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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan

4 Issues per year


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 11, Issue 2

Issues

A Query Suggestion Workflow for Life Science IR-Systems

Maria Esch
  • Corresponding author
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
  • Rothamsted Research, Department of Computational and Systems Biology, Harpenden, United Kingdom of Great Britain and Northern Ireland
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Jinbo Chen
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Stephan Weise
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Keywan Hassani-Pak
  • Rothamsted Research, Department of Computational and Systems Biology, Harpenden, United Kingdom of Great Britain and Northern Ireland
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  • De Gruyter OnlineGoogle Scholar
/ Uwe Scholz
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Matthias Lange
  • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2014-237

Summary

Information Retrieval (IR) plays a central role in the exploration and interpretation of integrated biological datasets that represent the heterogeneous ecosystem of life sciences. Here, keyword based query systems are popular user interfaces. In turn, to a large extend, the used query phrases determine the quality of the search result and the effort a scientist has to invest for query refinement.

In this context, computer aided query expansion and suggestion is one of the most challenging tasks for life science information systems. Existing query front-ends support aspects like spelling correction, query refinement or query expansion. However, the majority of the front-ends only make limited use of enhanced IR algorithms to implement comprehensive and computer aided query refinement workflows.

In this work, we present the design of a multi-stage query suggestion workflow and its implementation in the life science IR system LAILAPS. The presented workflow includes enhanced tokenisation, word breaking, spelling correction, query expansion and query suggestion ranking. A spelling correction benchmark with 5,401 queries and manually selected use cases for query expansion demonstrate the performance of the implemented workflow and its advantages compared with state-of-the-art systems.

About the article

Published Online: 2016-10-18

Published in Print: 2014-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 11, Issue 2, Pages 15–26, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2014-237.

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© 2014 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange, and Timothée Poisot
PLOS Computational Biology, 2018, Volume 14, Number 3, Page e1006058

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