Comparative analysis of five protein-protein interaction corpora

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 percentag...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski
• Keywords: BMCBI 2008, Diverse Ppi Corpora, Ppi Annotations, Ppi Extraction Methods