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BioMedical Information Retrieval: The BioTracer Approach

  • Conference paper
Information Technology in Bio- and Medical Informatics, ITBAM 2010 (ITBAM 2010)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 6266))

Abstract

With the large amount of biomedical information available today, providing a good search tool is vital. Such a tool should not only be able to retrieve the sought information, but also to filter out irrelevant documents, while giving the relevant ones the highest ranking. Focusing on biomedical information, the main goal of this work has been to investigate how to improve the ability for a system to find and rank relevant documents. To achieve this, we apply a series of information retrieval techniques to search in biomedical information and combine them in an optimal manner. These techniques include extending and using well-established information retrieval (IR) similarity models like the Vector Space Model (VSM) and BM25 and their underlying scoring schemes, and allowing users to affect the ranking according to their view of relevance. The techniques have been implemented and tested in a proof-of-concept prototype called BioTracer, extending a Java-based open source search engine library. The results from our experiments using the TREC 2004 Genomic Track collection seem promising. Our investigation have also revealed that involving the user in the search will indeed have positive effects on the ranking of search results, and that the approaches used in BioTracer can be used to meet the user’s information needs.

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Author information

Authors and Affiliations

  1. Department of Computer and Information Science, Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway

    Heri Ramampiaro

Authors
  1. Heri Ramampiaro
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Editors and Affiliations

  1. Department of Computer Science, San José State University, One Washington Square, 95192-0249, San José, CA, U.S.A.

    Sami Khuri

  2. Faculty of Electrical Engineering, Department of Cybernetics, Czech Technical University, Technicka 2, 166 27, Prague 6, Czech Republic

    Lenka Lhotská

  3. Dipartimento di Informatica, University of Pisa, Largo, Pontecorvo 3, 56127, Pisa, Italy

    Nadia Pisanti

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Ramampiaro, H. (2010). BioMedical Information Retrieval: The BioTracer Approach. In: Khuri, S., Lhotská, L., Pisanti, N. (eds) Information Technology in Bio- and Medical Informatics, ITBAM 2010. ITBAM 2010. Lecture Notes in Computer Science, vol 6266. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15020-3_14

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  • DOI: https://doi.org/10.1007/978-3-642-15020-3_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-15019-7

  • Online ISBN: 978-3-642-15020-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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