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 Zap! Graphene is bad news for bacteria
23.05.2017 | Rice University

nachricht Discovery of an alga's 'dictionary of genes' could lead to advances in biofuels, medicine
23.05.2017 | University of California - Los Angeles

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Turmoil in sluggish electrons’ existence

An international team of physicists has monitored the scattering behaviour of electrons in a non-conducting material in real-time. Their insights could be beneficial for radiotherapy.

We can refer to electrons in non-conducting materials as ‘sluggish’. Typically, they remain fixed in a location, deep inside an atomic composite. It is hence...

Im Focus: Wafer-thin Magnetic Materials Developed for Future Quantum Technologies

Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.

Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...

Im Focus: World's thinnest hologram paves path to new 3-D world

Nano-hologram paves way for integration of 3-D holography into everyday electronics

An Australian-Chinese research team has created the world's thinnest hologram, paving the way towards the integration of 3D holography into everyday...

Im Focus: Using graphene to create quantum bits

In the race to produce a quantum computer, a number of projects are seeking a way to create quantum bits -- or qubits -- that are stable, meaning they are not much affected by changes in their environment. This normally needs highly nonlinear non-dissipative elements capable of functioning at very low temperatures.

In pursuit of this goal, researchers at EPFL's Laboratory of Photonics and Quantum Measurements LPQM (STI/SB), have investigated a nonlinear graphene-based...

Im Focus: Bacteria harness the lotus effect to protect themselves

Biofilms: Researchers find the causes of water-repelling properties

Dental plaque and the viscous brown slime in drainpipes are two familiar examples of bacterial biofilms. Removing such bacterial depositions from surfaces is...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

AWK Aachen Machine Tool Colloquium 2017: Internet of Production for Agile Enterprises

23.05.2017 | Event News

Dortmund MST Conference presents Individualized Healthcare Solutions with micro and nanotechnology

22.05.2017 | Event News

Innovation 4.0: Shaping a humane fourth industrial revolution

17.05.2017 | Event News

 
Latest News

Scientists propose synestia, a new type of planetary object

23.05.2017 | Physics and Astronomy

Zap! Graphene is bad news for bacteria

23.05.2017 | Life Sciences

Medical gamma-ray camera is now palm-sized

23.05.2017 | Medical Engineering

VideoLinks
B2B-VideoLinks
More VideoLinks >>>