[OWW-Discuss] Fwd: Key biology databases go wiki (about time too!)

Thu Feb 15 21:06:14 EST 2007

It's a company doing this, so I wonder if the source for the tools will be
released for re-use -- take a look at the flash demo if you have a chance,
looks like this is definitely built on mediawiki.  And it looks pretty cool
in general.

http://www.wikiprofessional.info

Does anyone know if they will have to release their changes to the Mediawiki
source per the GNU license in this case?  Austin, I remember that you said
extensions didn't have to be released, but changes to the source would?

interesting stuff, I hope it turns out well.
jason

---------- Forwarded message ----------
From: John Cumbers <johncumbers at gmail.com>
Date: Feb 15, 2007 5:18 PM
Subject: [OWW-Discuss] Key biology databases go wiki (about time too!)
To: discuss at openwetware.org

News

*Nature* *445*, 691 (15 February 2007) | doi:10.1038/445691a; Published
online 14 February 2007
Key biology databases go wiki

Jim Giles
Top of page<http://www.nature.com/nature/journal/v445/n7129/full/445691a.html#top>
Abstract

Collaborative approach aims to keep pace with discoveries.

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.

A test version of the project, provisionally dubbed Wiki for
Professionals (http://www.wikiprofessional.info
), 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.

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.
[image: Key biology databases go wiki]

A. PASIEKA/SPL

Protein databases could be transformed by extra features.

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 *Drosophila
melanogaster*. 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."

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.

"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."

This will be a revolution.

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.

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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.

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

-- 
John Cumbers,  Graduate Student in Computational Biology
Brown University, Ecology and Evolutionary Biology, Box G-W
80 Waterman Street, Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166
UK to USA: 0207 617 7824
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