Special Issue papers |
Saccharomyces genome database: Underlying principles and organisation
team of scientists who commit their full time and energy to the design, maintenance, and enhancement of the Saccharomyces Genome Database, a resource for scientific information about the model organism Saccharomyces cerevisiae (baker's or budding yeast)
J. Michael Cherry, Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305-5120, USA Tel: +1 650 723 7541 Fax: +1 650 723 1534 E-mail: cherry{at}stanford.edu
A scientific database can be a powerful tool for biologists in an era where large-scale genomic analysis, combined with smaller-scale scientific results, provides new insights into the roles of genes and their products in the cell. However, the collection and assimilation of data is, in itself, not enough to make a database useful. The data must be incorporated into the database and presented to the user in an intuitive and biologically significant manner. Most importantly, this presentation must be driven by the user's point of view; that is, from a biological perspective. The success of a scientific database can therefore be measured by the response of its users — statistically, by usage numbers and, in a less quantifiable way, by its relationship with the community it serves and its ability to serve as a model for similar projects. Since its inception ten years ago, the Saccharomyces Genome Database (SGD) has seen a dramatic increase in its usage, has developed and maintained a positive working relationship with the yeast research community, and has served as a template for at least one other database. The success of SGD, as measured by these criteria, is due in large part to philosophies that have guided its mission and organisation since it was established in 1993. This paper aims to detail these philosophies and how they shape the organisation and presentation of the database.
Keywords: S. cerevisiae, database, genome-wide, analysis, bioinformatics, yeast
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. Piekna-Przybylska, W. A. Decatur, and M. J. Fournier The 3D rRNA modification maps database: with interactive tools for ribosome analysis Nucleic Acids Res., January 11, 2008; 36(suppl_1): D178 - D183. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Piekna-Przybylska, W. A. Decatur, and M. J. Fournier New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA RNA, March 1, 2007; 13(3): 305 - 312. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Chi, C. Huttenhower, L. Y. Geer, J. J. Coon, J. E. P. Syka, D. L. Bai, J. Shabanowitz, D. J. Burke, O. G. Troyanskaya, and D. F. Hunt Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry PNAS, February 13, 2007; 104(7): 2193 - 2198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Zuo, S. E. Mohr, Y. Hu, E. Taycher, A. Rolfs, J. Kramer, J. Williamson, and J. LaBaer PlasmID: a centralized repository for plasmid clone information and distribution Nucleic Acids Res., January 12, 2007; 35(suppl_1): D680 - D684. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Ruan and W. Zhang A bi-dimensional regression tree approach to the modeling of gene expression regulation Bioinformatics, February 1, 2006; 22(3): 332 - 340. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Hwang, J. J. Smith, D. M. Leslie, A. D. Weston, A. G. Rust, S. Ramsey, P. de Atauri, A. F. Siegel, H. Bolouri, J. D. Aitchison, et al. A data integration methodology for systems biology: Experimental verification PNAS, November 29, 2005; 102(48): 17302 - 17307. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Brockman, P. Singh, D. Liu, S. Quinlan, J. Salisbury, and J. H. Graber PACdb: PolyA Cleavage Site and 3'-UTR Database Bioinformatics, September 15, 2005; 21(18): 3691 - 3693. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. L. Tai, V. M. Boer, P. Daran-Lapujade, M. C. Walsh, J. H. de Winde, J.-M. Daran, and J. T. Pronk Two-dimensional Transcriptome Analysis in Chemostat Cultures: COMBINATORIAL EFFECTS OF OXYGEN AVAILABILITY AND MACRONUTRIENT LIMITATION IN SACCHAROMYCES CEREVISIAE J. Biol. Chem., January 7, 2005; 280(1): 437 - 447. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Balakrishnan, K. R. Christie, M. C. Costanzo, K. Dolinski, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman, E. L. Hong, R. Nash, et al. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD) Nucleic Acids Res., January 1, 2005; 33(suppl_1): D374 - D377. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Riffle, L. Malmstrom, and T. N. Davis The Yeast Resource Center Public Data Repository Nucleic Acids Res., January 1, 2005; 33(suppl_1): D378 - D382. [Abstract] [Full Text] [PDF]
|
|