<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Kiran,<div><br></div><div>You are right, the canonical transcript stable id is no longer available in BioMart as the changes made to the core schema (merging of the stable_id tables with their parent tables) made it impossible to add this data using the martbuilder tool. </div><div><br></div><div>Hope this helps,</div><div><br></div><div>Regards,</div><div>Thomas</div><div><br><div><div>On 11 Jul 2012, at 00:08, Kiran Mukhyala wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Thomas,<br>Thanks for the MTMP SQLs. <br><br>One more question - <br><br>The attribute canonical_transcript_stable_id has been missing from the Ensembl BioMart since e65. Is this attribute no longer supported?<br><br>-Kiran<br>
<br><div class="gmail_quote">On Mon, Jul 9, 2012 at 8:49 AM, Thomas Maurel <span dir="ltr"><<a href="mailto:maurel@ebi.ac.uk" target="_blank">maurel@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 style="word-wrap:break-word"><span style="background-color:transparent">Hi Kiran,</span><div><span style="background-color:transparent"><br></span></div><div><span style="background-color:transparent">I am sorry, I forgot to mention that we are now using these MTMP tables to help us build the ensembl, snp and functional genomics marts.</span></div>
<div><span style="background-color:transparent">You will have to create them before updating the mart schema.</span></div><div><span style="background-color:transparent"><br></span></div><div><span style="background-color:transparent">1) <span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">MTMP_probestuff_helper tables for the Ensembl mart: </span></span></div>
<div><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:transparent">This table need to be built for all the funcgen databases.</span></div>
<div><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none;background-color:transparent">You can use the iterate_tables.ksh script to iterate over multiple species databases and use the probestuff_helper.sql file to create this table in each database.</span></span></div>
<div><span style="background-color:transparent"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">2) </span><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Variation views for snp mart and Ensembl mart :</span></span></div>
<div><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none;background-color:transparent">You will need to run the variation_views.sql and the structural_variation.sql files for all the variation databases using the iterate_tables.ksh script.</span></span></div>
<div><span style="background-color:transparent"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">3) </span><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">eFG views for Functional genomics mart:</span></span></div>
<div><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:transparent">The functional genomics views and tables are created for all the funcgen databases </span><span style="line-height:17px">using the iterate_tables.ksh script.</span></div>
<div><span style="line-height:17px"><br></span></div><div><div style="text-align:left">Please find the<span style="background-color:transparent"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none"> sql files and the </span><span style="line-height:17px"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important">iterate_tables.ksh script</span></span><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none"> </span></span>at the following location: <span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none"> </span><a href="http://www.ebi.ac.uk/%7Emaurel/mart_prebuild_patches/" target="_blank">http://www.ebi.ac.uk/~maurel/mart_prebuild_patches/</a></div>
<div style="text-align:left"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none;background-color:transparent"><br>
</span></div><div style="text-align:left"><span style="font-variant:normal;letter-spacing:normal;line-height:17px;text-align:left;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none;background-color:transparent">Hope this helps,</span></div>
<div style="text-align:left"><span style="line-height:17px">Regards,</span></div><div style="text-align:left"><span style="line-height:17px;background-color:transparent">Thomas</span></div><div><div class="h5"><div><div>On 9 Jul 2012, at 06:40, Kiran Mukhyala wrote:</div>
<br><blockquote type="cite">Thanks Thomas for the mart builder files.<br><br>It looks like the Ensembl Mart building process has introduced usage of new tables like MTMP_transcript_variation and MTMP_probestuff_helper, etc.<br>
Would you please explain how to generate these tables? If its documented anywhere, please do point me to it.<br>
<br>Thanks,<br>-Kiran<br><br><div class="gmail_quote">On Sat, Jun 30, 2012 at 1:59 AM, Thomas Maurel <span dir="ltr"><<a href="mailto:maurel@ebi.ac.uk" target="_blank">maurel@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Kiran,<div><br></div><div>Please find the martbuilder xmls for release 67 at the following location : </div><div><a href="http://www.ebi.ac.uk/%7Emaurel/v67_xml/" target="_blank">http://www.ebi.ac.uk/~maurel/v67_xml/</a></div>
<div><br></div><div>Regards,</div><div>Thomas</div><div><br><div><div><div><div>On 29 Jun 2012, at 18:28, Kiran Mukhyala wrote:</div><br></div></div><blockquote type="cite"><div><div>Hi Rhoda,<br>
<br>
Could you please provide the e67 core, funcgen and variation martbuilder files?<br>
<br>
Thanks,<br>
-Kiran<br><br><div class="gmail_quote">On Wed, Jan 11, 2012 at 3:16 AM, Rhoda Kinsella <span dir="ltr"><<a href="mailto:rhoda@ebi.ac.uk" target="_blank">rhoda@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 style="word-wrap:break-word">Hi Kiran<div>I have provided the files you requested for release 64 and release 65 at the following location:</div><div><br></div><div><a href="http://www.ebi.ac.uk/%7Erhoda/v64_v65_xml/" target="_blank">http://www.ebi.ac.uk/~rhoda/v64_v65_xml/</a></div>
<div><br></div><div>Regards</div><div>Rhoda</div><div><br></div><div><div><div><br><div><div>On 9 Jan 2012, at 19:46, Kiran Mukhyala wrote:</div><br><blockquote type="cite">Hello Ensembl BioMart Team,<br> <br> Could you please provide the e64 core, funcgen and variation martbuilder files?<br>
<br> Thanks,<br> -Kiran<br><br><div class="gmail_quote">On Mon, May 9, 2011 at 5:38 AM, Rhoda Kinsella <span dir="ltr"><<a href="mailto:rhoda@ebi.ac.uk" target="_blank">rhoda@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">
Hi Kiran<br> You can find the files you need at:<br> <br> <a href="http://www.ebi.ac.uk/%7Erhoda/v62_xml/" target="_blank">http://www.ebi.ac.uk/~rhoda/<u></u>v62_xml/</a><br> <br> Regards<br> Rhoda<div><div><br> <br> On 7 May 2011, at 04:08, Kiran Mukhyala wrote:<br>
<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Hello,<br> <br> I'd like to upgrade my mart to e62, could you please provide the e62 core, funcgen and variation mart builder files?<br>
<br> Thanks,<br> -Kiran<br> </blockquote> <br></div></div><span><font color="#888888"> Rhoda Kinsella Ph.D.<br> Ensembl Bioinformatician,<br> European Bioinformatics Institute (EMBL-EBI),<br> Wellcome Trust Genome Campus,<br>
Hinxton<br> Cambridge CB10 1SD,<br> UK.<br> <br> </font></span></blockquote></div><br></blockquote></div><br></div></div><div> <div style="word-wrap:break-word"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:12px;white-space:normal;font-family:Helvetica;word-spacing:0px"><div style="word-wrap:break-word">
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<div>Rhoda Kinsella Ph.D.</div><div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Helvetica">Ensembl Production Project Leader,</div></div><div>
<div>European Bioinformatics Institute (EMBL-EBI),<br>Wellcome Trust Genome Campus, </div><div>Hinxton<br>Cambridge CB10 1SD,</div><div>UK.</div></div></div></span></div></span></div> </div><br></div></div></blockquote></div>
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<div>--</div><div>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<div><br>Wellcome Trust Genome Campus, Hinxton<br></div>Cambridge - CB10 1SD - UK</div>
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<div style="word-wrap:break-word"><div style="word-wrap:break-word"><div style="word-wrap:break-word"><div>--</div><div>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>
Wellcome Trust Genome Campus, Hinxton<br>Cambridge - CB10 1SD - UK</div></div></div></div>
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<div>--</div><div>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge - CB10 1SD - UK</div></div></span></div></span></div>
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