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Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions

Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jeppe Koivula, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions. In: Patrick Ruch Adeline Nazarenko Nigel Collier (Ed.), Proceedings of the International Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), 15-21, 2004.

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.

BibTeX entry:

@INPROCEEDINGS{inpPyGiPaKoBoJaSa04a,
  title = {Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions},
  booktitle = {Proceedings of the International Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA)},
  author = {Pyysalo, Sampo and Ginter, Filip and Pahikkala, Tapio and Koivula, Jeppe and Boberg, Jorma and Järvinen, Jouni and Salakoski, Tapio},
  editor = {Nigel Collier, Patrick Ruch Adeline Nazarenko},
  pages = {15-21},
  year = {2004},
}

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

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