Abstract
Increasing numbers of whole-genome sequences are available, but to interpret them fully requires more than listing all genes. Genome databases are faced with the challenges of integrating heterogenous data and enabling data mining. In comparison to a data warehousing approach, where integration is achieved through replication of all relevant data in a unified schema, distributed approaches provide greater flexibility and maintainability. These are important in a field where new data is generated rapidly and our understanding of the data changes. Interoperability between distributed data sources allows data maintenance to be separated from integration and analysis. Simple ways to access the data can facilitate the development of new data mining tools and the transition from model genome analysis to comparative genomics. With the MIPS Arabidopsis thaliana genome database (MAtDB, http://mips.gsf.de/proj/thal/db) our aim is to go beyond a data repository towards creating an integrated knowledge resource. To this end, the Arabidopsis genome has been a backbone against which to structure and integrate heterogenous data. The challenges to be met are continuous updating of data, the design of flexible data models that can evolve with new data, the integration of heterogenous data, e.g. through the use of ontologies, comprehensive views and visualization of complex information, simple interfaces for application access locally or via the Internet, and knowledge transfer across species.
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Selected References
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- Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796–815. doi: 10.1038/35048692. [DOI] [PubMed] [Google Scholar]
- Frishman D., Albermann K., Hani J., Heumann K., Metanomski A., Zollner A., Mewes H. W. Functional and structural genomics using PEDANT. Bioinformatics. 2001 Jan;17(1):44–57. doi: 10.1093/bioinformatics/17.1.44. [DOI] [PubMed] [Google Scholar]
- Haas Brian J., Volfovsky Natalia, Town Christopher D., Troukhan Maxim, Alexandrov Nickolai, Feldmann Kenneth A., Flavell Richard B., White Owen, Salzberg Steven L. Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol. 2002 May 30;3(6):RESEARCH0029–RESEARCH0029. doi: 10.1186/gb-2002-3-6-research0029. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hubbard T., Barker D., Birney E., Cameron G., Chen Y., Clark L., Cox T., Cuff J., Curwen V., Down T. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38–41. doi: 10.1093/nar/30.1.38. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sakata Katsumi, Nagamura Yoshiaki, Numa Hisataka, Antonio Baltazar A., Nagasaki Hideki, Idonuma Atsuko, Watanabe Wakako, Shimizu Yuji, Horiuchi Ikuo, Matsumoto Takashi. RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res. 2002 Jan 1;30(1):98–102. doi: 10.1093/nar/30.1.98. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schoof Heiko, Zaccaria Paolo, Gundlach Heidrun, Lemcke Kai, Rudd Stephen, Kolesov Grigory, Arnold Roland, Mewes H. W., Mayer Klaus F. X. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 2002 Jan 1;30(1):91–93. doi: 10.1093/nar/30.1.91. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wilkinson Mark D., Links Matthew. BioMOBY: an open source biological web services proposal. Brief Bioinform. 2002 Dec;3(4):331–341. doi: 10.1093/bib/3.4.331. [DOI] [PubMed] [Google Scholar]