The strategies WDK: a graphical search interface and web development kit for functional genomics databases

被引：8

作者：

Fischer, Steve ^{[1
,2
]}

Aurrecoechea, Cristina ^{[3
]}

Brunk, Brian P. ^{[1
,4
]}

Gao, Xin ^{[1
,4
]}

Harb, Omar S. ^{[1
,4
]}

Kraemer, Eileen T. ^{[5
]}

Pennington, Cary ^{[3
]}

Treatman, Charles ^{[1
,4
]}

Kissinger, Jessica C. ^{[3
,6
]}

Roos, David S. ^{[4
]}

Stoeckert, Christian J. ^{[1
,2
]}

机构：

[1] Univ Penn, Ctr Bioinformat, Philadelphia, PA 19104 USA

[2] Univ Penn, Dept Genet, Philadelphia, PA 19104 USA

[3] Univ Georgia, Ctr Trop & Emerging Global Dis, Athens, GA 30602 USA

[4] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA

[5] Univ Georgia, Dept Comp Sci, Athens, GA 30602 USA

[6] Univ Georgia, Dept Genet, Athens, GA 30602 USA

来源：

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2011年

基金：

美国国家卫生研究院;

关键词：

GENE ONTOLOGY; BIOLOGY; UNIFICATION; BROWSER; UCSC; TOOL;

D O I：

10.1093/database/bar027

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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

引用

页数：12

共 27 条

[11]

Eich B., A Z PROGRAMMING LANG

[12] Saccharomyces Genome Database provides mutant phenotype data [J].

Engel, Stacia R. ;

Balakrishnan, Rama ;

Binkley, Gail ;

Christie, Karen R. ;

Costanzo, Maria C. ;

Dwight, Selina S. ;

Fisk, Dianna G. ;

Hirschman, Jodi E. ;

Hitz, Benjamin C. ;

Hong, Eurie L. ;

Krieger, Cynthia J. ;

Livstone, Michael S. ;

Miyasato, Stuart R. ;

Nash, Robert ;

Oughtred, Rose ;

Park, Julie ;

Skrzypek, Marek S. ;

Weng, Shuai ;

Wong, Edith D. ;

Dolinski, Kara ;

Botstein, David ;

Cherry, J. Michael .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D433-D436

[13]

Fowler M., 2002, Patterns of Enterprise Application Architecture

[14]

Gamma E., 1995, DESIGN PATTERNS ELEM

[15]

Garrett J.J., 2005, ADAPTIVE PATH AJAX N

[16] Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences [J].

Goecks, Jeremy ;

Nekrutenko, Anton ;

Taylor, James .

GENOME BIOLOGY, 2010, 11 (08)

[17] WormBase: a comprehensive resource for nematode research [J].

Harris, Todd W. ;

Antoshechkin, Igor ;

Bieri, Tamberlyn ;

Blasiar, Darin ;

Chan, Juancarlos ;

Chen, Wen J. ;

De La Cruz, Norie ;

Davis, Paul ;

Duesbury, Margaret ;

Fang, Ruihua ;

Fernandes, Jolene ;

Han, Michael ;

Kishore, Ranjana ;

Lee, Raymond ;

Mueller, Hans-Michael ;

Nakamura, Cecilia ;

Ozersky, Philip ;

Petcherski, Andrei ;

Rangarajan, Arun ;

Rogers, Anthony ;

Schindelman, Gary ;

Schwarz, Erich M. ;

Tuli, Mary Ann ;

Van Auken, Kimberly ;

Wang, Daniel ;

Wang, Xiaodong ;

Williams, Gary ;

Yook, Karen ;

Durbin, Richard ;

Stein, Lincoln D. ;

Spieth, John ;

Sternberg, Paul W. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D463-D467

[18] Ensembl 2009 [J].

Hubbard, T. J. P. ;

Aken, B. L. ;

Ayling, S. ;

Ballester, B. ;

Beal, K. ;

Bragin, E. ;

Brent, S. ;

Chen, Y. ;

Clapham, P. ;

Clarke, L. ;

Coates, G. ;

Fairley, S. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Gordon, L. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Holland, R. ;

Howe, K. ;

Jenkinson, A. ;

Johnson, N. ;

Kahari, A. ;

Keefe, D. ;

Keenan, S. ;

Kinsella, R. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Pritchard, B. ;

Rios, D. ;

Schuster, M. ;

Slater, G. ;

Smedley, D. ;

Spooner, W. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. ;

Vogel, J. ;

White, S. ;

Wilder, S. ;

Zadissa, A. ;

Birney, E. ;

Cunningham, F. ;

Curwen, V. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D690-D697

[19] The human genome browser at UCSC [J].

Kent, WJ ;

Sugnet, CW ;

Furey, TS ;

Roskin, KM ;

Pringle, TH ;

Zahler, AM ;

Haussler, D .

GENOME RESEARCH, 2002, 12 (06) :996-1006

[20] EcoCyc: A comprehensive view of Escherichia coli biology [J].

Keseler, Ingrid M. ;

Bonavides-Martinez, Cesar ;

Collado-Vides, Julio ;

Gama-Castro, Socorro ;

Gunsalus, Robert P. ;

Johnson, D. Aaron ;

Krummenacker, Markus ;

Nolan, Laura M. ;

Paley, Suzanne ;

Paulsen, Ian T. ;

Peralta-Gil, Martin ;

Santos-Zavaleta, Alberto ;

Glennon Shearer, Alexander ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D464-D470

← 1 2 3 →