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Encyclopedia of Life in The Scientist magazine

Presenting an Encyclopedia Proteomica

Published 03/02/2004

The Scientist Magazine
Volume 18 | Issue 3 | 33 | Feb. 16, 2004

Biological databases are everywhere. From protein libraries in Switzerland to genome repositories in Maryland, one could spend hours tracking down all the sources of information on the Internet. An ambitious new project at the San Diego Supercomputer Center, University of California, aims to bring them all into one easy-to-use, centrally hosted place that is open to all.

Culling data from over a dozen databases, the Encyclopedia of Life project (EOL, http://eol.sdsc.edu/) seeks "to catalog the complete proteome of every living species in a flexible, powerful reference system." That's a tall order, yet the reference, still in alpha development, already contains information on over 570,000 open-reading frames from 139 genomes.

Available information includes functional annotations, predicted structural fold assignments, citations and references, a chromosome browser, and links to external databases, all presented with a simple-to-use, book-style graphical interface that caters to everyone from K-12 students to lab researchers. In addition, the data also can be exposed using Web services, for incorporation into third-party Web pages.

A monumental undertaking requiring 2,000 processor-years for the first full release, EOL's developers call the project an ideal application for the TeraGrid initiative. In the meantime, users can catch a glimpse of EOL's power as applied to Arabidopsis, at http://arabidopsis.sdsc.edu.

– Sam Jaffe

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