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Semantic Data Integration for Life Science Entities

  • Reference work entry
Encyclopedia of Database Systems

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Synonyms

Object identification; Data fusion; Duplicate detection;LSID

Definition

An entity is the representation of a (not necessarily physical) real-world object, such as a gene, a protein, or a disease, within a database. To integrate information about the same entities from different databases, these representations must be analyzed to uncover the corresponding underlying objects. This process is called entity identification. A variation of entity identification is duplicate detection, which analyses two or more entities to determine whether they represent the same real-world object or not. Finally, data fusion is the process of generating a single, homogeneous representation from multiple, possibly inconsistent entities that represent the same real-world object.

When entities have globally unique keys, such as ISBN numbers in the case of books, entity identification and duplicate detection are simple. However, in life science databases, one usually has only descriptive...

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Recommended Reading

  1. Bhat T.N., Bourne P., Feng Z., Gilliland G., Jain S., Ravichandran V., Schneider B., Schneider K., Thanki N., and Weissig H, et al. The PDB data uniformity project. Nucleic Acids Res., 29(1):214–218, 2001.

    Google Scholar 

  2. Brenner S.E. Errors in Genome Annotation. Trends Genet., 15(4):132–133, 1999.

    Google Scholar 

  3. Gibson G. and Muse S.V. A Primer of Genome Science. Sinauer Associates, Sunderland, MA.(2001)

    Google Scholar 

  4. Karp P.D. Models of identifiers. In Proc. Second Meeting on Interconnection of Molecular Biology Databases. Cambridge, UK, 1995.

    Google Scholar 

  5. Kingsbury D. Consensus, common entry, and community curation. Nat. Biotechnol., 14:679, 1996.

    Google Scholar 

  6. Krauthammer M. and Nenadic G. Term identification in the biomedical literature. J. Biomed. Inform., 37(6):512–526, 2004.

    Google Scholar 

  7. Leser U. and Hakenberg J. What Makes a Gene Name? Named Entity Recognition in the Biomedical Literature. Briefings in Bioinformatics, 6(4):357–369, 2005.

    Google Scholar 

  8. Müller H., Naumann F., and Freytag J.-C. Data quality in genome databases. In Proc. Conf. on Information Quality, 2003.

    Google Scholar 

  9. Smith T.F. and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol., 147:195–197, 1981.

    Google Scholar 

  10. Tamames J. and Valencia A. 2006.The success (or not) of HUGO nomenclature. Genome Biol., 7(5):402,

    Google Scholar 

  11. Trissl S., Rother K., Müller H., Koch I., Steinke T., Preissner R., Frömmel C., and Leser U. Columba: an integrated database of proteins, structures, and annotations. BMC Bioinformatics, 6:81, 2005.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Humboldt University of Berlin, Berlin, Germany

    Ulf Leser

Authors
  1. Ulf Leser
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Editor information

Editors and Affiliations

  1. College of Computing, Georgia Institute of Technology, 266 Ferst Drive, 30332-0765, Atlanta, GA, USA

    LING LIU (Professor) (Professor)

  2. Database Research Group David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, N2L 3G1, Waterloo, ON, Canada

    M. TAMER ÖZSU (Professor and Director, University Research Chair) (Professor and Director, University Research Chair)

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© 2009 Springer Science+Business Media, LLC

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Leser, U. (2009). Semantic Data Integration for Life Science Entities. In: LIU, L., ÖZSU, M.T. (eds) Encyclopedia of Database Systems. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-39940-9_627

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