[Bioc-devel] Change of schema of ENSEMBL biomart

Dear Tiphaine,

The Ensembl marts on the biomart.org portal were recently updated from Ensembl release 75 to release 77. In release 76, we renamed the "Associated Gene Name" attribute internal name from "external_gene_id" to "external_gene_name". We have also added a new "Associated Gene Name" id list limit filter in release 77.

From release 77 onward we have decided to declare all the attribute/filter internal names changes on the Ensembl website declaration page:  http://www.ensembl.org/info/website/news.html#cat-other. 

The data in the "hsapiens_gene_ensembl" dataset have also changed a lot since we moved from the human assembly GRCh37 to GRCh38 in Ensembl release 76. If you are still interested in the GRCh37 human assembly then you can access our archive Ensembl marts on the following page: http://grch37.ensembl.org/biomart/martview

Hope this helps,
Apologies for any inconvenience caused,
Regards,
Thomas

Hi Everybody,


Yesterday, I observed that ENSEMBL changed a little their schema of  the dataset "hsapiens_gene_ensembl".

In my case, some of my functions were impacted by the change from "external_gene_id" to

"external_gene_name".


Maybe there are other change in this dataset or other datasets.


Regards,

Tiphaine

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom