This article is part of the supplement: Proceedings of the Second International Symposium on Languages in Biology and Medicine (LBM) 2007

Open Access Proceedings

Comparative analysis of five protein-protein interaction corpora

Sampo Pyysalo*, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter and Tapio Salakoski

Author Affiliations

Turku Centre for Computer Science (TUCS) and the Department of IT, University of Turku, Joukahaisenkatu 3-5, 20520 Turku, Finland

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BMC Bioinformatics 2008, 9(Suppl 3):S6  doi:10.1186/1471-2105-9-S3-S6

Published: 11 April 2008

Abstract

Background

Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate.

Results

We present the first comparative evaluation of the diverse PPI corpora, performing quantitative evaluation using two separate information extraction methods as well as detailed statistical and qualitative analyses of their properties. For the evaluation, we unify the corpus PPI annotations to a shared level of information, consisting of undirected, untyped binary interactions of non-static types with no identification of the words specifying the interaction, no negations, and no interaction certainty.

We find that the F-score performance of a state-of-the-art PPI extraction method varies on average 19 percentage units and in some cases over 30 percentage units between the different evaluated corpora. The differences stemming from the choice of corpus can thus be substantially larger than differences between the performance of PPI extraction methods, which suggests definite limits on the ability to compare methods evaluated on different resources. We analyse a number of potential sources for these differences and identify factors explaining approximately half of the variance. We further suggest ways in which the difficulty of the PPI extraction tasks codified by different corpora can be determined to advance comparability. Our analysis also identifies points of agreement and disagreement in PPI corpus annotation that are rarely explicitly stated by the authors of the corpora.

Conclusions

Our comparative analysis uncovers key similarities and differences between the diverse PPI corpora, thus taking an important step towards standardization. In the course of this study we have created a major practical contribution in converting the corpora into a shared format. The conversion software is freely available at http://mars.cs.utu.fi/PPICorpora webcite.