Proteomics Identifications Database logo

Proteomics Identifications Database

spacer
Username: Password:

Accessing the PRIDE BioMart Web Service

Introduction

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 help page (linked from the Help button at the top of the page) and a Mini Tutorial 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 REST (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).




Page Contents


Additional PRIDE BioMart Help

Web Service Location

The PRIDE BioMart web service at the EBI can be accessed at: http://www.ebi.ac.uk/pride/biomart/martservice

Using the BioMart Web Service

the BioMart web service is very well documented in the complete BioMart Documentation (PDF) that is available from http://www.biomart.org/install.html.

Please see the section on pages 50 - 52, entitled "Web services API".


spacer