ebi-gene-expression-group / atlas-web-bulk

Bulk Expression Atlas web application
Apache License 2.0
0 stars 1 forks source link

Fix resources links for EGA datasets #209

Open ke4 opened 2 weeks ago

ke4 commented 2 weeks ago

The link to EGA dataset resources is broken.

Steps to reproduce:

  1. Open an experiment that has a linked EGA dataset resource
  2. Go to the Supplementary Information tab
  3. Click on the EGA resource

Example dataset: https://wwwdev.ebi.ac.uk/gxa/experiments/E-CURD-146/Supplementary%20Information

Expected result: The browser should open the EGA dataset's page.

Actual result: Page not found

ke4 commented 1 week ago

Here are 2 more example datasets that are already on public:

ke4 commented 1 week ago

The above 2 examples point to EGA studies with EGAS... accessions and using /studies/... in the URL. So the URL looks fine to me, but we got a 404.

I asked this last 2 from my EGA contact and waiting for his answer. :crossed_fingers:

ke4 commented 1 week ago

The answer was that we have to remove the / from the end of the URL and that should work. :-D

ke4 commented 3 days ago

Here is the resource mapping from a previous ticket (#195): accession to resource mappings:

ArrayExpress accessions E-MTAB<> -> ArrayExpress E-ERAD<> -> ArrayExpress E-GEUV<> -> ArrayExpress

Proteome Exchange accessions - can be viewed in PRIDE (and elsewhere) PXD<> -> PRIDE

GEO accessions GSE<> -> GEO GDS<> -> GEO

INSDC consortium project accessions - can be viewed in ENA (and elsewhere) ERP<> -> ENA SRP<> -> ENA DRP<> -> ENA

BioProject NSDC consortium accessions - can be viewed in ENA (and elsewhere) PRJEB<> -> ENA PRJNA<> -> ENA PRJDB<> -> ENA

EGA accessions EGAS<> -> EGA EGAD<> -> EGA

Some E-HCAD experiments (so these would be in SCEA only, not bulk) may have a 'bundle ID' in the secondary accession field in idf but I am not sure if that could be used to search and point to a project in the HCA Data portal