[ensembl-dev] Querying BioMart with XML

Thomas Maurel maurel at ebi.ac.uk
Tue Apr 7 13:55:55 BST 2020

Dear Jerry,

I am happy to report that your mart xml query is still valid and working. I am afraid that we have experienced some intermittent issues with BioMart recently so I am sorry about this. Please note that our website is still working with reduced functionality, please see more information here: http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/ <http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/>.

Hope this helps,
Kind Regards,

> On 7 Apr 2020, at 03:43, Jerry Vinokurov <jvinokurov at flatironinstitute.org> wrote:
> Hello all,
> I am a software engineer at the Flatiron Institute, where I inherited some code from a predecessor that obtained data from BioMart. From the code, it appears that the following query was being sent in XML format appended to the URL as a query parameter:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query  virtualSchemaName = "default" formatter = "FASTA" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
>   <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
>     <Filter name = "upstream_flank" value = "1000"/>
>     <Filter name = "with_entrezgene" excluded = "0"/>
>     <Attribute name = "ensembl_gene_id" />
>     <Attribute name = "gene_flank" />
>     <Attribute name = "ensembl_transcript_id" />
>   </Dataset>
>   </Query>
> This is a verbatim copy/paste from the code that was used by the person working on the project before me. Apparently at some point it worked, and I had even managed to download some data using this query, but lately it has been failing for me with the following error:
> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND
> Has something changed which renders the upstream_flank filter no longer valid? Could someone offer some guidance for what I should do to replicate the expected results of the query?
> thanks,
> Jerry
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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

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