Molecular Biology Wikis Launched

Central repository of information on genes and proteins requires participation by the scientific community

If you build it, will they come? That’s the question on everyone’s mind after the launch of two pioneering initiatives in community annotation: WikiProteins and Gene Wiki, announced, respectively, in the May 28 issue of Genome Biology and the July 8 issue of PLoS Biology. The efforts create a central repository of information on genes and proteins and call on the scientific community to keep it up-to-date and accurate.


Predictive behavior of a simulated microbe species at different points along an evolutionary trajectory. The resource (food) is always given shortly after giving either, but not both, of the two signals (environmental cues). Initially (subplot 1) the response seems random relative to the food and cues. Eventually, however (subplot 4), guided by the pattern of cues, the microbe evolves its feeding response to make it synchronize with the food availability. Courtesy of Ilias Tagkopoulos. Reprinted from the supporting online material for Predictive Behavior Within Microbial Genetic Networks, Ilias Tagkopoulis, et al.,  Science 320, 1313 (2008).“There’s no way we can handle the current growth of knowledge with central annotation only,” says Barend Mons, PhD, who leads the WikiProteins effort. “I’m a big fan of the authoritative databases like UniProt, but we have to make them grow faster. So what we need is a shell around them of community annotation.” Mons is associate professor of human genetics at the Leiden University Medical Centre and of medical informatics at Erasmus University, both in the Netherlands.


“WikiProteins is more than just a Wiki; it has the whole knowledge space hovering over it,” Mons says. Using text mining, WikiProteins imported structured content (adhering to computer-readable, controlled vocabularies) on 1.2 million unique biomedical concepts from existing databases, such as PubMed, Swiss-Prot, and Gene Ontology. The system also created profiles for about 1.6 million authors in PubMed, who are expected to serve as the knowledge guardians. “If you have 1.6 million people in PubMed publishing today and you have 1.2 million concepts in the Wiki, then roughly everyone could take one concept and make sure the page on that concept is correct. That’s doable,” Mons says.


Gene Wiki operates within Wikipedia and, in contrast to WikiProteins, emphasizes unstructured content, such as free text and images, “more akin to a review article,” says Andrew Su, PhD, of the Genomics Institute of the Novartis Research Foundation, who leads the effort. Using data from Entrez Gene, the system added or amended about 9000 Wikipedia “stub” entries on human genes, which anyone can edit. “Being part of the larger Wikipedia community is certainly an advantage of this system. The people there are experts at welcoming newcomers, fighting vandalism, and formatting things correctly,” Su says.


Su and Mons have plans to collaborate. WikiProtein and Gene Wiki entries will be linked through a common “entry page” (likely hosted in WikiProteins), making it easy to navigate between the systems. “This will allow users to take advantage of whichever system they feel comfortable with,” Su says.


Getting bench scientists to participate will be a challenge, Mons says, but he believes the incentives are high. The WikiProteins system mines PubMed for new information daily, finds new explicit and implicit associations—such as predicting protein-protein interactions—and alerts scientists of all edits and updates to concepts in their purview. “I hope it becomes a daily part of their knowledge discovery process,” Mons says. Since its launch, WikiProteins has also received requests to enable users to enter data as unstructured, free text, which should lower the barrier to participation.


Another factor that may boost participation is the development of ways to trace authorship for each entry, so that authors can get credit for their work and readers can assess the reliability of content. A recent proof of this possibility was demonstrated in  “WikiGenes,” (not to be confused with the GeneWiki!) a project described in Nature Genetics in September 2008. WikiGenes was developed by Robert Hoffmann, PhD, at the Massachusetts Institute of Technology. It’s part of his Mememoir project, which has, he says, “the ambitious goal to create a free collaborative knowledge base for all of science—where authorship matters.”


Though the creators of the various Wikis have not yet formally quantified participation, Su says that there’s been an uptick in Gene Wiki activity since the PLoS Biology paper came out. “It gives me hope that the system is right and that the framework is there, so if we are tapping into a desire in the community to share knowledge and harness community intelligence, then we have the structure to do it now.”


More information is available at:  (WikiProteins) and Gene_Wiki (Gene Wiki).

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