<h1 class="page-header">News</h1><p id="cite"><i>Nature</i> <b>445</b>, 691 (15 February 2007) | <span class="doi"><abbr title="Digital Object Identifier">doi</abbr>:10.1038/445691a</span>;
Published online 14 February 2007</p><h2 id="atl">Key biology databases go wiki</h2><p id="aug">Jim Giles</p><div id="abs"><a class="backtotop hidden" href="http://www.nature.com/nature/journal/v445/n7129/full/445691a.html#top">
Top<span class="hidden"> of page</span></a><h3 class="hidden">Abstract</h3><p class="lead">Collaborative approach aims to keep pace with discoveries.</p></div><div id="articlebody"><p class="norm">Barend
Mons's first objective would be ambitious enough for most people: to
meld some of the most important biomedical databases into a single
information resource. But that's just the beginning. Mons, a
bioinformatician at the Erasmus Medical Centre in Rotterdam, the
Netherlands, also wants to apply the Wikipedia philosophy. He's
inviting the whole research community to help update a vast store of
interlinked data. If he and his colleagues can pull it off — and even
the project's advocates are not sure they can — they could transform
the databases that are central to the work of many life scientists.</p><p class="norm">A test version of the project, provisionally dubbed Wiki for Professionals (<a href="http://www.wikiprofessional.info/">http://www.wikiprofessional.info
</a>),
is due to launch in the next month. It already contains data from key
sources, such as protein information from Swiss-Prot and gene
descriptions from Gene Ontology. Over the past year, Mons's team has
woven together these and other archives to create what, from a user's
point of view, seems to be a single database. The page on the
muscular-dystrophy protein dystrophin, for example, contains data from
Swiss-Prot together with links to disease information from the US
National Library of Medicine, as well as explanatory text. Links to
relevant publications in PubMed are also available.</p><p class="norm">Existing
databases interlink to an extent, although the new resource is more
comprehensive. But the next stage is the really radical bit. Biomedical
research produces hundreds of thousands of papers a year, overwhelming
database curators. To clear this bottleneck, Mons and his colleagues
are allowing anyone to edit the entries, modifying and adding text and
links as new work is published.</p><div id="illus1" class="image-legend"><img alt="Key biology databases go wiki" src="http://www.nature.com/nature/journal/v445/n7129/images/445691a-i1.0.jpg"><p>A. PASIEKA/SPL</p><p>Protein databases could be transformed by extra features.
</p></div><p class="norm">That's
an attractive proposition, say database administrators. Michael
Ashburner, a geneticist at the University of Cambridge, UK, helps run
FlyBase, a collection of gene data on the model organism <i>Drosophila melanogaster</i>.
The database receives around US$4 million a year from the US National
Institutes of Health and employs up to five full-time curators, but
still can't keep up with the relevant literature, says Ashburner, who
is working with Mons on the new project. "We have a list of around 12
journals that we try to cover. Even that's tough."</p><p class="norm">Anyone
motivated to register can curate Wiki for Professionals. Visitors to
the dystrophin entry, for example, can update almost any of the
information on the page, such as statements about the role of the
protein in disease. Users can also start new pages, and from later this
year will be given the option of creating pages for themselves, with
links to relevant publications. A final function, and the one that most
excites Mons, is the availability of text-mining software. This will
allow users to probe links between proteins, genes and disease that may
be revealed only by comparing a large number of papers and other data.</p><p class="norm">"Mons
is a visionary," says Amos Bairoch at the Swiss Institute of
Bioinformatics in Geneva, a collaborator on the project and the creator
of Swiss-Prot. "This will be a revolution."</p><blockquote class="box"><p class="quote"><img alt="" class="quoteleft" src="http://www.nature.com/nature/images/quoteleft.gif">This will be a revolution.<img alt="" class="quoteright" src="http://www.nature.com/nature/images/quoteright.gif">
</p></blockquote><p class="norm">Yet
realizing the vision will be difficult. Top of the list of challenges
is persuading the community to get involved. Adding one's own data is
likely to be the biggest motivator — Bairoch and Ashburner say they get
several calls a week asking for updates to databases, usually from
researchers who want their own papers added. Whether this will be
enough to keep the database fresh remains to be seen, given that
employers and funders tend not to value updating information highly.</p><p class="norm">
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<p class="norm">Wiki for Professionals will
also have to ensure that additions don't just reflect individual
researchers' pet theories. Mons hopes scientists will adopt entries
relevant to their work and use automated systems to alert them to
changes, which they can then amend if necessary. The original data in
Swiss-Prot and other databases will also be protected.</p><p class="norm">The
resource has been set up by Knewco, a scientific computing company
based in Rockville, Maryland, and co-founded by Mons. The firm raised
around $2 million in private funding to pay for the initial effort, and
says basic access will be free. Revenue will be generated by charging
drug firms and other users for premium services, such as the option to
run a private version of the system incorporating proprietary data.9999999</p></div><br clear="all"><br>-- <br> John Cumbers, Graduate Student in Computational Biology<br>Brown University, Ecology and Evolutionary Biology, Box G-W
<br>80 Waterman Street, Providence, Rhode Island, 02912, USA<br>Tel USA: +1 401 523 8190, Fax: +1 401 863-2166 <br>UK to USA: 0207 617 7824