Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

EBI and Ghent University launch PRIDE: an open source database of protein identifications

26.08.2005


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
Further information:
http://www.embl.org/aboutus/news/press/2005/press29aug05_2.html

More articles from Life Sciences:

nachricht How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH

nachricht A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>