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OntoGene in BioCreative II.5


Rinaldi, Fabio; Schneider, Gerold; Kaljurand, Kaarel; Clematide, Simon; Vachon, Thérèse; Romacker, Martin (2010). OntoGene in BioCreative II.5. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(3):472-480.

Abstract

We describe a system for the detection of mentions of protein-protein interactions in the biomedical scientific literature. The original system was developed as a part of the OntoGene project, which focuses on using advanced computational linguistic techniques for text mining applications in the biomedical domain. In this paper, we focus in particular on the participation to the BioCreative II.5 challenge, where the OntoGene system achieved best-ranked results. Additionally, we describe a feature-analysis experiment performed after the challenge, which shows the unexpected result that one single feature alone performs better than the combination of features used in the challenge.

We describe a system for the detection of mentions of protein-protein interactions in the biomedical scientific literature. The original system was developed as a part of the OntoGene project, which focuses on using advanced computational linguistic techniques for text mining applications in the biomedical domain. In this paper, we focus in particular on the participation to the BioCreative II.5 challenge, where the OntoGene system achieved best-ranked results. Additionally, we describe a feature-analysis experiment performed after the challenge, which shows the unexpected result that one single feature alone performs better than the combination of features used in the challenge.

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24 citations in Web of Science®
33 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:06 Faculty of Arts > English Department
06 Faculty of Arts > Institute of Computational Linguistics
Dewey Decimal Classification:000 Computer science, knowledge & systems
820 English & Old English literatures
410 Linguistics
Uncontrolled Keywords:Text Mining Parsinng Biomedicine
Language:English
Date:July 2010
Deposited On:21 Feb 2011 13:13
Last Modified:11 May 2016 07:21
Publisher:IEEE
ISSN:1545-5963
Funders:Swiss National Science Foundation (grant 100014-118396/1), Novartis Pharma AG, NITAS, Basel
Publisher DOI:10.1109/TCBB.2010.50
PubMed ID:20671319
Permanent URL: http://doi.org/10.5167/uzh-46282

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