Gene portals have become essential resources for modern biological research. Technologies for high-throughput experimentation are now commonly used in biomedical research, and scientists are often faced with evaluating many candidate genes which are unfamiliar to them. These researchers often turn to gene portals to quickly summarize and curate known gene annotation for their genes of interest from public databases, enabling them to quickly evaluate genes and formulate hypotheses for follow-up testing. Despite their current utility, there are also many opportunities to improve gene portals to better serve the scientific community. Here, we propose the construction of a new gene portal called BioGPS (Biology Gene Portal Services) which is based on recent concepts in web design and online collaboration. These principles, commonly referred to by the moniker ?Web 2.0?, were largely defined based on an analysis of successful web sites, including Wikipedia, Google, and Amazon. In the context of BioGPS, this proposal focuses on two key elements of Web 2.0. First, BioGPS will place heavy emphasis on maximizing usability. Development of BioGPS will draw on concepts and techniques from the discipline of computer science called Human Computer Interactions (HCI). These efforts will include continual usability testing, and utilizing techniques to maximize user interactivity. Second, BioGPS will also emphasize the concept of extensibility. Rather than develop a web site with a small community of web users, we will design a web platform that serves both the needs of web users and of bioinformatics scientists. Extensibility also applies to many different domain areas with BioGPS. BioGPS will be extensible in terms of data, allowing scientists to customize and contribute their own data sets to the gene portal. BioGPS will also be extensible in terms of knowledge, enabling scientists to collaborative share and edit free-text gene annotation through a gene wiki system. And finally, BioGPS will be extensible in terms of application development, allowing other bioinformatics programmers to extend functionality and link other bioinformatics analysis tools. In summary, the BioGPS gene portal will provide a platform for networks of users to synergistically leverage community knowledge and effort, allowing researchers across biological disciplines to efficiently translate high-throughput data to testable hypotheses. PROJECT NARRATIVE The development of the BioGPS gene portal will allow communities of biological researchers to effectively share knowledge and effort devoted to gene annotation. Generating a detailed and rich view of the function of every gene in the human genome will benefit our understanding of basic biological mechanisms, as well as the role of individual genes in human health.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM083924-05
Application #
8333335
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Hagan, Ann A
Project Start
2008-08-01
Project End
2013-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
5
Fiscal Year
2012
Total Cost
$371,458
Indirect Cost
$175,438
Name
Scripps Research Institute
Department
Type
DUNS #
781613492
City
La Jolla
State
CA
Country
United States
Zip Code
92037
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 MyGene.info: organizing online, gene-centric information. Nucleic Acids Res 41:D561-5
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; de Alfaro, Luca et al. (2012) The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res 40:D1255-61
Huss 3rd, Jon W; Lindenbaum, Pierre; Martone, Michael et al. (2010) The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res 38:D633-9
Wu, Chunlei; Orozco, Camilo; Boyer, Jason et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10:R130