GECKO missing imports?

[mcourtot]

I didn't see the BFO or IAO import at https://raw.githubusercontent.com/IHCC-cohorts/GECKO/master/gecko.owl

[jamesaoverton]

It's best-practise to merge all imports when creating a release artifact (such as gecko.owl), so that there are no owl:import elements left, and the release artifact is self-contained. If you don't do that, you have two problems:

1. every time someone opens gecko.owl they also need to connect to the Internet (or use a catalog file) to find the import files; network connections are never 100% reliable
2. those import files may have changed, so now GECKO looks different than it did when released, potentially causing it to break

You can see that all the BFO and IAO terms we need (and all the other imported terms) have been merged into gecko.owl.

Imports are updated/refreshed at build-time according to recipes in the Makefile, for example:

https://github.com/IHCC-cohorts/GECKO/blob/master/Makefile#L110

See also:

https://github.com/INCATools/ontology-development-kit/blob/master/docs/ReleaseArtefacts.md#release-artefact-2-full-required

[mcourtot]

hm - when I look at GECKO released version I do not see the BFO top-level though.

[jamesaoverton]

If you want to see the top-level of BFO (entity, continuant, independent continuant, generically dependent continuant, occurrent, etc.), then we will put it in to GECKO. The current top-level of GECKO is based on the subset of BFO terms used in COB, which were selected to be intuitive to a broad audience with minimal jargon. We've used this same top-level structure since the first draft of GECKO. It will, of course, merge cleanly with any other ontology based on BFO.

[mcourtot]

Thanks for the extra explanation. I had never noticed the top-level being different - I got used to preferred roots in OLS :) Happy to keep COB if that's what you recommend.