Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Mining biotech’s data mother lode

20.12.2005


A EU-sponsored project has developed a suite of tools that will enable biotech companies to mine through vast quantities of data created by modern life-science labs to find the nuggets of genetic gold that lie within.


A 3D structure of a kinase-inhibitor interaction predicted for the pancreas tumour gene expression data. The predicted interaction is important for the regulation of cell growth.



The BioGrid project brought together six partners from the UK, Germany, Cyprus and The Netherlands to address one of the key problems facing the life sciences today.

"How to integrate the huge volume of disparate data – on gene expression, protein interactions and the vast output of literature both inside and outside laboratories – to find out what is important," says Dr Michael Schroeder, Professor of the Bioinformatics group at Dresden Technical University and coordinator of this IST-funded project. "I attended a workshop recently, held by the W3 consortium, and many of the companies there said that this was the biggest problem they face."


Currently, pharmaceutical and biotech companies produce vast quantities of raw data on the problems that interests them. Microarrays process thousands of samples to discover what genes are over expressing. These over-expressing genes – numbering sometimes in their thousands, too – create proteins. The researchers then need to discover what protein interactions are taking place among all the different proteins created by the over-expressing genes. This is not trivial.

If a researcher can identify protein interactions they then need to do a search on their company intranet to see what other work company labs have produced relevant to the topic. Finally, the researcher must perform a search of academic journals to find relevant journal papers. Currently PubMed, the most important public literature database available, has 15,000,000 entries, and the number is growing every day. Finding relevant data there is again not a trivial task.

Dr Schroeder gives an example. "The medical faculty here were studying pancreatic tumours. They found 1,000 genes over expressing. Using our software they were able to find, among others, three protein interactions that were particularly relevant. Using our literature search ontology they were able to discover that two of these interactions were novel. They are now going to study these novel interactions more closely," he says.

BioGrid explained

This is how the project will help companies integrate all the data they need to make relevant discoveries using a BioGrid. A BioGrid is essentially a data and computational Grid created through a suite of tools developed by the project.

Here’s how it works. One element of the software suite analyses over-expressing genes discovered during micro assays to establish what proteins become encoded. This uses standard techniques.A second analysis tool in the suite predicts what possible protein-protein interactions are taking place. This is novel. When a gene encodes a protein, the protein folds up into a unique shape, forming a 3D structure. This structure can only interact, or fit, with some proteins, but not others, like pieces of a jigsaw puzzle.

BioGrid’s protein interaction software includes a database of the 20,000 known protein structures and uses that database to identify which ones could potentially interact, among the thousands of proteins created by the over-expressing genes. Once interesting potential protein interactions are known, BioGrid’s ontology-based search technology can mine company or journal data for any relevant information.

Linking all these software tools together is a rules-based Java scripting language called Prova, also developed by the BioGrid team. It is the glue the sticks the Gene Expression, Protein Interaction and ontology-based literature analysis together into an integrated, cohesive unit. "It’s an open source language, available at www.prova.ws, and about 20 groups are using it around the world right now. We made it open source because you need to develop a community to keep a programming language alive," says Dr Schroeder.

Tara Morris | alfa
Further information:
http://istresults.cordis.lu/index.cfm/section/news/tpl/article/BrowsingType/Features/ID/79828

More articles from Life Sciences:

nachricht Researchers identify potentially druggable mutant p53 proteins that promote cancer growth
09.12.2016 | Cold Spring Harbor Laboratory

nachricht Plant-based substance boosts eyelash growth
09.12.2016 | Fraunhofer-Institut für Angewandte Polymerforschung IAP

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Electron highway inside crystal

Physicists of the University of Würzburg have made an astonishing discovery in a specific type of topological insulators. The effect is due to the structure of the materials used. The researchers have now published their work in the journal Science.

Topological insulators are currently the hot topic in physics according to the newspaper Neue Zürcher Zeitung. Only a few weeks ago, their importance was...

Im Focus: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

Researchers identify potentially druggable mutant p53 proteins that promote cancer growth

09.12.2016 | Life Sciences

Scientists produce a new roadmap for guiding development & conservation in the Amazon

09.12.2016 | Ecology, The Environment and Conservation

Satellites, airport visibility readings shed light on troops' exposure to air pollution

09.12.2016 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>