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PRIDE, An Open Source Database of Protein Identifications

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The European Bioinformatics Institute, (EBI), and Flanders Interuniversity Institute for Biotechnology (VIB) -Ghent University have launched the PRoteomics IDEntifications database (PRIDE).

PRIDE is designed to allow scientists to exploit the growing mass of information on how the body's complement of proteins is altered in many disease states, paving the way towards predictive and diagnostic methods in medicine. While an individual's genome remains the same from one moment to the next, proteomes are extremely dynamic.

The high-throughput identification of proteins is gathering momentum, until recently there was no straightforward means of sharing or comparing the results. "Proteomics labs were publishing their protein identifications," explains Henning Hermjakob, leader of the EBI's Proteomics Services Team. He adds, "But they had no guidelines as what information should be captured or how the information should be formatted."

Further he said, "The proteomics community rapidly realized that researchers would only be able to exploit the results of their endeavours if they had a central repository that would allow them to make their results publicly available using agreed data standards."

"Once everyone makes their data available in the same format, it becomes possible to use powerful computational techniques to analyse the data" continues Joël Vanderkerckhove from VIB-Ghent University. He adds, "It then becomes trivial to analyse protein identifications from many different sources, or compare the proteins produced by a particular tissue under different conditions."

According to EBI, PRIDE is closely linked to the Human Proteomics Organization's Proteomics Standards Initiative and will allow users to transfer data using the standards that are currently being developed as part of PSI. EB have said that, large sets of data already available in PRIDE include the results of the Human Proteome Organization's Plasma Proteome Project, and a human platelet proteome set published by Ghent University.

The results of other international collaborations, such as the Human Proteome Organization's Liver Proteome Project, will follow as they are published.

PRIDE is an open source: the PRIDE database, source code, data, and support tools are freely available for web access or download and local installation."We hope that proteomics researchers and publishing companies will adopt PRIDE as the method of choice for making proteomics data freely available to and exploitable by the proteomics community" concludes Henning Hermjakob. "We also hope to collaborate with other providers of protein identification data to maximize the availability of comprehensive and up-to-date protein identification information"