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

Database

Volumn 2011, Issue , 2011, Pages

  Fischer, Steve ^a   Aurrecoechea, Cristina ^b   Brunk, Brian P ^a   Gao, Xin ^a   Harb, Omar S ^a   Kraemer, Eileen T ^c   Pennington, Cary ^b   Treatman, Charles ^a   Kissinger, Jessica C ^b,d   Roos, David S ^a   Stoeckert, Christian J ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c NONE   (United States)

^d University of Georgia   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

ARTICLE; COMPUTER INTERFACE; DATA BASE; GENETIC DATABASE; GENOMICS; INTERNET; METHODOLOGY;

DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENOMICS; INTERNET; USER-COMPUTER INTERFACE;

EID: 80053484719     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bar027     Document Type: Article

References (27)

1. Aurrecoechea, C., Brestelli, J., Brunk, B. P., Dommer, J. et al. (2009) PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res., 37(Database issue), D539-D543.
2. Engel, S. R., Balakrishnan, R., Binkley, G. et al. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res., 38(Database issue), D433-D436.
3. Hubbard, T. J. P., Aken, B. L., Ayling, S. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37(Database issue), D690-D697.
4. Aurrecoechea, C., Brestelli, J., Brunk, B. P. et al. (2010) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res., 38(Database issue), D415-D419.
5. Ashburner, M., Ball, C. A., Blake, J. A. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
6. Altschul, S. F., Gish, W., Miller, W. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
7. Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
8. Agüero, F., Al-Lazikani, B., Aslett, M. et al. (2008) Genomic-scale prioritization of drug targets: the TDR Targets database. Nat. Rev. Drug Discov., 7, 900-907.
9. Webb, E.; International Union of Biochemistry and Molecular Biology. (1992) Enzyme nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenc lature and classification of enzymes. 1984th edn. New York: Academic Press.
10. Davidson, S., Crabtree, J., Brunk, B. P. et al. (2001) K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources. IBM Systems J., 40, 512-531. (Pubitemid 32611100)
11. Trygve/MVC [Internet]. 1978. http://heim.ifi.uio.no/-trygver/themes/mvc/ mvc-index.html (19 January 2011, date last accessed).
12. Gamma, E. (1995) Design Patterns: Elements of Reusable Object-oriented Software. Addison-Wesley, Reading M A.
13. Fowler, M. (2002) Patterns of Enterprise Application Architecture. Addison-Wesley.
14. Data Transfer Object [Internet]. [date unknown]. http://msdn.microsoft. com/en-us/library/ms978717.aspx (19 January 2011, date last accessed).
15. Eich B. The A-Z of Programming Languages: JavaScript-a-z of programming languages-Computerworld [Internet]. [date unknown]. http://www.computerworld. com.au/article/255293/a-z-programming-languages-javascript/(19 January 2011, date last accessed).
16. Garrett, J. J. adaptive path ajax: a new approach to web applications [Internet]. 2005. http://www.adaptivepath.com/ideas/essays/archives/000385.php (19 January 2011, date last accessed).
17. Harris, T. W., Antoshechkin, I., Bieri, T. et al. (2010) WormBase: a comprehensive resource for nematode research. Nucleic Acids Res., 38(Database issue), D463-D467.
18. Twigger, S. N., Shimoyama, M., Bromberg, S. et al. (2007) The Rat Genome Database, update 2007-easing the path from disease to data and back again. Nucleic Acids Res., 35(Database issue), D658-D662. (Pubitemid 46056287)
19. Bult, C. J., Eppig, J. T., Kadin, J. A. et al. (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res., 36(Database issue), D724-D728. (Pubitemid 351149814)
20. Smedley, D., Haider, S., Ballester, B. et al. (2009) BioMart-biological queries made easy. BMC Genomics, 10, 22.
21. Lyne, R., Smith, R., Rutherford, K. et al. (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol., 8, R129.
22. Keseler, I. M., Bonavides-Martínez, C., Collado-Vides, J. et al. (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res., 37(Database issue), D464-D470.
23. Maglott, D., Ostell, J., Pruitt, K. D. et al. (2007) Entrez Gene: gene-centered information at NCB I. Nucleic Acids Res., 35(Database issue), D26-D31. (Pubitemid 46056164)
24. Tweedie, S., Ashburner, M., Falls, K. et al. (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res., 37(Database issue), D555-D559.
25. Birkland, A. and Yona, G. (2006) BIOZON: a system for unification, management and analysis of heterogeneous biological data. BMC Bioinformatics, 7, 70.
26. Kent, W. J., Sugnet, C. W., Furey, T. S. et al. (2002) The human genome browser at UCS C. Genome Res., 12, 996-1006. (Pubitemid 34662293)
27. Rhead,B, Karolchik, D., Kuhn, R. M. et al. (2010) The UCSC Genome Browser database: update 2010. Nucleic Acids Res., 38(Database issue), D613-D619.