The Gene Wiki: Community Intelligence Applied to Gene Annotation FaceBase Kick-off Meeting November 16, 2009 Andrew Su, Ph.D.

2 The biomedical literature is massive Centralized curation efforts do not scale with the rapid growth of the biomedical literature 811,214 articles in PubMed in 2008 Sooner or later, the research community will need to be involved in the annotation effort to scale up to the rate of data generation.

3 Wikipedia as a model Wikipedia: “the free encyclopedia that anyone can edit.” Contains a huge breadth of topics and volume of information > 2 million articles, > 1 billion words More accurate than one might think comparable to Britannica Online Epitomizes collaborative editing 300K+ active editors Displays both structured and unstructured data figures, images, photos July 2008

4 Gene “stubs” Active MCB community at WP had already developed ~650 gene articles Can we accelerate this process through stub creation? In total, created 8000 new articles and edited 650 previously existing articles.

5 Positive feedback loops Gene wiki page utility Number of users Number of contributors

6 25k gene-specific review articles? Goal: Create a continually-updated, collaboratively- written, and community-reviewed review article for every gene in the human genome. Figures and diagrams Inline PubMed citations Hyperlinks to related concepts Table of contents

Gene Wiki usage 7 Utility Users Contributors 85% of Gene Wiki pages are found on the first page of Google search results… Median: 303 views / page / month Total: 2.9 million views / month

8 Gene Wiki editing activity During Jan – Jun 2009… … 6848 edits were made by 1923 unique users of IP addresses … average of 1100 edits per month (SD=171) … additional 11,912 edits made by automated “bots” … total increase in text content by 2.28 megabytes, approximately equal to 19 research articles in PLoS Biology Utility Users Contributors

Positive feedback loop initiated? 9 Utility Users Contributors There is substantial evidence that Wikipedia and the Gene Wiki are used by both scientists and the general public, so we as a community better make it good. Monthly statistics

Dual FaceBase Wiki efforts Direct participation in the Gene Wiki –Goal: Scientific outreach and education –Pro: Existing critical mass of editors and content –Con: Bureaucracy Limited scope as a general encyclopedia Standalone FaceBase Wiki –Goal: Creation of a useful research tool –Pro: Greater editorial control Inclusion of unpublished data and findings Emphasis on content for craniofacial community –Con: Difficult to create and maintain critical mass –Q: How should we seed content? 10

11 Acknowledgements Funding and Support NIGMS, NIH Novartis Research Foundation John Hogenesch, UPenn Angel Pizzaro, UPenn Faramarz Valafar, SDSU Donabel Roberts, SDSU Pierre Lindenbaum, Fondation Jean Dausset Michael Martone, Rush Konrad Koehler, Karo Bio David Delano Jennifer Floyd James Goodale Phil McClurg Steve Su Richard Trager Julia Turner Serge Batalov Ghislain Bonamy Jason Boyer Jon Huss Yue Hu Jeff Janes Marc Leglise Camilo Orozco Chunlei Wu To access the Gene Wiki, Google “gene wiki portal” (or your favorite gene’s symbol) for more info… CollaboratorsCurrent group membersPast members