<div dir="ltr">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?<div><br></div><div>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.</div><div> </div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br> Duarte Miguel Paulo Molha <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div></div></div>
<br><div class="gmail_quote">On 1 July 2015 at 11:58, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Dear Duarte,<br>
<br>
The gene set in the GRCh37 database is a freeze from release 75.<br>
The variation and regulation annotation is updated when major data
sets are released.<br>
<br>
The gene set however is not updated given our major evidence sources
are updated to GRCh38.<br>
<br>
<br>
Regards,<br>
Magali<div><div class="h5"><br>
<br>
<div>On 01/07/2015 11:03, Duarte Molha
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">Dear developers
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>However I am finding inconsistencies in gene annotation
what have left me puzzled.</div>
<div><br>
</div>
<div>Take for example gene DNAAF5</div>
<div><br>
</div>
<div><a href="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=26013" target="_blank">http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=26013</a><br>
</div>
<div><br>
</div>
<div>If you query ensembl GRCh38 V80, the gene is there properly
annotated</div>
<div><br>
</div>
<div><a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000164818;r=7:726701-786475" target="_blank">http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000164818;r=7:726701-786475</a><br>
</div>
<div><br>
</div>
<div>However, on GRCh37 V80, the gene is still annotated with
the previous HGNC symbol HEATR2</div>
<div><br>
</div>
<div><a href="http://grch37.ensembl.org/Multi/Search/Results?q=HEATR2;site=ensembl;page=1" target="_blank">http://grch37.ensembl.org/Multi/Search/Results?q=HEATR2;site=ensembl;page=1</a><br>
</div>
<div><br>
</div>
<div>the ENSEMBL gene ID is the same in both cases : </div>
<div><br>
</div>
<div>ENSG00000164818</div>
<div><br>
</div>
<div>Is my thinking flawed? What is the reason for the
out-of-date gene annotation for this gene?</div>
<div><br>
</div>
<div>Many thanks</div>
<div><br>
</div>
<div>Duarte</div>
<div>
</div>
</div>
<br>
<fieldset></fieldset>
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</blockquote>
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