<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>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 <italic>Arabidopsis thaliana</italic>  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
<italic>Arabidopsis</italic> 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.</p>
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Comp Funct Genomics. 2003 Apr; 4(2):255-258