bridgedb/datasources

Incorrect linkout patterns for Gramene Rice and Rice Ensembl Gene

ariutta opened this issue · 1 comments

ariutta commented

I noticed a linkout that fails for a GeneProduct in the Geranylgeranyldiphosphate biosynthesis II pathway WP2211 at WikiPathways. The GeneProduct has a datasource of "Gramene Rice" and an identifier of "LOC_Os04g56210", as highlighted in green here.

Based on datasources.txt, the linkout should be
http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=LOC_Os04g56210`
but that link gives the following error:

  Database Error

  Could not connect to the core;g=LOC_Os04g56210 database.

  This view requires a gene, transcript or protein identifier in the URL. For example:

  http://ensembl.gramene.org/Oryza_sativa/Gene/Summary?g=OS05G0113900

The following URIs do work:

The URI from combining the linkout and sample identifier listed for Gramene Rice in datasources.txt also does not resolve:
http://www.gramene.org/Oryza_sativa/Gene/Summary?db=core;g=osa-MIR171a

Is this the URI describing osa-MIR171a?
http://archive.gramene.org/db/genes/search_gene?acc=GR:0100777

If so, the linkout for Gramene Rice should be http://archive.gramene.org/db/genes/search_gene?acc=$id and the sample identifier should be GR:0100777.

Maybe Rice Ensembl Gene is the datasource that should be used for LOC_Os04g54800 in WP2211, because the Rice Ensembl Gene sample identifier LOC_Os04g54800 resembles LOC_Os04g56210, unlike the sample identifier listed for Gramene Rice osa-MIR171a. However, the linkout pattern from datasources.txt would indicate the linkout should be
http://www.gramene.org/Oryza_sativa/geneview?gene=LOC_Os04g54800
which gives this error:

Gene 'LOC_Os04g54800' not found

The identifier 'LOC_Os04g54800' is not present in the current release of the Ensembl Plants database.

This view requires a gene, transcript or protein identifier in the URL. For example:

http://ensembl.gramene.org/Oryza_sativa/Gene/Summary?g=OS05G0113900

Then the linkout pattern in datasources.txt for Rice Ensembl Gene would need to be updated to http://ensembl.gramene.org/Oryza_sativa/Gene/Summary?g=$id;db=otherfeatures

egonw commented

Fixed in bd2b49c