OntoGene in BioCreative II
OntoGene in BioCreative II
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DOI：
10.1186/gb-2008-9-s2-s13
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发表时间：
2008-01-01
期刊：
影响因子：
12.3
通讯作者：
Vachon, Therese
中科院分区：
文献类型：
--
作者：
Rinaldi, Fabio;Kappeler, Thomas;Vachon, Therese
背景：在生物医学和基因组学领域工作的研究科学家和公司越来越面临着在大量已发表的科学发现中有效地定位指导当前和未来研究投资所需的关键信息的问题。结果：在本报告中，我们描述了在第二届BioCreative竞赛范围内为解决这一问题的两个方面所采取的方法：检测科学文章中报道的新的蛋白质相互作用，以及检测用于确认相互作用的实验方法。我们对前一个问题的方法是基于一个高召回率的蛋白质标注步骤，然后是两个严格的歧义消除步骤。然后，剩余的蛋白质根据一些词汇-句法过滤器进行组合，在保持合理召回率的同时提供高精度的结果。实验方法的检测通过模式匹配方法来解决，在官方的BioCreative评估中提供了最好的结果。结论：尽管BioCreative的结果清楚地表明没有足够可靠的工具来进行全自动标注，但一些提出的方法(包括我们自己的方法)已经达到了竞争的水平。这使得它们既可以作为初步文件检查的独立工具，也可以作为旨在支持生物医学文献整理过程的环境中的模块。
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 results while maintaining reasonable recall. The detection of the experimental methods is tackled by a pattern matching approach, which has delivered the best results in the official BioCreative evaluation.Conclusion: Although the results of BioCreative clearly show that no tool is sufficiently reliable for fully automated annotations, a few of the proposed approaches (including our own) already perform at a competitive level. This makes them interesting either as standalone tools for preliminary document inspection, or as modules within an environment aimed at supporting the process of curation of biomedical literature.