Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Allow the parsing of OBO files #36

Open
yum-yab opened this issue Sep 27, 2023 · 3 comments
Open

Allow the parsing of OBO files #36

yum-yab opened this issue Sep 27, 2023 · 3 comments
Labels
enhancement New feature or request

Comments

@yum-yab
Copy link
Contributor

yum-yab commented Sep 27, 2023

For example the bioregistry saves it's ontologies in the .obo format.

It would be nice to allow the parsing/loading of such files into Archivo, but currently rapper/rdflib do not support such files.

Also then the discovery process for the bioregistry needs to be adapted (add new key download_obo).

@cthoyt
Copy link
Contributor

cthoyt commented Sep 27, 2023

FYI the Bioregistry only keeps metadata about ontologies, it is not creating nor maintaining ontologies itself.

@matentzn
Copy link

There is no urgent need to parse OBO files as all OBO (Foundry, at least) ontologies are required to provide a primary RDF/XML release!

@cthoyt
Copy link
Contributor

cthoyt commented Sep 28, 2023

There are plenty of non obo foundry ontologies listed in Bioregistry that only have an obo flat file, eg, cellosaurus

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

3 participants