Support new HPO URL patterns in jax.org

bihealth / sodar-server

SODAR: System for Omics Data Access and Retrieval

https://github.com/bihealth/sodar-server

MIT License

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Support new HPO URL patterns in jax.org #1821

Closed Nicolai-vKuegelgen closed 10 months ago

Nicolai-vKuegelgen commented 11 months ago

Problem

I noticed this announcement on the website of the HPO ontology website:

We are currently moving our ontology API to https://ontology.jax.org and expect to fully switch by November 31, 2023 (this date is not firm). Please feel free to use this new API, however term annotation endpoints have not yet been moved.

I assume that could break a few things in Sodar, if no adjustments are made, so this issue is meant as a warning or maybe simply a reminder (I'm also really unsure if this fits bug report of feature request better ...)

Solution

References to the current API endpoint need to be identified & updated once HPO actually moves their ontology.

mikkonie commented 11 months ago

Can you link me to the original announcement? Is there some indication that the ontology will removed from obolibrary.org which we currently link to?

SODAR does not use the API but, instead, imports ontologies locally and uses its own internal Ajax views to search for ontology terems. This saves us the trouble of interfacing with different, potentially unstable APIs.

For term access. we link to obolibrary which is a general repository of ontologies. Unless HPO is removed from obolibrary, this should not affect SODAR.

mikkonie commented 10 months ago

Ok, so it appears that:

Obolibrary now forwards URLs to jax.org, so "pure" old ololibrary URLs still work
However, bioportal.org doesn't (yet?) support the jax.org URLs
This results in a 404 in bioportal if the new type of URL is used in the term accession

I need to do a workaround to ensure both old and new URLs work. For now, this can be doable by simply adding hpo.jax.org to SHEETS_ONTOLOGY_URL_SKIP.

The default accession pattern on the production server should probably be also updated to the new jax.org pattern.