Integrating biological databases

Nature Reviews Genetics

Volumn 4, Issue 5, 2003, Pages 337-345

  Stein, Lincoln D ^a  

^a Watson School of Biological Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGY; BIOTECHNOLOGY; COMPUTER PROGRAM; DATA BASE; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; INTEGRATION; NONHUMAN; ONLINE SYSTEM; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW; SEQUENCE HOMOLOGY;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER COMMUNICATION NETWORKS; DATABASES, FACTUAL; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET;

EID: 0038745614     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1065     Document Type: Review

References (17)

1. Wheeler, D. L. et al. Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res. 30, 13-16 (2002). A description of web services for biological databases that use the SOAP software infrastructure.
2. Hubbard, T. et al. The Ensembl genome database project. Nucleic Acids Res. 30, 38-41 (2002).
3. Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002)
4. The FlyBase Consortium. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 30, 106-108 (2002). A highly successful attempt to develop a common controlled vocabulary for describing gene-product function and location.
5. Harris, T. W. et al. WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 31, 133-137 (2003).
6. The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genet. 25, 25-29 (2000).
7. Zdobnov, E. M., Lopez, R., Apweiler, R. & Etzold, T. The EBI SRS server - new features. Bioinformatics 18, 1149-1150 (2002).
8. Davidson, S. B. et al. K2/Kleisli and GUS: experiments in integrated access to genomic data sources. IBM Syst, J. 40 [online] 〈http://www.research.ibm.com/journal/sj/402/davidson.html〉 (2001). This paper describes a web-services approach to sharing genome annotations.
9. Ritter, O., Kocab, P., Senger, M., Wolf, D. & Suhai, S. Prototype implementation of the integrated genomic database. Comput Biomed. Res. 27, 97-115 (1994).
10. Bahl, A. et al. PlasmoDB: the Plasmodium genome resource. An integrated database that provides tools for accessing, analysing and mapping expression and sequence data (both finished and unfinished). Nucleic Acids Res. 30, 87-90 (2002). This paper contrasts efforts by the same group to integrate biological data sources using the federated database and data warehousing approaches.
11. Dowell, R. D., Jokerst, R. M., Day, A., Eddy, S. R. & Stein, L. The distributed annotation system. BMC Bioinform. 2, 7 (2001).
12. Lewis, S. E. et al. Apollo: a sequence annotation editor. Genoma Biol. 3, R0082.1-R0082.14 (2002).
13. Stevens, R., Goble, C. A. & Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief. Bioinform. 1, 398-414 (2000). A description of web services for biological databases using the CORBA software infrastructure.
14. Wilkinson, M. D. & Links, M. BioMOBY: an open source biological web services proposal. Brief Bioinform. 3, 331-341 (2002).
15. Foster, I. & Kesselman, C. (eds) The Grid: Blueprint for a New Computing Infrastructure (Kaufmann, San Francisco, 1999).
16. Stein, L. Creating a bioinformatics nation. Nature 417, 119-120 (2002)
17. Gilberg, D. G. euGenes: a eukeryote genome information system. Nucleic Acids Res. 30, 145-148 (2002).