On the unification of syntactic annotations under the stanford dependency scheme: a case study on BioInfer and GENIA

Authors:
Sampo Pyysalo;Filip Ginter;Katri Haverinen;Juho Heimonen;Tapio Salakoski;Veronika Laippala
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
Venue:
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Year:
2007

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Abstract

Several incompatible syntactic annotation schemes are currently used by parsers and corpora in biomedical information extraction. The recently introduced Stanford dependency scheme has been suggested to be a suitable unifying syntax formalism. In this paper, we present a step towards such unification by creating a conversion from the Link Grammar to the Stanford scheme. Further, we create a version of the BioInfer corpus with syntactic annotation in this scheme. We present an application-oriented evaluation of the transformation and assess the suitability of the scheme and our conversion to the unification of the syntactic annotations of BioInfer and the GENIA Treebank. We find that a highly reliable conversion is both feasible to create and practical, increasing the applicability of both the parser and the corpus to information extraction.