Incomplete imports from AISM to COLAO

[JCGiron]

After the fix recommended by @matentzn a new release has been run but AISM terms are still missing.
Missing properties were added to the properties to keep file. All changes are now committed to the main repository.

One of such terms: AISM_0000407 is currently present in colao/src/ontology/imports/aism_import.owl but not in colao/imports/aism_import.owl

It looks like something is not right somewhere in the release process, even though the release was successfully run in the computer?

[anitacaron]

Hi @JCGiron, it seems that the colao/imports/aism_import.owl has never been updated for any of the 15 releases. Do you really need this update?

[JCGiron]

Thanks for checking, @anitacaron.
I think we do neeed the update, as we might need to add COLAO terms as subclasses of AISM terms that are currently missing in the import.

[anitacaron]

If I understood correctly, you said the class is in colao/src/ontology/imports/aism_import.owl. This is the right place to be present. Can you see it in Protégé?

[JCGiron]

If I open colao/src/ontology/imports/aism_import.owl in Protégé, the class AISM_0000407 is missing its label, which is present in the original AISM.

Class AISM_0000407 is completely absent in colao/src/ontology/colao-edit.owl.

Maybe I'm just misunderstanding what the import commands are supposed to do. I assumed that with the commands Nico suggested for the colao.Makefile, anytime we ran imports and release, we would get all the terms and annotations included in the latest version of AISM. Am I getting all this wrong?

In one of my tests I imported the colao/src/ontology/imports/aism_import.owl file into colao-edit.owl directly using Protégé, but it duplicated all the AISM annotations, which is not ideal.

[anitacaron]

It's a bit hard to understand the workflow in the ontology. You created an aism_import.owl, but many classes defined in colao-edit.owl are AISM, and there are also many classes from other ontologies. You don't import the aism_import.owl into colao-edit.owl because they have the same classes. Would you consider removing the AISM classes in colao-edit.owl and only importing aism_import.owl?

Anyway, I tried the aism_import command this way, and now it shows the label for AISM_0000407.

imports/aism_import.owl: mirror/aism.owl tmp/seed_aism_base.txt
	if [ $(IMP) = true ]; then $(ROBOT) remove -i $< -T tmp/seed_aism_base.txt --select complement --select "classes annotation-properties object-properties individuals" --signature true \
		annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output [email protected] && mv [email protected] $@; fi

But again, it's only in aism_import.owl. I'm not sure how you added the AISM classes in the colao-edit.owl before.

[JCGiron]

The AISM includes general terms for insects and is meant to be at the backbone of order-specific ontologies. COLAO is supposed to have all the terms used in AISM plus COLAO terms for beetle-specific terms.
This is the protocol we proposed to create AISM-based ontologies. Those were the steps we followed when COLAO was first created with a successful AISM import.

One problem that I see with removing the AISM classes in colao-edit.owl is that COLAO classes that are linked to AISM classes would lose those links. Is there a simple way to do that? the only way I would know how would be manually deleting each AISM class in Protégé.
Again, I'm not entirely sure that I fully understand how ODK works and why the newer or updated AISM terms are not getting imported with the release command.

[matentzn]

It seems you have aism configured as a component, not an import:

https://github.com/insect-morphology/colao/blob/main/src/ontology/colao-odk.yaml

[JCGiron]

Thanks for taking a look, @matentzn. How do I fix that?

[matentzn]

You may need help but try to follow the steps for PATO:

https://pato-ontology.github.io/pato/odk-workflows/RepoManagement/

Could you ask Istvan for help?