Paper Info
Title
The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.
Abstract
Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets. For example, PlasmoDB users seeking novel therapeutic targets may wish to locate putative enzymes that distinguish pathogens from their hosts, and that are expressed during appropriate developmental stages. When a researcher runs one of the approximately 100 searches available on the site, the search is presented as a first step in a strategy. The strategy is extended by running additional searches, which are combined with set operators (union, intersect or minus), or genomic interval operators (overlap, contains). A graphical display uses Venn diagrams to make the strategy's flow obvious. The interface facilitates interactive adjustment of the component searches with changes propagating forward through the strategy. Users may save their strategies, creating protocols that can be shared with colleagues. The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects. The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk. Database URL: www.eupathdb.org
Year
DOI
Venue
2011
10.1093/database/bar027
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
Keywords
Field
DocType
database management systems,genomics,internet
Web development,Venn diagram,Data mining,Computer science,Graphical user interface,Operator (computer programming),The Internet,World Wide Web,Architecture,PlasmoDB,Information retrieval,Usability,Bioinformatics,Database
Journal
Volume
ISSN
Citations 
2011
1758-0463
5
PageRank 
References 
Authors
0.54
12
11
Name
Order
Citations
PageRank
Steve Fischer114815.80
Cristina Aurrecoechea236136.70
B. P. Brunk333742.80
Xin Gao450.54
Omar S Harb511610.70
Eileen Kraemer655065.47
Cary Pennington7827.76
Charles Treatman8888.02
Jessica C. Kissinger927031.73
David S Roos1042438.47
C. J. Stoeckert, Jr.1172889.50