On 22 Nov 2006, at 06:40, Twigger Simon wrote:
Hi there,
Im working on the martservice to use our various biomarts as data
sources for other scripts. If I was using the Ensembl Mouse web
interface in the Gene - ID List limit section I would enter a Uniprot
Accession (eg. P63101) and select attributes for UniProt/Swiss-Prot ID
and UniProt/Swiss-Prot Accession to get the output that I want.
I'm trying to mimic this call via the webservice route and I'm having
difficulties formulating the XML query, specifically I'm not sure how
to enter the list of IDs into the XML query. Here's what I have
currently but the id_list_limit_filters_list filter isnt being
recognized so I think Im doing something wrong in my attempt to enter
the various IDs that I want results for.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" count = "0" >
<Dataset name = "mmusculus_gene_ensembl">
<Attribute name = "uniprot_swissprot" />
<Attribute name = "uniprot_swissprot_accession" />
<Filter name = "id_list_limit_filters_list" value =
"P63101"/>
<Filter name = "id_list_limit_filters" value =
"uniprot_swissprot_accession"/>
</Dataset>
</Query>
Can anyone tell me how I should encode the list of uniprot accessions
in the XML document so they get submitted as the
uniprot_swissprot_accession IDs that get used in the filter?
Hi Simon,
you need to use the actual filter name and the values are the
identifiers (comma separated) eg
<Filter name = "uniprot_swissprot_accession" value = "P63101,Q23444"/>
see if this works
a.
Cheers,
Simon.
--
Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595
AIM/iChat: simontatmcw
------------------------------------------------------------------------
-------
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
------------------------------------------------------------------------
-------
