Nico Matentzoglu

Adding a preprocessing intermediate file to the ODK build process

1

This allows injecting custom preprocessing steps

We allow people to customise their ROBOT reports, but we have no facilitate to update the profiles when new checks are added to ROBOT report (i.e. the profile.txt once it...

1. It should be very easy to do the standard stuff, and make it possible for knowledgeable people to be able to customise.

right now, external_imports cannot handle if unknown prefixes.

Replace base specification by introducing the possibility of reasoning

1

The current base specification is simply "all axioms belonging into that ontology, and not to one of its imports, merged into a single file". After thorough discussions with @cmungall @dosumis...

probably using isDefinedBy, whatever is standard. This way we can easily remove external axioms at a later step, also helps with provenance.

Add `make reason_test` to do a quick check if ontology has no unsats.

For some use cases, like building application ontologies, we may not want to run the reasoner again at release time. We should provide an option to skip reasoning operations.

Files managed in OBO format have replaced by values as CURIE strings

9

We should try and make sure they are correctly rewritten to URIs before moving out. Maybe use the new intermediate call #639 see https://github.com/monarch-initiative/mondo/issues/2636