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Nucleic Acids Research Advance Access originally published online on June 11, 2009
Nucleic Acids Research 2009 37(Web Server issue):W160-W165; doi:10.1093/nar/gkp484
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W160-W165
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction

Martin Krallinger1,*, Carlos Rodriguez-Penagos2, Ashish Tendulkar1 and Alfonso Valencia1

1Structural Biology and Biocomputing programme, Spanish National Cancer Center (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain and 2Barcelona Media - Centre d'Innovacio, Av. Diagonal 177, 08018 Barcelona, Spain

*To whom correspondence should be addressed. Tel: +34 91 224 6900; Fax: +34 91 224 6980; Email: mkrallinger{at}cnio.es

Received March 16, 2009. Revised May 13, 2009. Accepted May 19, 2009.

There is an increasing interest in using literature mining techniques to complement information extracted from annotation databases or generated by bioinformatics applications. Here we present PLAN2L, a web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. Our system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. PLAN2L does not require registration and is freely accessible at http://zope.bioinfo.cnio.es/plan2l.


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