Versioning of OBO ontologies?

[justaddcoffee]

Is there a versioning system for OBO Foundry ontologies, or a plan to make one?

We are currently building a pipeline to transform OBO foundry ontologies into a format that is more amenable to graph machine learning, and it would be great to have information about versions so we could, for example, make previous versions available for reanalysis.

[balhoff]

Every ontology has (or should have) a version IRI which is stated within the ontology. Each version should be retrievable in perpetuity from its version IRI. In practice this doesn't always work, but it works for most. What we don't have, but need, is an actual listing of what versions of each ontology are available. This information is available idiosyncratically from particular ontologies (e.g. http://release.geneontology.org) but it would be great to keep this in RDF, for the whole library. I have some vague plans to do this. 😄

[justaddcoffee]

Thanks @balhoff!

[nlharris]

See also #771 and #1414

Are there action items here? Should this ticket be kept open?

[justaddcoffee]

I think for our purposes we can close this, since I think we can just use the version IRI

Thanks for the link to the existing tickets - the discussions of versioning there are along the lines of what I was hoping to find, but version IRIs should work fine too

[cthoyt]

I’ve been interested in this recently as well and am keeping track of the current versions of all ontologies and other biomedical resources I can at https://github.com/cthoyt/bioversions

[alanruttenberg]

You should be able to scrape the versions from https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config

[cmungall]

Most ontologies I'm aware of use a generic redirect for versions so this won't work

…

On Mon, Aug 23, 2021, 21:21 Alan Ruttenberg ***@***.***> wrote: You should be able to scrape the versions from https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1576 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOP4TP4CLV52QHTKGITT6MM5TANCNFSM5CVHTUFQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .