OntoGene in BioCreative II 英文参考文献.docVIP

Open Access Re rch 2008RinaldietVoal.lumesea9, Suppl 2, Article S13 OntoGene in BioCreative II Fabio Rinaldi1, Thomas Kappeler1, Kaarel Kaljurand1, Gerold Schneider1, Manfred Klenner1, Simon Clematide1, Michael Hess1, Jean-Marc von Allmen2, Pierre Parisot2, Martin Romacker2 and Therese Vachon2 Addresses: 1Institute of Computational Linguistics, University of Zurich, Binzmühlestrasse, CH-8050 Zurich, Switzerland. 2Novartis Pharma AG, NITAS, Text Mining Services, CH-4002, Basel, Switzerland. Correspondence: Fabio Rinaldi. Email: rinaldi@cl.uzh.ch Published: 01 September 2008 doi: 10.1186/gb-2008-9-S2-S13 Genome Biology 2008, 9(Suppl 2):S13 The electronic version of this article is the complete one and can be found online at /2008/9/S2/S13 ? 2008 Rinaldi et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the critical pieces of information that are needed to direct current and future research investment. Results: In this report we describe approaches taken within the scope of the second BioCreative competition in order to solve two aspects of this problem: detection of novel protein interactions reported in scientific articles, and detection of the experimental method that was used to confirm the interaction. Our approach to the former problem is based on a high-recall protein annotation step, followed by two strict disambiguation steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which deliver high-precision re