UPHENO status

[bschilder]

Is your feature request related to a problem? Please describe.
I was wondering what the current status and plans were for the UPHENO ontology. It doesn't seem to be currently accessible via OLS (in the browser or the rols R package which uses the API).
I noticed some old issues and PRs that removed it, but I'm not sure why:

• Upheno removal #564
• Remove upheno for next data release #563

I also noticed that mappings to UPHENO terms do still exist in relation to other ontologies (e.g. DOID):
https://www.ebi.ac.uk/ols4/ontologies/doid/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUPHENO_0001001

Both v1 and v2 or UPHENO are available via the OBO Foundry
https://obofoundry.org/ontology/upheno.html
As well as on GitHub:
https://github.com/obophenotype/upheno/

Describe the solution you'd like
Have UPHENO be available via OLS.

Describe alternatives you've considered
Currently, I'm downloading UPHENO directly from their OBO Foundry ("https://purl.obolibrary.org/obo/upheno/v2/upheno.owl") and importing it into R with simona::import_ontology

Additional context
I'm asking in part as it relates to a new package I'm making to help use, filter, and manipulate ontologies and knowledge graphs in R:
https://github.com/neurogenomics/KGExplorer

Thanks for your help!,
Brian

[haideriqbal]

Thank you for your inquiry about the inclusion of UPHENO ontology in the OLS. UPHENO is managed by OBO (Open Biological and Biomedical Ontology) Foundry and we're glad to inform you that UPHENO is in the process of being recognized by the OBO Foundry community. It's the efforts of the OBO community that determine the inclusion of new ontologies into the OBO.

Once UPHENO is formally part of the OBO, it will automatically be integrated into OLS and then you can query it via OLS.

[matentzn]

Just to be clear: there is a slightly confusing situation as there is a "upheno (1)" that has already been accepted in OBO, and a new one developed by @jamesamcl and his team which you can see, for now, here: https://ols.monarchinitiative.org/ontologies/upheno2

It is odd that upheno1 is not at all in OLS (it should be), but its probably because it has 40K unsatisfiable classes..

[bschilder]

Thanks so much for the info @matentzn @haideriqbal !

Just to be clear: there is a slightly confusing situation as there is a "upheno (1)" that has already been accepted in OBO, and a new one developed by @jamesamcl and his team which you can see, for now, here: https://ols.monarchinitiative.org/ontologies/upheno2

Thanks for the link! I'm guessing this page is still under development though? based on the fact that the ontology isn't actually available for download (at least not that I can find there):
https://ols.monarchinitiative.org/ontologies/upheno2/download

It is odd that upheno1 is not at all in OLS (it should be), but its probably because it has 40K unsatisfiable classes..

This seemed strange to me as well since upheno1 has been out for a quite a while. @haideriqbal am I mistaken in thinking that if it's on OBO Foundry already (see here) it should also be available on OLS? Is the issue due to the errors reported here? Not sure is this is the same issue with 40k 40K unsatisfiable classes that @matentzn mentioned.

[haideriqbal]

Hi @bschilder after further investigating the issue on our end we've come to know that there is an issue with one of the imports of UPHENO ontology. The import is not in the correct format and hence is not loaded in OLS. I've opened an issue with the UPHENO team as well. You can have a look here obophenotype/upheno#929.

Once the UPHENO team fixes the issue with the import then the UPHENO ontology would automatically load in the OLS.

[bschilder]

@haideriqbal thanks so much for looking into this! Glad to hear there's activity on this