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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks Burt, I’m kind of a detailed guy who looks at specific situations when I manage data. So while your explanation sounds reasonable, lets look at the first of the two examples I chose: C4A<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Vega: Search Vega for C4, and you get nothing related to C4A. Searches for C4A and C4B and you get useful information. Specifically C4A OTTSUSG00000001346 .<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Uniprot: Searching for C4: After leafing through pages of tobacco and tomatoes, I found F1RQW2 (F1RQW2_PIG) that says “The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.” Search for C4A, leads to the various C4As in mostly mammals, and I find A5A8W8 (A5A8W8_PIG) with no Cautions under the General annotation (Comments). So clearly Uniprot has them both, one from a curated source and one from ensembl’s preliminary predictions.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Search for C4 in the Pig on Ensembl.org, you get 4 genes, one of which is 4 Genes match your query ('C4') in Pig ENSSSCG00000001427 that maps to C4A OTTSUSG00000001346 in Vega.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Search for C4A in ensemble.org, and you get <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Results Summary - Your search of Pig with 'C4A' returned no results.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Taken together, it would seem your predicted protein “C4” made it to Uniprot and then somehow that allowed you to think deleting the name C4A was in order.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Finally, just look at ncbi for C4 and C4A: <a href="http://www.ncbi.nlm.nih.gov/gquery/?term=C4A">http://www.ncbi.nlm.nih.gov/gquery/?term=C4A</a> vs <a href="http://www.ncbi.nlm.nih.gov/gquery/?term=C4">http://www.ncbi.nlm.nih.gov/gquery/?term=C4</a> . Which is the correct name to use??<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>So while I understand, appreciate and support your desire to make sense of the big uncoordinated mess we all have called gene annotations. However, in this case it seems that there is something not entirely productive with your approach since it seems to add more confusion.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Also since C4A is a valid protein and apparently gene name in Uniprot, I don’t think I can report a bug to them. Thank you for your attention and assistance!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ed<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Bert Overduin<br><b>Sent:</b> Monday, June 24, 2013 1:48 PM<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] RE Lesser annotation names in sscrofa in V72??<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Dear Ed,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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 <span style='color:black'><a href="mailto:help@uniprot.org"><span style='font-family:"Arial","sans-serif";text-decoration:none'>help@uniprot.org</span></a>. Unless the removal is a bug, I assume they must have had a valid reason to do this, though.</span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>With kind regards,<o:p></o:p></p></div><div><p class=MsoNormal>Bert<o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Mon, Jun 24, 2013 at 6:35 PM, Ed <<a href="mailto:gray_ed@hotmail.com" target="_blank">gray_ed@hotmail.com</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> 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??</span><o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dear Magali,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thank you so much for responding. Your answer seems reasonable.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best wishes,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ed</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> 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??</span><o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;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<o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On 20/06/13 19:27, Ed wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Dear Ensembl developers,<o:p></o:p></pre><pre> <o:p></o:p></pre><pre>We extract ensembl annotations for sus scrofa 10.2 and load them into a<o:p></o:p></pre><pre>GBrowse database. When we updated to ensembl V71, there were a few hundred<o:p></o:p></pre><pre>additional annotations, a generally expected result.<o:p></o:p></pre><pre> <o:p></o:p></pre><pre>A test load of ensembl 72 yielded an unexpected result, fewer annotations.<o:p></o:p></pre><pre>The 1241 'names' I believe were removed are listed below.<o:p></o:p></pre><pre> <o:p></o:p></pre><pre>I normally expect a few additional annotations and seeing so many removed<o:p></o:p></pre><pre>was a little unsettling.<o:p></o:p></pre><pre> <o:p></o:p></pre><pre>Any ideas or comments if this is a bug or a feature?<o:p></o:p></pre><pre> <o:p></o:p></pre><pre>Ed<o:p></o:p></pre></blockquote></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><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><o:p></o:p></p></div><p class=MsoNormal><br><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>-- <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><o:p></o:p></p><div><p style='mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Ensembl browser: <a href="http://www.ensembl.org/" target="_blank">http://www.ensembl.org</a></span><o:p></o:p></p><p style='mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Mailing lists: </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:blue'><a href="http://www.ensembl.org/info/about/contact/mailing.html" target="_blank">http://www.ensembl.org/info/about/contact/mailing.html</a></span><span style='font-family:"Arial","sans-serif"'><o:p></o:p></span></p><p style='mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>Blog: </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:blue'><a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info</a></span><span style='font-family:"Arial","sans-serif"'><o:p></o:p></span></p><p style='mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'>YouTube: </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#000099'><a href="http://www.youtube.com/user/EnsemblHelpdesk" target="_blank">http://www.youtube.com/user/EnsemblHelpdesk</a></span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><br>Facebook: </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:blue'><a href="http://www.facebook.com/Ensembl.org" target="_blank">http://www.facebook.com/Ensembl.org</a></span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black'><br>Twitter: </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:blue'><a href="http://twitter.com/Ensembl" target="_blank">http://twitter.com/Ensembl</a> </span><span style='font-family:"Arial","sans-serif"'><o:p></o:p></span></p></div></div></div></div></body></html>