This proposal describes the continued maintenance and development of the Gene Wiki, the goal of which is to create a continuously-updated, community-reviewed, and collaboratively-written review article for every human gene. The Gene Wiki was created directly within Wikipedia as an informal collection of 10,646 gene-specific articles. In the first funding period, the infrastructure to keep Gene Wiki "infoboxes" in sync wit the source databases in the genomics community was developed. Next, methods to assess and quantify the trustworthiness of each word of a Gene Wiki article were developed and implemented in a system called WikiTrust. And finally, simple text-mining applied to Gene Wiki was able to identify thousands of novel gene annotations. During the next project period, the Gene Wiki is poised to make further strides. First, the scope of the Gene Wiki will be expanded to also include review articles on diseases and drugs. Thousands of articles will either be created or maintained through this initiative with a particular emphasis on rare diseases. Second, a dedicated outreach component will ensure that the community of editors is poised to grow. This outreach effort will engage both faculty members who are experts on specific genes of interest, as well as classroom instructors at all levels who want to design curriculum based on the Gene Wiki for a class project. Third, a "Centralized Model Organism Database" will be constructed in the Wikidata environment, which will serve as a clearing house of microbial gene and genome annotation data. And fourth an entirely new crowdsourcing application will be created that taps into crowds of patient-aligned individuals and their desire to advance research. These individuals will be a novel crowd that will be applied to the challenge of systematically annotating the biomedical literature. In summary, the Gene Wiki is a useful tool for biomedical research. Successful completion of this proposal will result in more efficient knowledge management and dissemination through crowdsourcing.

Public Health Relevance

The Gene Wiki is a highly used resource for understanding gene function. The goal of this project is to create a collaboratively-written, community-reviewed, and continuously-updated review article for every human gene, drug, and disease.

National Institute of Health (NIH)
Research Project (R01)
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Application #
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Lyster, Peter
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Scripps Research Institute
La Jolla
United States
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Peterson, Scott N; Meissner, Tobias; Su, Andrew I et al. (2014) Functional expression of dental plaque microbiota. Front Cell Infect Microbiol 4:108
Good, Benjamin M; Ainscough, Benjamin J; McMichael, Josh F et al. (2014) Organizing knowledge to enable personalization of medicine in cancer. Genome Biol 15:438
Loguercio, Salvatore; Good, Benjamin M; Su, Andrew I (2013) Dizeez: an online game for human gene-disease annotation. PLoS One 8:e71171
Good, Benjamin M; Su, Andrew I (2013) Crowdsourcing for bioinformatics. Bioinformatics 29:1925-33
Wu, Chunlei; Macleod, Ian; Su, Andrew I (2013) BioGPS and organizing online, gene-centric information. Nucleic Acids Res 41:D561-5
Clarke, Erik L; Loguercio, Salvatore; Good, Benjamin M et al. (2013) A task-based approach for Gene Ontology evaluation. J Biomed Semantics 4 Suppl 1:S4
Grogan, Shawn P; Duffy, Stuart F; Pauli, Chantal et al. (2013) Zone-specific gene expression patterns in articular cartilage. Arthritis Rheum 65:418-28
Good, Benjamin M; Clarke, Erik L; Loguercio, Salvatore et al. (2012) Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. Database (Oxford) 2012:bar060
Good, Benjamin M; Clarke, Erik L; de Alfaro, Luca et al. (2012) The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res 40:D1255-61
Good, Benjamin M; Howe, Douglas G; Lin, Simon M et al. (2011) Mining the Gene Wiki for functional genomic knowledge. BMC Genomics 12:603

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