Navigation Links
Mining biotech's data mother lode

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 s tudy these novel interactions more closely," he says.

BioGrid explainedThis 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.


'"/>

Source:IST Results


Related biology news :

1. Mining for gems in the fungal genome
2. Adding Radiation Therapy To Chemotherapy Improves Survival In Patients With High-risk Breast Cancer
3. New Treatment Rivals Chemotherapy For Lymphoma, Study Finds
4. Bevacizumab Combined With Chemotherapy Improves Progression-Free Survival for Patients With Advanced Breast Cancer
5. Report that delayed motherhood decreases life expectancy of mouse offspring
6. Tendency to hair loss inherited from the mother
7. USC researchers determine mechanism of action of chemotherapy drug
8. Studies clarify risk factors for mother-to-child transmission of hepatitis C virus
9. Gene expression profile helps predict chemotherapy response in ovarian cancer patients
10. Ultrasounds show mothers drinking shrinks fetal brain
11. Hyena mothers give their cubs a helpful dose of hormones
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:4/19/2016)... 2016 The new GEZE SecuLogic ... web-based "all-in-one" system solution for all door components. It ... the door interface with integration authorization management system, and ... The minimal dimensions of the access control and the ... installations offer considerable freedom of design with regard to ...
(Date:4/13/2016)... April 13, 2016  IMPOWER physicians supporting Medicaid patients ... a new clinical standard in telehealth thanks to a ... the higi platform, IMPOWER patients can routinely track key ... body mass index, and, when they opt in, share ... visit to a local retail location at no cost. ...
(Date:3/23/2016)... WAKEFIELD, Massachusetts , March 23, 2016 ... kombiniert im Interesse erhöhter Sicherheit Gesichts- und ... Xura, Inc. (NASDAQ: MESG ... heute bekannt, dass das Unternehmen mit SpeechPro ... insbesondere aus der Finanzdienstleistungsbranche, wird die Möglichkeit ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... ... June 27, 2016 , ... Cancer experts from ... believe could be a new and helpful biomarker for malignant pleural mesothelioma. Surviving ... to read it now. , Biomarkers are components in the blood, tissue ...
(Date:6/27/2016)... Ginkgo Bioworks , a leading organism design company ... as one of the World Economic Forum,s Technology ... companies. Ginkgo Bioworks is engineering biology to manufacture ... the nutrition, health and consumer goods sectors. The ... Fortune 500 companies to design microbes for their ...
(Date:6/23/2016)... ... June 23, 2016 , ... ... of its second eBook, “Clinical Trials Patient Recruitment and Retention Tips.” Partnering with ... in this eBook by providing practical tips, tools, and strategies for clinical researchers. ...
(Date:6/23/2016)... , June 23, 2016 Houston ... with the Cy-Fair Sports Association to serve as ... the agreement, Houston Methodist Willowbrook will provide sponsorship ... and connectivity with association coaches, volunteers, athletes and ... with the Cy-Fair Sports Association and to bring ...
Breaking Biology Technology: