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ABSTRACT A prerequisite to systems biology is the integration of heterogeneous experimental data, which are stored in numerous life-science databases. However, a wide range of obstacles that

relate to access, handling and integration impede the efficient use of the contents of these databases. Addressing these issues will not only be essential for progress in systems biology,

it will also be crucial for sustaining the more traditional uses of life-science databases. Access through your institution Buy or subscribe This is a preview of subscription content, access

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Article  CAS  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS The authors would like to thank C. Rawlings and P. Verrier for commenting on an earlier version of

this article. Furthermore we would like to thank the following individuals for exploring with us the pitfalls of life-science databases over the past years: J. Baumbach, J. Butz, E.

Kirchem, F. Klingert, S. Knop, B. Kormeier, I. Kupp, A. Neu, A. Rüegg, A. Skusa, B. Steuernagel, J. Taubert, P. Verrier and R. Winnenburg. S.P. gratefully acknowledges funding by the

European Science Foundation. Rothamsted Research receives grant-aided support from the UK Biotechnological and Biological Science Research Council. AUTHOR INFORMATION AUTHORS AND

AFFILIATIONS * Stephan Philippi is at the Department of Computer Science, University of Koblenz, PO Box 201602, Koblenz, 56016, Germany Stephan Philippi * Jacob Köhler is at the

Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK Jacob Köhler Authors * Stephan Philippi View author publications You can also search

for this author inPubMed Google Scholar * Jacob Köhler View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence to Stephan

Philippi. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. RELATED LINKS RELATED LINKS FURTHER INFORMATION BioJava BioPAX — Biological Pathways

Exchange BioPerl BioRuby CellML DiscoveryLink DNA Data Bank of Japan EC (enzyme class) numbers of the enzyme nomenclature Ensembl Trace Server European Bioinformatics Institute SRS server

European Bioinformatics Institute Extensible Markup Language (XML) Gene Ontology homepage Kyoto Encyclopedia of Genes and Genomes Microarray Gene Expression Data Society mySQL NCBI taxonomy

Nucleic Acids Research Database Categories List ONDEX Open Biomedical Ontologies Open Source Initiative License Index PostgreSQL Proteomics Standards Initiative — molecular interaction

Systems biology markup language Universal Protein Resource Web Services Activity GLOSSARY * Controlled vocabulary A standardized set of terms that can be used in a given application domain.

A prominent example is the enzyme class nomenclature, which describes classes of biochemical reaction. * Database management system A system that provides a means of storing, modifying and

extracting data from a database. * Evidence code A controlled vocabulary that is used to track the types of evidence that support a gene annotation. * Flat file Human readable,

non-standardized files that can be used to exchange the contents of life-science databases. * Ontology A commonly agreed definition of real-world concepts, such as 'protein' and

'enzyme', and their particular relationships, for example, an enzyme 'is a' protein. * Parser Software that reads a given input, such as a flat file, for further

processing. * Web service A standardized way to allow for interoperable machine-to-machine interaction over a network. * XML The extensible markup language (XML) is a standard for the

creation of application-specific, self-descriptive markup languages, which, for example, can be used for the definition of data-exchange formats. RIGHTS AND PERMISSIONS Reprints and

permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Philippi, S., Köhler, J. Addressing the problems with life-science databases for traditional uses and systems biology. _Nat Rev Genet_ 7,

482–488 (2006). https://doi.org/10.1038/nrg1872 Download citation * Published: 09 May 2006 * Issue Date: 01 June 2006 * DOI: https://doi.org/10.1038/nrg1872 SHARE THIS ARTICLE Anyone you

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