Accessing the PRIDE BioMart Web Service
BioMart is developed jointly by the
European Bioinformatics Institute (EBI)
and Cold Spring Harbor Laboratory (CSHL).
For quick help with the BioMart interface, linked both from here and directly from the
PRIDE BioMart page itself, you
will find a short
(linked from the Help button at the top of the page) and a
describing how to build and run a query on any BioMart.
(Install Adobe Flash to view this tutorial)
BioMart allows you to retrieve public PRIDE data from a query-optimised data warehouse that is synchronized with the
main PRIDE database each week. The BioMart web service allows you to build simple or complex
queries, with total control over both how the data is filtered (to restrict which records are included) and
also which attributes (equivalent to columns in a spreadsheet) are included in the results.
The BioMart web service is a simple
(Representational State Transfer) web service
that involves building an HTTP request including an XML file that encodes the filters and attributes
of the request.
The response is in the form of tab-delimited plain text file. The number and order of the columns in this file
are specified in the XML file that forms the request (the selected attributes).
Web Service Location
The PRIDE BioMart web service at the EBI can be accessed at:
Using the BioMart Web Service
the BioMart web service is very well documented in the
complete BioMart Documentation
that is available from
Please see the section on pages 50 - 52, entitled "Web services API".