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The phenomenon that is Wikipedia, a free online reference resource that allows users to edit or create articles, has revolutionized the way many people obtain encyclopedic information. Wiki-based platforms can also be very useful for sharing scientific information. In one recent report, Andrew Su of the Genomics Institute of the Novartis Research Foundation and his colleagues describe their efforts to build up a comprehensive gene wiki within Wikipedia (Huss et al., 2008). In another report, Bruce Conklin of the University of California, San Francisco, Chris Evelo of Maastricht University and their colleagues introduce WikiPathways, a community-based tool for biological pathway curation (Pico et al., 2008).

Su and his colleagues saw great potential in using Wikipedia for community-curated gene annotations as a resource for both researchers and students. To rapidly build up a gene wiki, they 'seeded' Wikipedia with 7,500 new gene stub pages, based on data from Entrez Gene. “If you create minimally useful content you will attract readers; ... the hope is that some percentage of those readers will actually stay to make an edit,” explains Su. “It can be as trivial as fixing a typo, to summarizing a paper from the literature.” This often generates a positive feedback loop; as pages gain more useful content they attract more readers and more editors. Indeed, Su and his colleagues observed a substantial amount of editing to the stub pages even before they published a paper reporting their efforts.

Conklin and his colleagues thought that a wiki platform also had great potential for capturing biological pathway information, which is difficult to synthesize from static images in publications and from information scattered across different databases. Because such information is often visual rather than text-based, they amended the open-source software behind Wikipedia to make WikiPathways, which incorporates a new visual pathway editor. However, explains Conklin, “we are maintaining as much of the Wikipedia software as possible so that we can use their solutions for dealing with diverse communities as well as efficient curation methods.”

Since WikiPathways has gone live, Conklin and his colleagues have already observed strong participation from diverse pathway communities. “There are communities that are already formed but didn't have a forum to push their pathway data out into the world,” says Conklin. Alexander Pico, lead author on the report, also notes that “for our internal team and our collaboration with [colleagues from] the Netherlands, WikiPathways has made it so much easier to edit and curate content.” Evelo describes another important benefit: “Pathways created on WikiPathways are not just representations of knowledge; they can also be used for analysis of new results.”

Using a wiki-based platform for managing gene or pathway data is very different from the traditional model, in which researchers submit their data to databases that are curated by a relatively small number of experts (Fig. 1). Neither Su's nor Conklin's teams intend their wiki platforms to replace traditional databases, but they both emphasize that wikis can serve as highly complementary resources. “Even the people behind the gene portals recognize that their crew of 50 people can't keep on top of all the literature; ... essentially you're empowering a large community to serve as amateur curators,” explains Su. However, he stresses that with a wiki platform, “at any moment there may be a misleading statement, or it may be incorrect or incomplete—it's an eternal work in progress,” and as such, wikis are not meant to serve as primary sources.

Figure 1: Two models for managing biological data.
figure 1

The traditional database model (left) and the wiki-based model (right) are shown. FTP, file transfer protocol; API, application programming interface. Reprinted from PLoS Biology (Pico et al., 2008).

Perhaps one of the main reasons the wiki format works so well for communicating scientific data is because it is so simple and requires little effort to use. In using a wiki platform, Pico says, “an average biologist who's quite busy doesn't notice that at the same time that they're helping themselves they're also helping everyone else.”