Fix ORCID individuals import

[anitacaron]

Related to #3253 (ORCID names are being removed in diff)

I chose to have a separate import because the merged_import excludes individuals, and I wanted to enable this only for Orcidio. I created a custom rule for imports/orcidio_import.owl and imported it in uberon-edit.obo.

What do you think?

[anitacaron]

Can I please merge this PR and move the discussion to another place?

[gouttegd]

I don’t like the fact that the PR only works because of what is likely to be either (1) a bug in ROBOT’s STAR extraction or (2) an undefined behaviour due to the fact that the seed is a list of individuals, while SLME is supposed to work from a list of class or property names.

I am not discussing just for the sake of discussing. Relying on a bug/undefined behaviour that we can’t explain is not great, even if it appears to work the way we want.

[anitacaron]

I can change it to BOT and then get all individuals, which is the expected behaviour.

[gouttegd]

But then all the individuals defined in orcidio would end up in the orcidio_import.owl module, including those who have nothing to do with Uberon.

[gouttegd]

This works as I believe it should:

robot filter -i mirror/orcidio.owl -T imports/orcidio_terms_combined.txt --trim false  -o imports/orcidio_import.owl

The key option here is --trim false, which is necessary to ensure we get the annotations associated with the individuals. Without that option, the annotation assertion axioms are filtered out because their signature contains entities that are not in the seed. This is exactly as expected:

When using filter --trim true (the default), if all objects for the axiom are in the target set then that axiom is copied to the new ontology. When using filter --trim false, if any object for the axiom are in the target set, then that axiom is copied.

[gouttegd]

Looks good.

You don’t need to do anything about my remark regarding the use of Make conditionals. It’s something we can do later, maybe by doing a single overhauling pass over the custom Makefile to replace all shell conditionals in one step.