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Bioinformatics 2007 23(13):i424-i432; doi:10.1093/bioinformatics/btm184
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© 2007 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.

Negation of protein–protein interactions: analysis and extraction

Olivia Sanchez-Graillet 1 and Massimo Poesio 1,2,*

1Department of Computer Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK and 2DIT and Center for Mind/Brain Sciences, University of Trento, Via Sommarive 14 I-38050 POVO (TN), Italy

*To whom correspondence should be addressed.


  Abstract

Motivation: Negative information about protein–protein interactions—from uncertainty about the occurrence of an interaction to knowledge that it did not occur—is often of great use to biologists and could lead to important discoveries. Yet, to our knowledge, no proposals focusing on extracting such information have been proposed in the text mining literature.

Results: In this work, we present an analysis of the types of negative information that is reported, and a heuristic-based system using a full dependency parser to extract such information. We performed a preliminary evaluation study that shows encouraging results of our system. Finally, we have obtained an initial corpus of negative protein–protein interactions as basis for the construction of larger ones.

Availability: The corpus is available by request from the authors.

Contact: osanch{at}essex.ac.uk or poesio{at}essex.ac.uk


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