Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification
Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification
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DOI：
10.1016/j.jbi.2006.09.002
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发表时间：
2007-06-01
影响因子：
4.5
通讯作者：
Kors, Jan A.
中科院分区：
文献类型：
--
作者：
Schuemie, Martijn J.;Mons, Barend;Kors, Jan A.
在文本中识别基因和蛋白质名称需要字典方法来将同义词与相同的基因或蛋白质联系起来，并将名称链接到外部数据库。然而，现有的字典是不完整的。我们研究了两种互补的方法自动生成一个全面的字典：结合现有的基因和蛋白质数据库的信息和基于规则的生成拼写变化。这两种方法在文献中已有报道，但迄今尚未进行系统的组合和评价。我们结合了来自四种不同生物的几个现有数据库的基因和蛋白质名称。与任何单一数据库相比，组合字典在三个不同的测试集上显示出召回率的大幅增加。应用23拼写变化规则的组合字典进一步增加召回。然而，许多规则似乎没有效果，有些规则似乎对精确度有不利影响。(C)2006年爱思唯尔公司All rights reserved.
Gene and protein name identification in text requires a dictionary approach to relate synonyms to the same gene or protein, and to link names to external databases. However, existing dictionaries are incomplete. We investigate two complementary methods for automatic generation of a comprehensive dictionary: combination of information from existing gene and protein databases and rule-based generation of spelling variations. Both methods have been reported in literature before, but have hitherto not been combined and evaluated systematically. We combined gene and protein names from several existing databases of four different organisms. The combined dictionaries showed a substantial increase in recall on three different test sets, as compared to any single database. Application of 23 spelling variation rules to the combined dictionaries further increased recall. However, many rules appeared to have no effect and some appear to have a detrimental effect on precision. (C) 2006 Elsevier Inc. All rights reserved.