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OntoGene in Biocreative II


Rinaldi, Fabio; Kappeler, T; Kaljurand, K; Schneider, G; Klenner, M; Hess, M; von Allmen, J M; Romacker, M; Vachon, T (2007). OntoGene in Biocreative II. In: Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, 23 April 2007 - 25 April 2007.

Abstract

Research scientists and companies working in the domains of biomedicine and genomics are increasingly
faced with the problem of efficiently locating, in the vast amount of published scientific results, the critical
pieces of information that are needed in order to assess current and future research investment.
In this paper we describe approaches taken within the scope of the second Biocreative competition in
order to solve two aspects of this problem: the detection of novel protein interactions reported in scientific
articles, and the detection of the experimental method that was used to confirm the interaction.
Our approach is based on a high-recall protein annotation step, followed by two sharp disambiguation
steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which
deliver high-precision results, while maintaining a reasonable recall.

Abstract

Research scientists and companies working in the domains of biomedicine and genomics are increasingly
faced with the problem of efficiently locating, in the vast amount of published scientific results, the critical
pieces of information that are needed in order to assess current and future research investment.
In this paper we describe approaches taken within the scope of the second Biocreative competition in
order to solve two aspects of this problem: the detection of novel protein interactions reported in scientific
articles, and the detection of the experimental method that was used to confirm the interaction.
Our approach is based on a high-recall protein annotation step, followed by two sharp disambiguation
steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which
deliver high-precision results, while maintaining a reasonable recall.

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Additional indexing

Item Type:Conference or Workshop Item (Paper), refereed, original work
Communities & Collections:06 Faculty of Arts > Institute of Computational Linguistics
Dewey Decimal Classification:000 Computer science, knowledge & systems
410 Linguistics
Language:English
Event End Date:25 April 2007
Deposited On:30 Mar 2010 12:37
Last Modified:20 Sep 2018 03:19
ISBN:84-933255-6-2
OA Status:Green
Official URL:http://biocreative.sourceforge.net/bc2ws/index.html

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