotype organisation:
   • Wait until a member of obophenotype deals with your PR

How to become a maintainer?

Open a an issue on the issue tracker with a request to join.

How to run a release?

1. Clone the repo
2. From within the repo run sh odk.sh make all (you need to have docker installed)
3. Commit any changed files to branch, make PR
4. Ask for a review from another maintainer
5. After a single approval, merge
6. Make a GitHub release with the usual OBO tag (i.e. v2022-09-21)

Note that running the sh odk.sh make all command above will forcefully refresh the local CHEBI mirror by downloading the latest available version of CHEBI. If that is not desired (if for some reasons you want to make a new release based on the exact same version as a previous release, without updating to a more recent CHEBI), you may call that command as sh odk.sh make all MIR=false. You may only do that if you also ran the previous release. If the previous release was made by someone else, you must ensure that you are using a version of CHEBI that is at least as recent as the one used for the last release, and the easiest way to ensure that is to always get the latest version (which is the default behaviour, when you do not use MIR=false).