On 12 Mar 2007, at 03:48, Julian Catchen wrote:
Hello,
Does anyone have any example XML queries they are using to poll the
Ensembl biomart interface? I have gotten some simple examples working
that pull down lists of ensembl IDs by using examples from the
documentation. However, I can't seem to find any examples of how to
query for FASTA formatted cDNA sequences or translations. Also, I
can't find any documentation of how to request gzipped data.
Hi Julian,
please go to www.biomart.org/biomart/martview, create your favourite
query using MView and click
XML button. This will give you the exact xml format required for your
web service query. In principle anything
that you can do with MView you should be also able to do with
webservice XML. If not, that we need
to fix it.
In order to invoke a formatter you simply need to add
'formatter="FASTA' to your xml query.
For example the below query will give you peptides from chromosome 22
in FASTA format:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" Header = "1" count = ""
softwareVersion = "0.5" formatter="FASTA" >
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Attribute name = "peptide" />
<Attribute name = "str_chrom_name" />
<Attribute name = "gene_stable_id" />
<Attribute name = "biotype" />
<Filter name = "chromosome_name" value = "22"/>
</Dataset>
</Query>
you can run this query using the webExample.pl script:
http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/scripts/
webExample.pl?view=markup
I used to have all of these automated through simple URL GET queries
that no longer seem to work with Ensembl post version 41.
URL GET query still work but the format has changed. We have not yet
documented it properly.
I am cc-ing your email to mart-dev so someone from there will send you
a few examples
hope that helps,
a.
Any pointers to examples or documentation for XML queries would be
appreciated.
Thanks,
julian
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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