Upcoming Ensembl API and data access changes

[guidohooiveld]

Hi Johannes,

You are likely aware of this, but a heads-up as I just saw this post at the Bioconductor support forum:
https://support.bioconductor.org/p/9162883/

https://www.ensembl.info/2025/12/02/updates-to-programmatic-access-to-ensembl-and-transitioning-to-the-new-ensembl-platform/

I cannot fully oversee the implications of this new API in the context of ensembldb, but I am afraid they are substantial. (Hopefully I am wrong!)

G

[jorainer]

Hi @guidohooiveld ! yes, I have seen that. I'm afraid this might break the package completely. but it could also be a nice MSc project to update the package to use the upcoming API from ensembl - the database layout we have would stay the same, it's just the way to retrieve the data from Ensembl that need to change.

[jorainer]

Or, do you want to give it a shot @guidohooiveld - or do you have anybody in your group - or access to MSc / BSc students who could work on that? I'm afraid I will not have the time to spent on this, in particular since I'm now mostly working with mass spectrometry and metabolomics data...