CL release 2023-10-19

[ghost]

CL release 2023-10-19

Cursory review revealed expected updates.

[github-actions]

Here's a diff of how this release impacts cl.owl

[ghost]

FYI @gouttegd as I noticed some edits involving "namespace: fly_anatomy.ontology".

[gouttegd]

The disappearance of the oboInOwl#hasOBONamespace annotations with a value of fly_anatomy.ontology is a consequence of FBbt having recently stopped to use OBO shorthands for some RO relations. I am not sure why such annotations were even present in CL in the first place (CL does not import FBbt), but in any case their removal is a healthy thing.

I am more concerned by things like this:

-property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI
+property_value: depicted:by "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI

in some of the OBO artefacts. That depicted:by seems very wrong.

[ghost]

The disappearance of the oboInOwl#hasOBONamespace annotations with a value of fly_anatomy.ontology is a consequence of FBbt having recently stopped to use OBO shorthands for some RO relations. I am not sure why such annotations were even present in CL in the first place (CL does not import FBbt), but in any case their removal is a healthy thing.

@gouttegd, thank you for confirming.

I am more concerned by things like this:

-property_value: depicted_by "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI
+property_value: depicted:by "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI

in some of the OBO artefacts. That depicted:by seems very wrong.

@anitacaron, is this expected?

[anitacaron]

unsure if this is related to obophenotype/uberon#3091. Is this expected?

They're unrelated, but it seems we don't have any control over the OBO format. Maybe it can be related to the change in CL that I removed the annotation declaration. It'll be fixed on the next Uberon release.

[aleixpuigb]

All the expected changes from PRs are reflected in the diff file.

Once the issues raised in the previous comments are solved, I will approve the PR.

[ghost]

All the expected changes from PRs are reflected in the diff file.

Once the issues raised in the previous comments are solved, I will approve the PR.

Thanks for reviewing.
It seems like the OBO formatting issue is benign (@anitacaron has approved) and will be resolved after a new Uberon release is available.