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Published online 3 September 2008 | Nature 455, 22-25 (2008) | doi:10.1038/455022a
News Feature
Big data: Wikiomics
Pioneering biologists are trying to use wiki-type web pages to manage and interpret data, reports Mitch Waldrop. But will the wider research community go along with the experiment?
Alexander Pico remembers just when the idea hit him. In January 2007, he and his boss, Bruce Conklin, were discussing how to push their software tool for visualizing intracellular signalling pathways to the next level of interactivity — when Pico blurted out, "What we really need is a wiki!"
Well, it was an original thought at the time, says Pico, a software engineer in Conklin's laboratory in the Gladstone Institute of Cardiovascular Disease at the University of California, San Francisco.
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This is a really great idea! I have been working as a contributor and as a developer on various wiki projects in the life-sciences. To try to increase communication and to get the community together I have created the 'BioWiki' group on Nature Networks: http://network.nature.com/group/biowiki Although this is still a fledgeling group, I would encourage 'wikomics' practitioners, users and anyone who is simply just interested to sign up and take part in this ever evolving 'community experiment' known as wiki! Please leave ideas about how the BioWiki group should develop on the groups forum pages. Dan Bolser
With reference to Table 1 (and in keeping with the theme of this article!) I have created a 'BioWiki' category on the MetaBase wiki: http://MetaDatabase.org/index.php/Category:BioWiki MetaBase is the user contributed database of biological databases: http://metadatabase.org If you would like to add your favourite BioWiki project to those listed in MetaBase, please just follow the instructions on that site. Please leave comments regarding MetaBase using the standard wiki tools.
Our experience developing SNPedia (www.SNPedia.com) as the wiki for DNA variation information differs in two significant ways from the views presented in this very interesting article. First: wikis created by scientists may actually have quite large (non-scientific) audiences. While SNPedia - and associated software such as Promethease (www.promethease.com) - are certainly used by researchers, they can also be used by every "personal genomics" consumer who has access to their own genomic data and wants either initial or continously updated knowledge beyond whatever they are told by the company or lab producing the data. This will only grow as the cost of getting your genome fully sequenced decreases, and the number of meaningful medical conclusions that can be drawn from your DNA increases. Second: While historically it's always been a struggle to get proper funding for biodatabases, wikis at least have a theoretical advantage of being cheaper to develop, maintain, and expand. For this reason, funding agencies that are seeking to stretch their "data-dollars" should encourage the long-term growth of wikis.
One approach to making big data more useful is to provide a way in which people can ask unexpected questions in English, and can also can get English explanations of the answers. It's a challenge to do this, particularly if people are to be able to use their own words and phrases, rather than sticking to a fixed vocabulary and grammar. However there is progress. There's a free "Wiki for *executable* English" over databases, that you can find via Google.
It is not likely to replace a database system in its current functionality. Originally designed as an electronic communication board, pages on wiki are independent from each other, i.e., without mechanism to check consistency among pages. As long as wiki is used as a weblog or encyclopaedia, this independent design is more than natural because authors take the responsibility for page contents. For a database, the should-be design is the opposite: original, consistent contents are registered as the background data in tables, and its change should affect all page views that users create by issuing queries (these views correspond to wiki pages). This is exactly what the relational database model provides. In other words, current wiki-based systems do not provide pages whose contents depend on, or constrained by, other page contents. This condition results in the absence of page for automated statistics, indexes, or errata list because all these pages must depend on other pages in some way. To disentangle this situation, we recently published a measure to install "page-dependency" in MediaWiki system (BMC BioData Mining 1:7, 2008 http://www.biodatamining.org/). I wish many wiki-based projects notice the drawback of wiki, and plan some measures before becoming too late.