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Using the OntoGene pipeline for the triage task of BioCreative 2012

Rinaldi, F, Clematide, S, Hafner, S, Schneider, G, Grigonyte, G, Romacker, M and Vachon, T (2013) Using the OntoGene pipeline for the triage task of BioCreative 2012. Database-the Journal of Biological Databases and Curation.


In this article, we describe the architecture of the OntoGene Relation mining pipeline and its application in the triage task of BioCreative 2012. The aim of the task is to support the triage of abstracts relevant to the process of curation of the Comparative Toxicogenomics Database. We use a conventional information retrieval system (Lucene) to provide a baseline ranking, which we then combine with information provided by our relation mining system, in order to achieve an optimized ranking. Our approach additionally delivers domain entities mentioned in each input document as well as candidate relationships, both ranked according to a confidence score computed by the system. This information is presented to the user through an advanced interface aimed at supporting the process of interactive curation. Thanks, in particular, to the high-quality entity recognition, the OntoGene system achieved the best overall results in the task

Item Type: Article
Additional Information: pubid: 244 nvp_institute: NIBR contributor_address: [Rinaldi, Fabio; Clematide, Simon; Hafner, Simon; Schneider, Gerold; Grigonyte, Gintare] Univ Zurich, Inst Computat Linguist, CH-8050 Zurich, Switzerland. [Romacker, Martin; Vachon, Therese] Novartis Pharma AG, NIBR IT, Text Min Serv, Basel, Switzerland.
Date Deposited: 13 Oct 2015 13:12
Last Modified: 13 Oct 2015 13:12


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