<div dir="ltr">Dear Ed,<div><br></div><div style>I am afraid this is not something that can be changed in Ensembl. As Magali explained, Ensembl retrieves the gene names from UniProt and they have removed the names in question. So, if you want to enquire whether these gene names can be reinstated, you have to contact UniProt at <font color="#000000"><a href="mailto:help@uniprot.org" style="text-decoration:none;font-family:sans-serif;line-height:26px">help@uniprot.org</a>. Unless the removal is a bug, I assume they must have had a valid reason to do this, though.</font></div>
<div style><br></div><div style>I appreciate that this possibly is not the answer you'd like to hear, but these kind of things have to be fixed at the source, otherwise it would become one big uncoordinated mess. I hope this makes sense.</div>
<div style><br></div><div style>With kind regards,</div><div style>Bert</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jun 24, 2013 at 6:35 PM, Ed <span dir="ltr"><<a href="mailto:gray_ed@hotmail.com" target="_blank">gray_ed@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="white" lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><div><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> Ed [mailto:<a href="mailto:gray_ed@hotmail.com" target="_blank">gray_ed@hotmail.com</a>] <br>
<b>Sent:</b> Monday, June 24, 2013 9:35 AM<br><b>To:</b> 'Magali'; '<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>'<br><b>Subject:</b> RE: [ensembl-dev] Lesser annotation names in sscrofa in V72??<u></u><u></u></span></p>
</div></div><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Dear Magali,<u></u><u></u></span></p><p class="MsoNormal">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thank you so much for responding. Your answer seems reasonable.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I guess I was a little taken aback that a number of gene names removed were, I believe, the preferred HUGO name for the gene.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Take for instance C4A. By changing it to C4, it creates some confusion in the ensembl comparative genomics section on what is mapped. C4B seems clearly mapped to C4B, while it looks like what is now C4 (used to be C4A) maps to both C4A and C4B.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Another example is PDX-1, an important Gene for sure. Recent news stories (<a href="http://www.telegraph.co.uk/science/science-news/8584443/Pigs-could-grow-human-organs-in-stem-cell-breakthrough.html" target="_blank">http://www.telegraph.co.uk/science/science-news/8584443/Pigs-could-grow-human-organs-in-stem-cell-breakthrough.html</a> ) are based on work on the PDX-1 gene. While Hugo has the gene listed as PDX1, PDX-1 is an approved synonym and many of the papers in academic journals use (and still use) PDX-1.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Those two were notable only with 30 second review of the eliminated names from a single researcher.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thank you for your consideration and explanation, however, I’d suggest you may want to reconsider.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best wishes,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Ed<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><div><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> Magali [<a href="mailto:mr6@ebi.ac.uk" target="_blank">mailto:mr6@ebi.ac.uk</a>] <br>
<b>Sent:</b> Friday, June 21, 2013 4:57 AM<br><b>To:</b> Ensembl developers list<br><b>Cc:</b> Ed<br><b>Subject:</b> Re: [ensembl-dev] Lesser annotation names in sscrofa in V72??<u></u><u></u></span></p></div></div><p class="MsoNormal">
<u></u> <u></u></p><p class="MsoNormal" style="margin-bottom:12.0pt">Hi Ed,<br><br>In release 72, we updated the external references for pig.<br><br>This means we use the latest sets of data from external sources, like Uniprot for example.<br>
A number of gene names assigned in Uniprot have been removed in the latest set used in 72, causing the drop you notice.<br><br>The number of assigned external references is still comparable or higher than in 71, but no trustworthy gene name was available for these annotations.<br>
<br>See <a href="http://www.uniprot.org/uniprot/F1SF30?version=12&version=13" target="_blank">http://www.uniprot.org/uniprot/F1SF30?version=12&version=13</a> for example.<br>Uniprot entry F1SF30 in pig has had its name remove between versions 12 and 13.<br>
So we still assign that uniprot entry to ensembl gene ENSSSCG00000015625, but we cannot deduce a gene name from it.<br><br><br>Hope that helps,<br>Magali<u></u><u></u></p><div><p class="MsoNormal">On 20/06/13 19:27, Ed wrote:<u></u><u></u></p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"><pre>Dear Ensembl developers,<u></u><u></u></pre><pre><u></u> <u></u></pre><pre>We extract ensembl annotations for sus scrofa 10.2 and load them into a<u></u><u></u></pre>
<pre>GBrowse database. When we updated to ensembl V71, there were a few hundred<u></u><u></u></pre><pre>additional annotations, a generally expected result.<u></u><u></u></pre><pre><u></u> <u></u></pre><pre>A test load of ensembl 72 yielded an unexpected result, fewer annotations.<u></u><u></u></pre>
<pre>The 1241 'names' I believe were removed are listed below.<u></u><u></u></pre><pre><u></u> <u></u></pre><pre>I normally expect a few additional annotations and seeing so many removed<u></u><u></u></pre><pre>was a little unsettling.<u></u><u></u></pre>
<pre><u></u> <u></u></pre><pre>Any ideas or comments if this is a bug or a feature?<u></u><u></u></pre><pre><u></u> <u></u></pre><pre>Ed<u></u><u></u></pre></blockquote></div></div><br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Bert Overduin, Ph.D.<br>Vertebrate Genomics Team<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>
United Kingdom<br><br><a href="http://www.ebi.ac.uk/~bert" target="_blank">http://www.ebi.ac.uk/~bert</a><div><p style="margin-bottom:0in;margin-bottom:.0001pt"><font face="Arial"></font></p><p style="margin-bottom:0in;margin-bottom:.0001pt">
<font face="Arial">
</font></p><p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><font face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:black">Ensembl
browser: <a href="http://www.ensembl.org/" target="_blank"><span style="color:blue">http://www.ensembl.org</span></a></span><span style="font-size:10.0pt;font-family:Arial"></span></font></p><font face="Arial">
<p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:Arial;color:black">Mailing
lists: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://www.ensembl.org/info/about/contact/mailing.html" target="_blank"><span style="color:blue">http://www.ensembl.org/info/about/contact/mailing.html</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"></span></p>
<p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:Arial;color:black">Blog: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://www.ensembl.info/" target="_blank"><span style="color:blue">http://www.ensembl.info</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"></span></p>
<p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:Arial;color:black">YouTube: </span><span style="font-size:10.0pt;font-family:Arial;color:#000099"><a href="http://www.youtube.com/user/EnsemblHelpdesk" target="_blank"><span style="color:blue">http://www.youtube.com/user/EnsemblHelpdesk</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"><br>
Facebook: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://www.facebook.com/Ensembl.org" target="_blank"><span style="color:blue">http://www.facebook.com/Ensembl.org</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"><br>
Twitter: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://twitter.com/Ensembl" target="_blank"><span style="color:blue">http://twitter.com/Ensembl</span></a> </span><span style="font-size:10.0pt;font-family:Arial;color:black"></span></p>
<p></p>
</font><p></p><font face="Arial">
</font><p></p>
</div>
</div></div>