<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"><base href="x-msg://2552/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Beat<div>The missing information has now been added to the Ensembl gene 72 mart database on <a href="http://www.ensembl.org">www.ensembl.org</a>. Thanks again for reporting this.</div><div>Regards</div><div>Rhoda</div><div><br><div><div>On 19 Jun 2013, at 11:07, Beat Wolf <<a href="mailto:wolf@fryx.ch">wolf@fryx.ch</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="font-size: 9pt; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-family: Ubuntu; "><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Hi Rhoda,</div><p style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Thank you for your fast help!</div><p style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Regards</div><p style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Beat</div><p style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">On Wednesday 19 June 2013 10.49:23 Rhoda Kinsella wrote:<br></div><p style="white-space: pre-wrap; margin: 12px 40px; text-indent: 0px; ">Hi Beat</p><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">The Ensembl release 71 archive is now working. Apologies for the inconvenience.</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Regards</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Rhoda</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">On 19 Jun 2013, at 09:03, Rhoda Kinsella <<a href="mailto:rhoda@ebi.ac.uk"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">rhoda@ebi.ac.uk</span></a>> wrote:</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Hi Beat</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">We don't produce beta builds of future releases so i'm afraid there is no way to test your pipeline before a release is made live. We make every effort to inform our users about what changes to expect in a future release via our blog. We also extensively test and QC all our data and infrastructure before every release. </div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Unfortunately, as with any project dealing with large volumes of data, some issues do arise. Any issues that are discovered once we release are dealt with as swiftly as possible. I will email as soon as our archive website is back up for release 71 so that you can start your pipeline and we will aim to replace the missing data in the Ensembl gene mart as soon as possible.</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Kind regards</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Rhoda</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">On 19 Jun 2013, at 08:11, Beat Wolf <<a href="mailto:wolf@fryx.ch"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">wolf@fryx.ch</span></a>> wrote:</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><p style="white-space: pre-wrap; margin: 12px 40px 0px; text-indent: 0px; ">Hello Rhoda,</p><p style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">great to hear that the isse can be fixed today or tomorrow. As i said, quite a lot of code depends on it. If the archive can be fixed even earlier that would be even better.</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">For the future, are there any beta builds available of future releases? I would be happy to test my software before the official release to see if anything is broken. As this is the second time in a row a functionallity i depend on disapears, this would be a great way to avoid future problems.</div><p style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Best regards</div><p style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Beat Wolf</div><p style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">On Tuesday 18 June 2013 19.52:44 Rhoda Kinsella wrote:<br></div><p style="white-space: pre-wrap; margin: 12px 80px; text-indent: 0px; ">Hi Beat</p><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Thank you for reporting these issues. You are correct, we are missing the information you mentioned. We will try to rectify this as quickly as possible but it may take a day or two to generate and add to the live BioMart database. In the mean time, I will report the issue with the archive BioMart to our web team and hopefully you should be able to get the data from there until we reinstate the data. Apologies for any inconvenience caused and thanks again for reporting the bugs.</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Regards</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Rhoda</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">On 18 Jun 2013, at 19:13, Beat Wolf <<a href="mailto:wolf@fryx.ch"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">wolf@fryx.ch</span></a>> wrote:</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "><br></div><p style="white-space: pre-wrap; margin: 12px 120px 0px; text-indent: 0px; ">I also couldn't get the 71 archive to work. The url should be <a href="http://apr2013.archive.ensembl.org/biomart/"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://apr2013.archive.ensembl.org/biomart/</span></a></p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">right?</div><p style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">The changelog doesn't seem to indicate that the functionality i need was <span style="color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">removed. Also, in the changelog of </span><span style="font-size: 13px; color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">Ensembl Genes 72</span><span style="color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">there is this entry:</span></div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "><span style="font-size: 13px; color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">-Reinstated PolyPhen prediction and score filters and attributes</span></div><p style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">That should go into<span style="color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); "> </span><span style="font-size: 13px; color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">Ensembl Variation 72 i guess. Thank you for fixing that by the way, i reported that when 71 got online.</span></div><p style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "><span style="font-size: 13px; color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">I hope the functionality lost this time can be recovered before the 73 release in a few months... quite some code depends on it. If at least the archive would work that would be perfect.</span></div><p style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "><span style="font-size: 13px; color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">Thank you for your help</span></div><p style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "><span style="font-size: 13px; color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">Greetings</span></div><p style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "><span style="font-size: 13px; color: rgb(31, 28, 27); background-color: rgb(255, 255, 255); ">Beat Wolf</span></div><p style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; "> </p><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">On Tuesday 18 June 2013 19.38:37 Beat Wolf wrote:</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> Hello,</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> </div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> i have a problem. In the new biomart update that just got out, i can't find</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> a way to get the following information on an exon:</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> </div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> 5_utr_start</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> 5_utr_end</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> 3_utr_start</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> 3_utr_end</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> genomic_coding_end</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> cdna_coding_start</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> cds_start</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> cds_end</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> </div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> Did it move to some place else? Where can i find this information? Thank you</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> for your help!</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> </div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> Best regards</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> </div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> Beat Wolf</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> </div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> _______________________________________________</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> Dev mailing list <a href="mailto:Dev@ensembl.org"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">Dev@ensembl.org</span></a></div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> Posting guidelines and subscribe/unsubscribe info:</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> <a href="http://lists.ensembl.org/mailman/listinfo/dev"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://lists.ensembl.org/mailman/listinfo/dev</span></a> Ensembl Blog:</div><div style="white-space: pre-wrap; margin: 0px 120px; text-indent: 0px; ">> <a href="http://www.ensembl.info/"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://www.ensembl.info/</span></a></div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">Dev@ensembl.org</span></a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://lists.ensembl.org/mailman/listinfo/dev</span></a><br>Ensembl Blog: <a href="http://www.ensembl.info/"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://www.ensembl.info/</span></a></div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Rhoda Kinsella Ph.D.</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Ensembl Production Project Leader,</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">European Bioinformatics Institute (EMBL-EBI),</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Wellcome Trust Genome Campus,</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Hinxton,</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">Cambridge,</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; ">CB10 1SD</div><div style="white-space: pre-wrap; margin: 0px 80px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "><br><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">Dev@ensembl.org</span></a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://lists.ensembl.org/mailman/listinfo/dev</span></a><br>Ensembl Blog: <a href="http://www.ensembl.info/"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://www.ensembl.info/</span></a></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Rhoda Kinsella Ph.D.</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Ensembl Production Project Leader,</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">European Bioinformatics Institute (EMBL-EBI),</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Wellcome Trust Genome Campus,</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Hinxton,</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">Cambridge,</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">CB10 1SD</div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; ">_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">Dev@ensembl.org</span></a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://lists.ensembl.org/mailman/listinfo/dev</span></a><br>Ensembl Blog: <a href="http://www.ensembl.info/"><span style="text-decoration: underline; color: rgb(0, 87, 174); ">http://www.ensembl.info/</span></a><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Rhoda Kinsella Ph.D.</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Ensembl Production Project Leader,</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">European Bioinformatics Institute (EMBL-EBI),</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Wellcome Trust Genome Campus,</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Hinxton,</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">Cambridge,</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; ">CB10 1SD</div><div style="white-space: pre-wrap; margin: 0px 40px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br></div><div style="white-space: pre-wrap; margin: 0px; text-indent: 0px; "><br><br></div>_______________________________________________<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">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a></div></blockquote></div><br><div>
<div>Rhoda Kinsella Ph.D.</div><div>Ensembl Production Project Leader,</div><div>European Bioinformatics Institute (EMBL-EBI),</div><div>Wellcome Trust Genome Campus,</div><div>Hinxton,</div><div>Cambridge,</div><div>CB10 1SD</div><div><br></div><br class="Apple-interchange-newline">
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