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On the Unification of Syntactic Annotations under the Stanford Dependency Scheme: A Case Study on BioInfer and GENIA

Sampo Pyysalo, Filip Ginter, Veronika Laippala, Katri Haverinen, Juho Heimonen, Tapio Salakoski, On the Unification of Syntactic Annotations under the Stanford Dependency Scheme: A Case Study on BioInfer and GENIA. In: Proceedings of BioNLP 2007: Biological, Translational, and Clinical Language Processing, 25-32, ACL, 2007.

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 syntactic 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.

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BibTeX entry:

@INPROCEEDINGS{inpPyGiLaHaHeSa07a,
  title = {On the Unification of Syntactic Annotations under the Stanford Dependency Scheme: A Case Study on BioInfer and GENIA},
  booktitle = {Proceedings of BioNLP 2007: Biological, Translational, and Clinical Language Processing},
  author = {Pyysalo, Sampo and Ginter, Filip and Laippala, Veronika and Haverinen, Katri and Heimonen, Juho and Salakoski, Tapio},
  publisher = {ACL},
  pages = {25-32},
  year = {2007},
}

Belongs to TUCS Research Unit(s): Turku BioNLP Group

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