BioMart

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Version 0.7 MartService

RESTful Access

Querying BioMart

To submit a query using our webservices generate an XML document conforming to our Query XML syntax. This can be achieved simply by building up your query using MartView and hitting the XML button. This XML should be posted to /martservice attached to a single parameter of query. For example you could either:

save your query as Query.xml and then POST this using the webExample.pl script in our biomart-perl/scripts installation.
submit using wget: wget -O results.txt '/biomart/martservice?query=MY_XML' replacing MY_XML with the XML obtained above, first removing any new lines.

Retrieving Meta Data

to retrieve registry information: /biomart/martservice?type=registry
to retrieve datasets available for a mart: /biomart/martservice?type=datasets&mart=ensembl
to retrieve attributes available for a dataset: /biomart/martservice?type=attributes&dataset=oanatinus_gene_ensembl
to retrieve filters available for a dataset: /biomart/martservice?type=filters&dataset=oanatinus_gene_ensembl
to retrieve configuration for a dataset: /biomart/martservice?type=configuration&dataset=oanatinus_gene_ensembl

SOAP Access

The SOAP based access is functionally equivalent to the REST style access described above. For description on BioMart SOAP based Web Service (MartServiceSoap), see:

MartServiceSoap Endpoint (for SOAP based access only): /biomart/martsoap
MartServiceSoap WSDL: /biomart/martwsdl
MartServiceSoap XSD: /biomart/martxsd