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Build pipeline and Releases

Usual obo workflow applies:

  • make test for running tests
  • make for building staged release

You can use run.sh to use the ODK Docker container

Tests

See Makefile for details

  • Robot reason - detects logically inconsistency and equivalence between names classes in Mondo
  • Sparql checks
    • Standard obo
      • ...
    • Mondo specific
      • ...

Releases

All release products are described on the OBO page: http://obofoundry.org/ontology/mondo.html

  • mondo.owl:
    • Includes owl definitional axioms plus imports
    • Includes owl equivalence axioms to OMIM/Orphanet/DOID/EFO/NCIT/MESH
      • Note: these ontologies are not imported
    • Monarch loads this
  • Mondo.obo
    • Excludes owl definitional axioms that reference external ontologies
    • Excludes owl equivalence axioms
    • This is what OLS loads
    • Applications use xrefs

The release mondo.owl will look like this in Protege: How release looks in Protege

Release process:

Currently Chris makes releases, but top priority is Dockerizing this so anyone can run it

The size of the OWL file causes some problems with standard GH-based release management. We are currently using OSF.io but this is a pain. We also make GH releases with all main artefacts, we may switch to this mechanism.