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BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats

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Data Integration in the Life Sciences (DILS 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5109))

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Abstract

BioWarehouse is an open-source project for integrating bioinformatics databases within a relational database warehouse. It has two key features. A comprehensive database schema models many different bioinformatics datatypes. A set of loader tools permits loading of public bioinformatics databases, and of standard bioinformatics formats, into that database schema. Thus, multiple databases can be queried together within a single common schema. The supported databases are BioCyc, CMR, ENZYME, Eco2DBase, Genbank, Gene Ontology, KEGG, NCBI Taxonomy, and UniProt. The supported formats are BioPAX (protein interactions subset only) and MAGE-ML.

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References

  1. BioWarehouse home page, http://bioinformatics.ai.sri.com/biowarehouse/

  2. Lee, T.J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D.W.J., Tenenbaum, J.D., Karp, P.D.: BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics 7, 170 (2006)

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  3. Pouliot, Y., Lee, T.J., Wagner, V., Karp, P.D.: Identifying candidate genes using the biowarehouse: A case study. In: Proceedings of the Eighteenth International Conference on Systems Engineering, pp. 332–340. IEEE Computer Society, Los Alamitos (2005)

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Authors and Affiliations

  1. SRI International, Menlo Park, CA, USA

    Peter D. Karp, Thomas J. Lee & Valerie Wagner

Authors
  1. Peter D. Karp
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  2. Thomas J. Lee
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  3. Valerie Wagner
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Amos Bairoch Sarah Cohen-Boulakia Christine Froidevaux

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© 2008 Springer-Verlag Berlin Heidelberg

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Karp, P.D., Lee, T.J., Wagner, V. (2008). BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds) Data Integration in the Life Sciences. DILS 2008. Lecture Notes in Computer Science(), vol 5109. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69828-9_2

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  • DOI: https://doi.org/10.1007/978-3-540-69828-9_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-69827-2

  • Online ISBN: 978-3-540-69828-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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