Introducing the PRIDE Archive RESTful web services.

Florian Reisinger,Juan Antonio Vizcaíno,Henning Hermjakob,Tobias Ternent,Noemi Del-Toro

doi:10.1093/nar/gkv382

Florian Reisinger, Juan Antonio Vizcaíno + Show 3 more

Open Access

https://doi.org/10.1093/nar/gkv382

Copy DOI

Abstract

The PRIDE (PRoteomics IDEntifications) database is one of the world-leading public repositories of mass spectrometry (MS)-based proteomics data and it is a founding member of the ProteomeXchange Consortium of proteomics resources. In the original PRIDE database system, users could access data programmatically by accessing the web services provided by the PRIDE BioMart interface. New REST (REpresentational State Transfer) web services have been developed to serve the most popular functionality provided by BioMart (now discontinued due to data scalability issues) and address the data access requirements of the newly developed PRIDE Archive. Using the API (Application Programming Interface) it is now possible to programmatically query for and retrieve peptide and protein identifications, project and assay metadata and the originally submitted files. Searching and filtering is also possible by metadata information, such as sample details (e.g. species and tissues), instrumentation (mass spectrometer), keywords and other provided annotations. The PRIDE Archive web services were first made available in April 2014. The API has already been adopted by a few applications and standalone tools such as PeptideShaker, PRIDE Inspector, the Unipept web application and the Python-based BioServices package. This application is free and open to all users with no login requirement and can be accessed at http://www.ebi.ac.uk/pride/ws/archive/.

Highlights

Mass spectrometry (MS)-based proteomics analysis techniques are increasingly used in the life sciences
Within the Consortium, PRIDE fully supports the storage of tandem MS data, data coming from other proteomics workflows can be stored
Among the other major public proteomics data resources, GPMDB [10] has REST-style web services available [11] whereas PeptideAtlas [12] does not provide this functionality. In this manuscript we describe the main features of these new web services, which can be freely accessed at http:// www.ebi.ac.uk/pride/ws/archive/

Summary

Introduction

Mass spectrometry (MS)-based proteomics analysis techniques are increasingly used in the life sciences. RESTful web services have been developed to replace the most popular functionality available in the BioMart and to serve the data access requirements of the newly developed PRIDE Archive.

Results

Conclusion