This project is an attempt to bring together key terms from a wide range of Open Biological and Biomedical Ontology (OBO) projects into a single, small ontology. The goal is to improve interoperabilty and reuse across the OBO community through better coordination of key terms. Our plan is to keep this ontology small, but ensure that one or more COB terms can be used as the root of any given OBO library ontology.
COB is split into three "modules" that contain distinct sets of terms:
- BASE has only terms in the COB ID space
- FULL has all the terms in BASE, plus other OBO terms used in the axioms of those terms
- ROOT has all the terms in FULL, plus "root" terms from various OBO ontologies, which anchor those ontologies in COB and provide points from which other ontologies can expand
Most ontologies that import COB will want to use cob-root.owl.
COB makes use of the ODK workflows, but with a few additional steps that are unique to COB. Unlike most OBO ontologies, all of the terms in COB are housed in a single ROBOT template: cob-edit.tsv. All changes should be made in this template.
After making changes to cob-edit.tsv, run the following command in src/ontology/ to update the files:
sh run.sh make prepare_release -B
This command:
- Runs the script
split-cob-edit.py, which separatescob-edit.tsvinto templates for each module - Builds the base, full, and root modules using ROBOT
- Annotates the resulting files with an updated release date
- Reports on any violations found by
robot report - Sets literals to use
@en(preferred) orxsd:string(if used by the source ontology) (see PR #295 for more info)
Once the release files have been updated, run the following command to check imported terms against their source ontology:
make crosscheck
The crosscheck process compares imported terms to OntoFox import files (see PR #295 for more info). If the results from crosscheck look good, commit the changes and open a PR.