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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM089820-09
Application #
9265870
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Ravichandran, Veerasamy
Project Start
2009-12-01
Project End
2018-04-30
Budget Start
2017-05-01
Budget End
2018-04-30
Support Year
9
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Scripps Research Institute
Department
Type
DUNS #
781613492
City
La Jolla
State
CA
Country
United States
Zip Code
92037
Xia, Di; Tang, Wai Kwan; Ye, Yihong (2016) Structure and function of the AAA+ ATPase p97/Cdc48p. Gene 583:64-77
Hettne, Kristina M; Thompson, Mark; van Haagen, Herman H H B M et al. (2016) The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PLoS One 11:e0149621
Katsuoka, Fumiki; Yamamoto, Masayuki (2016) Small Maf proteins (MafF, MafG, MafK): History, structure and function. Gene 586:197-205
Hanukoglu, Israel; Hanukoglu, Aaron (2016) Epithelial sodium channel (ENaC) family: Phylogeny, structure-function, tissue distribution, and associated inherited diseases. Gene 579:95-132
Tatetsu, Hiro; Kong, Nikki R; Chong, Gao et al. (2016) SALL4, the missing link between stem cells, development and cancer. Gene 584:111-9
Dex, Sarah; Lin, Dasheng; Shukunami, Chisa et al. (2016) Tenogenic modulating insider factor: Systematic assessment on the functions of tenomodulin gene. Gene 587:1-17
Burgstaller-Muehlbacher, Sebastian; Waagmeester, Andra; Mitraka, Elvira et al. (2016) Wikidata as a semantic framework for the Gene Wiki initiative. Database (Oxford) 2016:
Yokota, Tomohiro; Wang, Yibin (2016) p38 MAP kinases in the heart. Gene 575:369-76
Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin et al. (2016) A comprehensive and scalable database search system for metaproteomics. BMC Genomics 17:642
Panchenko, Maria V (2016) Structure, function and regulation of jade family PHD finger 1 (JADE1). Gene 589:1-11

Showing the most recent 10 out of 64 publications