Integrating various resources for gene name normalization.
Integrating various resources for gene name normalization.
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整合各种资源进行基因名称标准化
DOI：
10.1371/journal.pone.0043558
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Cheng L
中科院分区：
文献类型：
--
作者：
Hu Y;Li Y;Lin H;Yang Z;Cheng L
The recognition and normalization of gene mentions in biomedical literature are crucial steps in biomedical text mining. We present a system for extracting gene names from biomedical literature and normalizing them to gene identifiers in databases. The system consists of four major components: gene name recognition, entity mapping, disambiguation and filtering. The first component is a gene name recognizer based on dictionary matching and semi-supervised learning, which utilizes the co-occurrence information of a large amount of unlabeled MEDLINE abstracts to enhance feature representation of gene named entities. In the stage of entity mapping, we combine the strategies of exact match and approximate match to establish linkage between gene names in the context and the EntrezGene database. For the gene names that map to more than one database identifiers, we develop a disambiguation method based on semantic similarity derived from the Gene Ontology and MEDLINE abstracts. To remove the noise produced in the previous steps, we design a filtering method based on the confidence scores in the dictionary used for NER. The system is able to adjust the trade-off between precision and recall based on the result of filtering. It achieves an F-measure of 83% (precision: 82.5% recall: 83.5%) on BioCreative II Gene Normalization (GN) dataset, which is comparable to the current state-of-the-art.
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结合丰富的背景知识进行基因命名实体分类和识别
影响因子：
3
作者：
Li Y;Lin H;Yang Z
通讯作者：
Yang Z
生物公约概述：生物学信息提取的批判性评估。
影响因子：
3
作者：
Hirschman L;Yeh A;Blaschke C;Valencia A
通讯作者：
Valencia A
影响因子：
5.8
作者：
Settles, B
通讯作者：
Settles, B
影响因子：
3
作者：
Neves ML;Carazo JM;Pascual-Montano A
通讯作者：
Pascual-Montano A
影响因子：
5.8
作者：
Hakenberg, Joerg;Plake, Conrad;Gonzalez, Graciela
通讯作者：
Gonzalez, Graciela