Press
Release 4 February 2003 [PDF]
From genes to cellular processes with the
Genome Knowledge Base
The
best place to learn about a small town you plan to visit would
be a travel brochure or a history book. If none exists, you
might have to spend days combing libraries and archives for
information before your trip. A similar problem confronts
scientists when they search genome databases for information
about genes. "What they want to know may be there," says Ewan
Birney, of the European Bioinformatics
Institute [EBI] in the UK, "but figuring out what it means,
and whether it's important, may require days in the library."
Birney has teamed up with Lincoln Stein of Cold
Spring Harbor Laboratory [New York] to launch the "Genome
Knowledge Base" [GKB], a sort of "travellogue" of the
human genome. It goes online for the first time today at www.genomeknowledge.org.
The information is directly linked to Ensembl, the public
database of human, mice, and other genomes run by Birney's
team and the Sanger
Institute.
Scientists are rapidly learning new things about how individual
genes participate in processes like cell division, cell differentiation,
or cancer. In Ensembl
and other databases, these discoveries appear as a sort of
exhaustive series of footnotes. This often makes it hard to
see the forest for the trees. The Genome
Knowledge Base aims to make things much simpler.
"When scientists talk about the cell," Birney says, "they
say things like, "Once this molecule recruits its partner
kinase, the resulting complex switches on a number of other
target genes." It is a process view, in contrast to the gene-centric
or protein-centric view of most databases." Representing biological
processes in a database is regarded as one of the biggest
current challenges for bioinformatics.
In the past, discoveries came at a slower pace, so researchers
had the time to spend a day or two in the library. And the
current system generally works fine, Birney says, if a scientist
is working on a specific process and comes to a database for
information about a gene.
But new types of experiments have changed things. For example,
work at the EBI's parent institute, the European Molecular
Biology Laboratory in Heidelberg [EMBL], has recently turned
up over two hundred genes that might be involved in how mosquitoes
transmit malaria. Looking them all up would be a gargantuan
task that the GKB aims to make easier. "You might find that
twenty of those genes are part of a very common biological
process," Birney says. "But if you can¨t spot that easily
in the database, you might overlook them as unconnected single
genes."
While this is not the first effort to tackle the problem,
three things make the resource special. First, it will be
entirely in the public domain, and Birney and Stein invite
scientists everywhere to use it, link into it, and add to
it. Secondly, researchers can move smoothly back and forth
between the GKB and Ensembl, which many scientists regard
as the world's best public version of human and other genomes.
Finally, the researchers are taking painstaking steps to ensure
a very high quality of information. "Everything in the Knowledge
Base points back to original experimental sources," Birney
says. "Some of what we know about basic processes like metabolism
goes back fifty years or more, and you have to crack old textbooks
to find it. New or old, all the information is reviewed by
a top expert, and we invite help from scientists in each field."
The initial version of the GKB presents four major
processes in human cells. Several more will be
covered in a second release planned for March.
With active support from the research community,
the resource should quickly grow by leaps and
bounds.
Scientific
Contacts
Ewan
Birney
European Bioinformatics Institute [EBI], Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U. K.
Tel: +44 [0] 1223 494 420
Fax: +44 [0] 1223 494 468
E-mail: birney@ebi.ac.uk
Lincoln Stein
Cold Spring Harbor Laboratory,
P. O. Box 100, 1 Bungtown Road, Cold Spring
Harbor, USA NY 11724
Tel: +1 516 367 8380
Fax: +1 516 367 8389
E-mail: steinl@cshl.edu |
