EBI and Ghent University launch PRIDE: an open source database of protein identifications
The European Bioinformatics Institute and Flanders Interuniversity Institute for Biotechnology (VIB)–Ghent University have launched the PRoteomics IDEntifications database (PRIDE; www.ebi.ac.uk/pride). PRIDE allows researchers who work in the field of proteomics – the large-scale study of proteins – to share information much more readily than was previously possible. This will allow them 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 new predictive and diagnostic methods in medicine.
Proteomics is the identification and characterization of all the proteins produced by a particular type of cell, tissue or organism under certain conditions. While an individual’s genome remains the same from one moment to the next, proteomes are extremely dynamic. For example, the set of proteins produced by your liver will change in response to eating a meal, and a healthy liver produces a different set of proteins than a diseased liver. Proteomics therefore has great potential, not only for helping us to understand how our environment affects the healthy body, but also for understanding disease mechanisms and developing new ways of diagnosing disease. Large international efforts to document all the proteins produced by several tissues, including liver, brain and blood plasma, are now underway. But although 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, “but they had no guidelines as what information should be captured or how the information should be formatted. 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. “It then becomes trivial to analyse protein identifications from many different sources, or compare the proteins produced by a particular tissue under different conditions.” PRIDE is closely linked to the Human Proteomics Organization’s Proteomics Standards Initiative (HUPO-PSI; psidev.sourceforge.net) and will allow users to transfer data using the standards that are currently being developed as part of PSI.
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 completely 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. 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” concludes Henning Hermjakob.
Sarah Sherwood | alfa
The most recent press releases about innovation >>>
Die letzten 5 Focus-News des innovations-reports im Überblick:
Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.
As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...
Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.
Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...
For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.
While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...
An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.
The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...
A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.
Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...