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Columba: Multidimensional Data Integration of Protein Annotations

  • Kristian Rother
  • Heiko Müller
  • Silke Trissl
  • Ina Koch
  • Thomas Steinke
  • Robert Preissner
  • Cornelius Frömmel
  • Ulf Leser
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2994)

Abstract

We present COLUMBA, an integrated database of protein annotations. COLUMBA is centered around proteins whose structure has been resolved and adds as much annotations as possible to those proteins, describing their proper-ties such as function, sequence, classification, textual description, participation in pathways, etc. Annotations are extracted from seven (soon eleven) external data sources. In this paper we describe the motivation for building COLUMBA, its integrational architecture and the software tools we developed for the integrated data sources and keeping COLUMBA up-to-date. We put special focus on two aspects: First, COLUMBA does not try to remove redundancies and overlaps in data sources, but views each data source as a proper dimension describing a protein. We explain the advantages of this approach compared to a tighter semantic integration as pursued in many other projects. Second, we highlight our current investigations regarding the quality of data in COLUMBA by identification of hot spots of poor data quality.

Keywords

Protein Data Bank Global Schema Nucleic Acid Research Protein Annotation Protein Data Bank Entry 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Kristian Rother
    • 1
  • Heiko Müller
    • 2
  • Silke Trissl
    • 2
  • Ina Koch
    • 3
  • Thomas Steinke
    • 4
  • Robert Preissner
    • 1
  • Cornelius Frömmel
    • 1
  • Ulf Leser
    • 2
  1. 1.Institut für BiochemieUniversitätskrankenhaus Charité BerlinBerlinGermany
  2. 2.Institut für InformatikHumboldt-Universität zu BerlinBerlinGermany
  3. 3.Technische Fachhochschule BerlinBerlinGermany
  4. 4.Zuse Institut BerlinBerlinGermany

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