The Gene Wiki: community intelligence applied to human gene annotation

Abstract

Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model based on the principle of community intelligence. Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Previously, we described the creation of Gene Wiki 'stubs' for approximately 9000 human genes. Here, we describe ongoing systematic improvements to these articles to increase their utility. Moreover, we retrospectively examine the community usage and improvement of the Gene Wiki, providing evidence of a critical mass of users and editors. Gene Wiki articles are freely accessible within the Wikipedia web site, and additional links and information are available at http://en.wikipedia.org/wiki/Portal:Gene_Wiki.

Figure 1.

Analysis of links between the Entrez Gene and PubMed databases. (A) Examining the degree of gene annotation from the perspective of Entrez Gene, we found that while a few genes are very well annotated with links to PubMed references, the vast majority of genes have few or no linked references. (B) Examining links from the perspective of PubMed, we found that only a small fraction of published articles are linked to human genes. Taken together, these findings suggest that the traditional model of centralized curation is not scaling well with the rate of scientific research, and that complementary approaches based on community intelligence may be worth exploring.

Figure 2.

Average monthly page views of pages in the Gene Wiki. Calculated over the first 6 months of 2009, this histogram shows the average number of page views per month over all Gene Wiki articles. Each page receives an average of 304 page views per month (median = 80).

Figure 3.

Google rank of Gene Wiki pages. When searching by gene symbol, >85% of Gene Wiki pages are found within the first eight hits by the search engine Google.

Figure 4.

Analysis of page size versus change in page size. The change in size of each Gene Wiki article during the first 6 months of 2009 is plotted as a function of the page size at the end of June 2009. Larger markers indicate more page views, and marker color indicates the Google rank of the page when searching by gene symbol. Labels are shown for a few representative pages.

Figure 5.

Timelines of Wikipedia views and Google Trends information for HCG (A) and catalase (B). Blue dots represent editing events, with bigger size corresponding to more editing events. The asterisks mark major events in the popular press for HCG and catalase, where Manny Ramirez was linked to performance-enhancing drugs and catalase was linked to premature gray hair, respectively.