Analysis of link grammar on biomedical dependency corpus targeted at protein-protein interactions

Authors:
Sampo Pyysalo;Filip Ginter;Tapio Pahikkala;Jorma Boberg;Jouni Järvinen;Tapio Salakoski;Jeppe Koivula
Affiliations:
University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland;University of Turku, Turku, Finland;MediCel Ltd., Helsinki, Finland
Venue:
JNLPBA '04 Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications
Year:
2004

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Abstract

In this paper, we present an evaluation of the Link Grammar parser on a corpus consisting of sentences describing protein-protein interactions. We introduce the notion of an interaction subgraph, which is the subgraph of a dependency graph expressing a protein-protein interaction. We measure the performance of the parser for recovery of dependencies, fully correct linkages and interaction subgraphs. We analyze the causes of parser failure and report specific causes of error, and identify potential modifications to the grammar to address the identified issues. We also report and discuss the effect of an extension to the dictionary of the parser.