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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 8, Issue 2

Issues

Automatic extraction of microorganisms and their habitats from free text using text mining workflows

BalaKrishna Kolluru
  • Corresponding author
  • National Centre for Text Mining, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK United Kingdom of Great Britain and Northern Ireland
  • School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, United Kingdom of Great Britain and Northern Ireland
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/ Sirintra Nakjang
  • Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK United Kingdom of Great Britain and Northern Ireland
  • School of Computing Science, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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/ Robert P. Hirt
  • Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom of Great Britain and Northern Ireland
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/ Anil Wipat
  • Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK United Kingdom of Great Britain and Northern Ireland
  • School of Computing Science, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom of Great Britain and Northern Ireland
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/ Sophia Ananiadou
  • National Centre for Text Mining, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK United Kingdom of Great Britain and Northern Ireland
  • School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester, M13 9PL, United Kingdom of Great Britain and Northern Ireland
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2011-184

Summary

In this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of the workflows, to extract the mention of microorganisms, habitats and the inter-relation between organisms and their habitats.

Results indicate a good performance for extraction of microorganisms and the relation extraction aspects of the task (with a precision of over 80%), while habitat recognition is only moderate (a precision of about 65%). We also conjecture that pdf-to-text conversion can be quite noisy and this implicitly affects any sentence-based relation extraction algorithms.

About the article

Published Online: 2016-10-18

Published in Print: 2011-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 8, Issue 2, Pages 176–186, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2011-184.

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© 2011 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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