[ensembl-dev] Querying BioMart with XML

Jerry Vinokurov jvinokurov at flatironinstitute.org
Tue Apr 7 03:43:56 BST 2020

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 Has something changed which renders the upstream_flank filter no longer
valid?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?

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