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EU Team to Coordinate Gen2Phen Data


A consortium of European research groups and bioinformatics firms has kicked off an effort to integrate the growing body of information on human genotype-to-phenotype relationships enabled by the rise of low-cost genotyping technologies.

The five-year project, called Gen2Phen, for Genotype-to-Phenotype, began earlier this month with €11.9 million in funding from the European Union's Seventh Framework Program. The goal of the project is to create tools and standards that will seamlessly integrate numerous genetic variation databases and provide a unified view of these disparate data sources.

"This is not a database," says Anthony Brookes, a professor in the department of genetics at the UK's University of Leicester and the coordinator of the project. "It's trying to help organize, orchestrate, and coordinate the general field of genotype-to-phenotype databasing."

Brookes says that the project is a response to the "tidal wave of information" that is now coming online from low-cost genome-wide association studies that link genotypic data with phenotypic information.

Brookes says that the informatics community has not yet developed standardized database infrastructures, data standards, or data models for the rise of so-called G2P data. Unlike genomic data, which is "unidimensional, so it's very easy to design databases, and very easy to manage and handle," Brookes notes that "there are a lot more complex challenges involved in handling phenotype data because it's an infinite universe of information."

As a result, different databases have chosen to handle and represent this information in very different ways, which has made it difficult for researchers to access data from multiple studies and compare it. Current efforts to solve the problem are "nowhere near enough for the absolute torrent of genotype-phenotype information that's now flowing and will continue to flow," he says.

Bernadette Toner

Bioinformatics  Notes

The National Library of Medicine will give $5 million over a three-year period to fund several research groups aiming to advance biomedical informatics. The grant will support between 12 and 15 research programs in areas of public health, complex modeling, and clinical translational research.

The US Environmental Protection Agency's National Center for Computational Toxicology will license Gene Logic's bioinformatics platform. The EPA will use the company's Genesis Enterprise System, GXR Connect software, and parts of its ToxExpress and BioExpress systems for use in the agency's ToxCast program.

The CDC extended an existing deal for a multi-site license to DNAStar's sequence analysis software for use at its facilities in Colorado, Alaska, and Puerto Rico.


$50 million
Amount the National Science Foundation has doled out to establish a cyberinfrastructure center for plant biology.

Funded grants

Sp Base: A Sea Urchin Genome Database
Grantee: Robert Andrew Cameron, California Institute of Technology
Began: Sep.1, 2007; Ends: Jun.30, 2012
Through this grant, Cameron will continue to expand and extend SpBase, a genome database for sea urchins that collects data produced by the Sea Urchin Genome Sequencing Project, composed of the Baylor College of Medicine Human Genome Sequencing Center and the Sea Urchin Genome Annotation team. SpBase is being developed to include a user interface that allows for easy updating, editing, and installation of additional features.

Shotgun Lipidomics and Alterations in Sphingolipidomes in Alzheimer's Diseases
Grantee: Xianlin Han, Washington University
Began: Sep. 1, 2007; Ends: July 31, 2012
Han and his colleagues are developing a bioinformatics approach to yield high-throughput processing of complex lipidomics data, including the identification of altered lipid molecular species induced by a disease state and the construction of a lipid metabolic network map. This project will also attempt to identify the altered pathways of the sphingolipidome networks present in very mild Alzheimer's disease.

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