[ensembl-dev] Question regarding gene Annotations discrepancies between GRCh38 and 37 on the latest API.

Duarte Molha duartemolha at gmail.com
Wed Jul 1 12:57:04 BST 2015


I understand... But shouldn't at least genes that you have maintained from
one assembly to the next be updated in terms of gene names? Or at least add
the most up-to-date gene symbol to the alias field?

It is a bit annoying because we will not be able to search for a correct
gene name on the GRCh37 because it will only be listed on the database with
its previous alias.


=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================

On 1 July 2015 at 11:58, mag <mr6 at ebi.ac.uk> wrote:

>  Dear Duarte,
>
> The gene set in the GRCh37 database is a freeze from release 75.
> The variation and regulation annotation is updated when major data sets
> are released.
>
> The gene set however is not updated given our major evidence sources are
> updated to GRCh38.
>
>
> Regards,
> Magali
>
>
> On 01/07/2015 11:03, Duarte Molha wrote:
>
> Dear developers
>
>  It was my understanding that ensembl would be keeping 2 databases
> running in parallel for both GRCh38 and GRCh37 and so all genes would be
> receiving annotation updates and both databases could be queried with the
> latest and greatest ensembl perl api.
>
>  However I am finding inconsistencies in gene annotation what have left
> me puzzled.
>
>  Take for example gene DNAAF5
>
>  http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=26013
>
>  If you query ensembl GRCh38 V80, the gene is there properly annotated
>
>
> http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000164818;r=7:726701-786475
>
>  However, on GRCh37 V80, the gene is still annotated with the previous
> HGNC symbol HEATR2
>
>
> http://grch37.ensembl.org/Multi/Search/Results?q=HEATR2;site=ensembl;page=1
>
>  the ENSEMBL gene ID is the same in both cases :
>
>  ENSG00000164818
>
>  Is my thinking flawed? What is the reason for the out-of-date gene
> annotation for this gene?
>
>  Many thanks
>
>  Duarte
>
>
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