Databases

Databases

Model organism sequence data. Genetic markers of drug metabolism and efficacy.

Shared Facilities:

Aspergillus Genome Database (AspGD)

• Description — The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data.
• Location — online
• Questions — Contact Us  
• Website — http://www.aspgd.org
• Selected References

  The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G. Nucleic Acids Res. 2010; 38 (Database issue): D420-7. PubMedID: 19773420.

  The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, Crabtree J, Howarth C, Orvis J, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G, Wortman JR. Nucleic Acids Res. 2012; Jan;40 (Database issue): D635-9. Epub 2011 Nov 12. PubMedID: 22080559.

Candida Genome Database (CGD)

• Description — The Candida Genome Database provides free online access to data, including genomic sequence and manually curated functional information, about genes and proteins of the human pathogen Candida albicans and related species.
• Location — online
• Questions — Contact Us  
• Website — http://www.candidagenome.org
• Selected References

  New tools at the Candida Genome Database: biochemical pathways and full-text literature search. Skrzypek MS, Arnaud MB, Costanzo MC, Inglis DO, Shah P, Binkley G, Miyasato SR, Sherlock G. Nucleic Acids Res. 2010; 38 (Database issue): D428-32. PubMedID: 19808938.

  The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G. Nucleic Acids Res. 2012 January; 40(Database Issue): D667–D674. Epub 2011 November 7. PubMedID: 22064862.

  Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G. Trends Microbiol. 2009 Jul;17(7):295-303. Epub 2009 Jul 3. PubMedID: 19577928.

The Pharmacogenomics Knowledgebase (PharmaGKB)

• Description — PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. We curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.
  
  The knowledge base offers information as a research tool and will:
  • Collect and disseminate knowledge about the impact of human genetic variation on drug responses
  • Curate and display primary genotype and phenotype data
  • Annotate gene variants and gene-drug-disease relationships via literature reviews
  • Summarize important pharmacogenomic genes and drug pathways
  • Enable consortia examining important questions in pharmacogenomics
• Location —online
• Questions — Contact Us  
• Website — http://www.pharmgkb.org/index.jsp
• Selected References

  From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. McDonagh EM, Whirl-Carrillo M, Garten Y, Altman RB and Klein TE. Biomarkers in Medicine (2011) Dec; 5(6):795-806. PubMedID: 22103613.

  Pharmacogenomics Knowledge for Personalized Medicine. M. Whirl-Carrillo, E.M. McDonagh, J. M. Hebert, L. Gong, K. Sangkuhl, C.F. Thorn, R.B. Altman and T.E. Klein.Clinical Pharmacology & Therapeutics (2012) 92(4): 414-417. PubMedID: 22992668.

  CPIC: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network. Clinical pharmacology and therapeutics. 2011. Relling MV, Klein TE. PubMedID: 21270786; PMCID: PMC3098762.

Saccharomyces Genome Database (SGD)

• Description — SGD is an organized collection of genetic and molecular biological information about Saccharomyces cerevisiae, bakers' and brewers' yeast. It contains the sequences of yeast genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; links to literature information; links to functional genomics datasets; and tools for analysis and comparison of sequences.
• Location — online
• Website — http://genome-www.stanford.edu/Saccharomyces/
• Selected References

  Genetic and physical maps of Saccharomyces cerevisiae. Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. PubMedID: 9169866.

  Saccharomyces Genome Database provides mutant phenotype data. Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM (2010) Nucleic Acids Res 38(Database issue):D433-6 PubMedID: 19906697.

  New mutant phenotype data curation system in the Saccharomyces Genome Database. Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM. (2009) Database (Oxford):bap001. PubMedID: 20157474.