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dieterich-lab / scimodom

Sci- ModoM: A quantitative database of transcriptome-wide high-throughput RNA modification sites
https://dieterich-lab.github.io/scimodom/
GNU Affero General Public License v3.0
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Inconsistent versions between application and Ensembl (genome browser) #148

Open eboileau opened 2 months ago

eboileau commented 2 months ago

Aims/objectives.

What if we use e.g. Ensembl 110 (for sequence context, annotation in general such as features, gene assigment, and complementing RBP annotation) and link reported sites to Ensembl genome browser, which is likely to be a few versions above e.g. at the time of opening this issue it was 112.

A clear and concise description of todo items.

We will eventually have to consider database/application upgrade (and liftover), but we want to do that on a per-species basis only when absolutely required, e.g. when a new assembly is available. We could consider upgrading annotation only, but need to carefuly consider whether this is necessary, and how frequently, see also https://dieterich-lab.github.io/scimodom/database.html#annotation.

CDieterich commented 2 months ago

Dear @eboileau - there is a nice feature of EnsEMBL. They keep old releases on the archive site with permanent links. see https://www.ensembl.org/Help/ArchiveList

eboileau commented 1 month ago

The archive service seems unstable... for instance https://jul2023.archive.ensembl.org does not work at the moment...

eboileau commented 1 month ago

I leave this open, this needs to be refactored. The version is hard coded separately in BE and FE. We need a single source, and this must match the assembly version set in the DB.