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Hi there,</div>
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I have an issue when submitting requests to biomart on grch37. The requests take a very long time, to the point where its not really useable in some circumstances.</div>
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So one example is, getting the swissprot ID for all transcripts on a particular chromosome.</div>
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Here is the query:</div>
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<pre><?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Filter name = "with_uniprotswissprot" excluded = "0"/>
<Filter name = "chromosome_name" value = "16"/>
<Attribute name = "uniprotswissprot" />
<Attribute name = "ensembl_transcript_id" />
<Attribute name = "ensembl_gene_id" />
<Attribute name = "ensembl_gene_id_version" />
</Dataset>
</Query></pre>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">here is the grch37 url for this query:</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"> </span><a href="http://grch37.ensembl.org/biomart/martservice?query=%3C%3Fxml+version%3D%221.0%22+encoding%3D%22UTF-8%22%3F%3E%3C%21DOCTYPE+Query%3E%3CQuery++virtualSchemaName+%3D+%22default%22+formatter+%3D+%22TSV%22+header+%3D+%220%22+uniqueRows+%3D+%220%22+count+%3D+%22%22+datasetConfigVersion+%3D+%220.6%22+%3E%3CDataset+name+%3D+%22hsapiens_gene_ensembl%22+interface+%3D+%22default%22+%3E%3CFilter+name+%3D+%22chromosome_name%22+value+%3D+%2216%22%2F%3E%3CFilter+name+%3D+%22with_uniprotswissprot%22+excluded+%3D+%220%22%2F%3E%3CAttribute+name+%3D+%22ensembl_gene_id%22+%2F%3E%3CAttribute+name+%3D+%22ensembl_transcript_id%22+%2F%3E%3CAttribute+name+%3D+%22uniprotswissprot%22+%2F%3E%3C%2FDataset%3E%3C%2FQuery%3E" id="LPlnk702620" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">http://grch37.ensembl.org/biomart/martservice?query=%3C%3Fxml+version%3D%221.0%22+encoding%3D%22UTF-8%22%3F%3E%3C%21DOCTYPE+Query%3E%3CQuery++virtualSchemaName+%3D+%22default%22+formatter+%3D+%22TSV%22+header+%3D+%220%22+uniqueRows+%3D+%220%22+count+%3D+%22%22+datasetConfigVersion+%3D+%220.6%22+%3E%3CDataset+name+%3D+%22hsapiens_gene_ensembl%22+interface+%3D+%22default%22+%3E%3CFilter+name+%3D+%22chromosome_name%22+value+%3D+%2216%22%2F%3E%3CFilter+name+%3D+%22with_uniprotswissprot%22+excluded+%3D+%220%22%2F%3E%3CAttribute+name+%3D+%22ensembl_gene_id%22+%2F%3E%3CAttribute+name+%3D+%22ensembl_transcript_id%22+%2F%3E%3CAttribute+name+%3D+%22uniprotswissprot%22+%2F%3E%3C%2FDataset%3E%3C%2FQuery%3E</a><br>
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and here the one using grch38:</div>
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<a href="http://ensembl.org/biomart/martservice?query=%3C%3Fxml+version%3D%221.0%22+encoding%3D%22UTF-8%22%3F%3E%3C%21DOCTYPE+Query%3E%3CQuery++virtualSchemaName+%3D+%22default%22+formatter+%3D+%22TSV%22+header+%3D+%220%22+uniqueRows+%3D+%220%22+count+%3D+%22%22+datasetConfigVersion+%3D+%220.6%22+%3E%3CDataset+name+%3D+%22hsapiens_gene_ensembl%22+interface+%3D+%22default%22+%3E%3CFilter+name+%3D+%22chromosome_name%22+value+%3D+%2216%22%2F%3E%3CFilter+name+%3D+%22with_uniprotswissprot%22+excluded+%3D+%220%22%2F%3E%3CAttribute+name+%3D+%22ensembl_gene_id%22+%2F%3E%3CAttribute+name+%3D+%22ensembl_transcript_id%22+%2F%3E%3CAttribute+name+%3D+%22uniprotswissprot%22+%2F%3E%3C%2FDataset%3E%3C%2FQuery%3E" id="LPlnk832592">http://ensembl.org/biomart/martservice?query=%3C%3Fxml+version%3D%221.0%22+encoding%3D%22UTF-8%22%3F%3E%3C%21DOCTYPE+Query%3E%3CQuery++virtualSchemaName+%3D+%22default%22+formatter+%3D+%22TSV%22+header+%3D+%220%22+uniqueRows+%3D+%220%22+count+%3D+%22%22+datasetConfigVersion+%3D+%220.6%22+%3E%3CDataset+name+%3D+%22hsapiens_gene_ensembl%22+interface+%3D+%22default%22+%3E%3CFilter+name+%3D+%22chromosome_name%22+value+%3D+%2216%22%2F%3E%3CFilter+name+%3D+%22with_uniprotswissprot%22+excluded+%3D+%220%22%2F%3E%3CAttribute+name+%3D+%22ensembl_gene_id%22+%2F%3E%3CAttribute+name+%3D+%22ensembl_transcript_id%22+%2F%3E%3CAttribute+name+%3D+%22uniprotswissprot%22+%2F%3E%3C%2FDataset%3E%3C%2FQuery%3E</a><br>
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The difference is massive, 4 seconds (GRCH38) vs 130 seconds (GRCH37) (if it doesn't time out).</div>
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I'm doing something wrong? Is there any fix for this problem?</div>
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Kind regards</div>
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Beat Wolf</div>
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<p style="margin-top:0px; margin-bottom:0px"><b><span style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont">Dr Beat Wolf, PhD ▪ Assistant Professor ▪ Member of iCoSys Institute<br>
</span></b><span style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont">University of Applied Sciences and Arts Western Switzerland ▪ Pérolles 80 ▪ CH-1700 Fribourg<br>
Member of University of Applied Sciences of Western Switzerland<br>
</span><span lang="FR" style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont; color:blue"><a href="https://eia-fr.ch/" target="_blank" rel="noopener noreferrer" style="margin:0px"><span lang="EN-GB" style="margin:0px">https://www.heia-fr.ch</span></a></span><span style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont; color:blue"> </span><span style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont">▪ <a href="http://humantech.institute/" target="_blank" rel="noopener noreferrer" style="margin:0px"></a><a href="https://icosys.ch/" target="_blank" rel="noopener noreferrer" style="margin:0px">https://icosys.ch/</a></span></p>
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