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OpenLHS / CVDO

Cardiovascular disease ontology
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Imports not resolvable from http://purl.obolibrary.org/obo/cvdo.owl #4

Open psiotwo opened 1 year ago

psiotwo commented 1 year ago

Resolving http://purl.obolibrary.org/obo/cvdo.owl required resolution of a few more ontologies, three of which however are not resolvable (as shown in https://psiotwo.github.io/ontology-version-extractor/output.html):

serjoshua commented 1 year ago

Following up on this since loading in OLS of CVDO from http://purl.obolibrary.org/obo/cvdo.owl is having issues. In summary, there is a failure importing http://purl.obolibrary.org/obo/cvdo/external/doid_import.owl.

Refer to https://github.com/EBISPOT/ols4/issues/453 for details regarding the error message in our pipeline.

ethierjf commented 1 year ago

Thanks for pointing this out. Our colleague in charge of this is currently not available but should be back early September.

JF Ethier - GRIIS.ca - Université de Sherbrooke

From: Josh Lagrimas @.> Sent: Friday, August 4, 2023 9:37:06 AM To: OpenLHS/CVDO @.> Cc: Subscribed @.***> Subject: Re: [OpenLHS/CVDO] Imports not resolvable from http://purl.obolibrary.org/obo/cvdo.owl (Issue #4)

Following up on this since loading in OLS of CVDO from http://purl.obolibrary.org/obo/cvdo.owl is having issues. In summary, there is a failure importing http://purl.obolibrary.org/obo/cvdo/external/doid_import.owl.

Refer to EBISPOT/ols4#453https://github.com/EBISPOT/ols4/issues/453 for details regarding the error message in our pipeline.

— Reply to this email directly, view it on GitHubhttps://github.com/OpenLHS/CVDO/issues/4#issuecomment-1665620380, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEY2LXUIULNLJN7MRKQAWRDXTT3IFANCNFSM6AAAAAAWOKO2G4. You are receiving this because you are subscribed to this thread.Message ID: @.***>

matentzn commented 3 months ago

Following up on this - as is, the ontology is not usable by anyone using standard OWL tools. Do you have an ETA on when this will be fixed?

ethierjf commented 3 months ago

Thanks for the follow up. Should be fixed now

pfabry commented 3 months ago

An updated version with versioned imports is now available. cf. PR https://github.com/OpenLHS/CVDO/pull/5

anitacaron commented 2 months ago

I just tested the new version and imports are still not revolving.

Could not load imported ontology: <http://purl.obolibrary.org/obo/CVDO/releases/2013-04-04/imports/doid_import.owl> Cause: http://www.berkeleybop.org/ontologies/CVDO/releases/2013-04-04/imports/doid_import.owl
matentzn commented 2 months ago

@pfabry for this to work,

  1. CVDO in the IRI should be lower case (cvdo)
  2. You need to create a corresponding release (2013-04-04) - this is ancient

But despite all this:

Its not good practice anymore to have imports in the release versions of ontologies. If you just use ROBOT and merge them it at release time, then the problem will go away without the need of changing anything about the IRIs!

pfabry commented 2 months ago

There is a merged version available in the repo, but it is not the release target. Our goal is to migrate this repo to an ODK pipeline, that should be done soon-ish. In the meantime I will make a new release with the merged version.

ethierjf commented 2 months ago

Honestly this is not a priority at this point for the team and others have been using the cvdo namespace for a different ontology.

Thanks for your feedback. It is on our roadmap and will be addressed accordingly 🙂

JF Ethier - GRIIS.ca - Université de Sherbrooke

From: Paul Fabry @.> Sent: Monday, June 17, 2024 10:50:45 AM To: OpenLHS/CVDO @.> Cc: Jean-François Ethier @.>; Comment @.> Subject: Re: [OpenLHS/CVDO] Imports not resolvable from http://purl.obolibrary.org/obo/cvdo.owl (Issue #4)

There is a merged version available in the repo, but it is not the release target. Our goal is to migrate this repo to an ODK pipeline, that should be done soon-ish. In the meantime I will make a new release with the merged version.

— Reply to this email directly, view it on GitHubhttps://github.com/OpenLHS/CVDO/issues/4#issuecomment-2173626391, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEY2LXUDDRCSGDVMXSFAYNDZH3ZULAVCNFSM6AAAAAAWOKO2G6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZTGYZDMMZZGE. You are receiving this because you commented.Message ID: @.***>

anitacaron commented 1 month ago

Great news! The ontology is now loading correctly! However, the version IRI is not resolving. It might need to update the purl configuration.