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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">How does Biomart handle such issues when stable id may not be unique?<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>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><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>Luke Goodsell<br>
<b>Sent:</b> 21 July, 2015 10:53 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] (v80) "RefSeq_gene_name" DBLink missing for ACKR1?<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Fergal,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">That is indeed very helpful.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Many thanks,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Luke<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><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"">
<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Fergal<br>
<b>Sent:</b> 21 July 2015 15:20<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] (v80) "RefSeq_gene_name" DBLink missing for ACKR1?<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">Hi Luke,<o:p></o:p></span></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">The quick answer is to change your script to do the following:<o:p></o:p></span></p>
</div>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
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<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">foreach my $query ('NM_002036.3', 'NM_001122951.2') {<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> print "q: " . $query . "\n";<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> my $transcripts = $external_transcript_adaptor->fetch_all_versions_by_stable_id($query);<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> foreach my $transcript (@{$transcripts}) {<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> print " t: " . $transcript->stable_id . "\n";<o:p></o:p></span></p>
</div>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> foreach my $dbe (<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> @{ $transcript->get_Gene->get_all_DBEntries() },<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> @{ $transcript->get_all_DBEntries() },<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> @{ $transcript->get_Gene->get_all_DBLinks() },<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> @{ $transcript->get_all_DBLinks() }<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> ) {<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> printf " XREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();<o:p></o:p></span></p>
</div>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> }<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"> }<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">}<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">The issue you ran into is because of the assumption that stable ids are unique in the otherfeatures db (as they are in the core db). This is not the case. The reason is that the otherfeatures
db has external gene sets and we do not really create stable ids for the genes and transcripts in it. For example for refseq genes we take things like the NM accession and make it the stable id. This does not mean it’s unique, an NM corresponds to an mRNA
that may map to multiple places in the genome. Refseq often map these mRNAs in multiple places and thus you get duplicate stable ids. In addition, there are actually two refseq genesets in the db (‘refseq_human_import’, which is a curated set closely linked
to the CCDS set, and ‘refseq_import’, which is the full public annotation from the gff3 file on the refseq ftp site), leading to duplicate ids between the transcripts in each set.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">The problem occurs when you request a transcript by stable_id. Currently the API returns a single transcript as it assumes that stable ids are unique. In e80 the public set, ‘refseq_import’, has
no xrefs (these are present in e81 though). The ‘fetch_by_stable_id’ call was returning only the transcript from the public set and thus no xrefs were showing. In e81 you should get xrefs back from both so there isn’t really a problem. For e80 the above code,
which uses ‘fetch_all_versions_by_stable_id’ will give back all transcripts and thus you will be able to get the xrefs from the curated refseq set.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">It is worth keeping in mind that mRNAs may be mapped to multiple places, that stable ids are not unique and that there are two different refseq geneset when working with otherfeatures db. In future
we are considering the removal of the curated set as it is confusing and is a subset of the public set. For the moment, if you only want to work with one of the two sets you can use fetch_all_by_logic_name('refseq_import’) or fetch_all_by_logic_name('refseq_human_import’),
though you’ll need to move to e81 if you want the xrefs for the ‘refseq_import’ set.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">Hope this helps,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">Fergal.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB">On 21 Jul 2015, at 10:15, Luke Goodsell <<a href="mailto:Luke.Goodsell@ogt.com">Luke.Goodsell@ogt.com</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<span lang="EN-GB"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi EnsEMBL Devs,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Querying an external transcript adaptor for ‘NM_002036.3’ or ‘NM_001122951.2’ (transcripts of ACKR1/DARC) and calling get_all_DBEntries
or get_all_DBLinks on either the returned transcript or the transcripts’ gene objects returns nothing in v80, but in v75 it returns the expected RefSeq_gene_name links.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Have the DBLinks/Entries been intentionally removed, is this in error, or have I missed something?<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Example code below.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Kind regards,<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Luke<o:p></o:p></span></p>
</div>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#!/usr/bin/perl<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">use strict;<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">use warnings;<o:p></o:p></span></p>
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<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">use Bio::EnsEMBL::Registry;<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">my $registry = 'Bio::EnsEMBL::Registry';<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">$registry->load_registry_from_db(<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> -host => '<a href="http://ensembldb.ensembl.org/"><span style="color:purple">ensembldb.ensembl.org</span></a>',<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> -user => 'anonymous',<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">);<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">my $external_transcript_adaptor = $registry->get_adaptor( 'Human', 'otherfeatures', 'Transcript' );<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">foreach my $query ('NM_002036.3', 'NM_001122951.2') {<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> print "q: " . $query . "\n";<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> my $transcript = $external_transcript_adaptor->fetch_by_stable_id($query);<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> print " t: " . $transcript->stable_id . "\n";<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> foreach my $dbe (<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> @{ $transcript->get_Gene->get_all_DBEntries() },<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> @{ $transcript->get_all_DBEntries() },<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> @{ $transcript->get_Gene->get_all_DBLinks() },<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> @{ $transcript->get_all_DBLinks() }<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> ) {<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> printf " XREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();<o:p></o:p></span></p>
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