Current version of CCO accessed on web does not import BFO!

[alanruttenberg]

http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AllCoreOntology
retrieves http://www.ontologyrepository.com/CommonCoreOntologies/Mid/2024-02-14/AllCoreOntology

which doesn't have a BFO imports, so only IDs are shown at the top level.

[alanruttenberg]

The merged version does have BFO in it.

[alanruttenberg]

But the merged version IRIs don't resolve.
What am I missing?

[alanruttenberg]

Maybe the readme should say what the official IRIs are...

[mark-jensen]

Is this related to #221?

All Core is just an import handler. It pulls in 5 or 6 ontologies, which themselves all eventually pull in the 11 CCO modules plus BFO via ERO.

I don't like the way we currently do this. We are now exploring alternatives to improve CCO modularization, the release, and import methodology.

[alanruttenberg]

All core does not import BFO, even indirectly. Try it: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AllCoreOntology

[alanruttenberg]

This is what I see in Protege

[ewrayjohnson]

I would appreciate a online meeting (with @alanruttenberg and @mark-jensen) to discuss this issue and #221.

[alanruttenberg]

@ewrayjohnson I am available this afternoon.

[ewrayjohnson]

@ewrayjohnson I am available this afternoon.
See my direct email

[mark-jensen]

@alanruttenberg @ewrayjohnson I believe I have discovered the problem here. If you open this link in your browser, or download the file and look at it in a text editor, you see the import statement for BFO is absent in ERO.

https://www.ontologyrepository.com/CommonCoreOntologies/Mid/ExtendedRelationOntology

The version of ERO that is part of the 1.5 release contains it however. Not sure what happened. I'll get the server updated asap.

[alanruttenberg]

Mark, please add a BFO import to each of the domain ontologies.

…

On Thu, May 30, 2024 at 3:35 PM Mark Jensen ***@***.***> wrote: @alanruttenberg <https://github.com/alanruttenberg> @ewrayjohnson <https://github.com/ewrayjohnson> I believe I have discovered the problem here. If you open this link in your browser, or download the file and look at it in a text editor, you see the import statement for BFO is absent in ERO. https://www.ontologyrepository.com/CommonCoreOntologies/Mid/ExtendedRelationOntology The version of ERO that is part of the 1.5 release contains it however. Not sure what happened. I'll get the server updated asap. — Reply to this email directly, view it on GitHub <#255 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAB3CDWANCXW35LGC45C2PLZE55RXAVCNFSM6AAAAABIANEPDOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBQG42DGMBWHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[mark-jensen]

@ewrayjohnson @alanruttenberg This problem has been fixed. The version of ERO loaded up on the server has the correct import for BFO2020. Loading it, or All Core, or any of the other CCO ontologies, will find and load BFO as intended.

[alanruttenberg]

@mark-jensen Well, I'll say it one more time for emphasis. It is bad practice to rely on an indirect import. Ontologies that use terms in imported ontologies should directly import those ontologies.

[neilotte]

@alanruttenberg Has this ticket been resolved?