Gene annotation from scientific literature using mappings between keyword systems
Gene annotation from scientific literature using mappings between keyword systems
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DOI：
10.1093/bioinformatics/bth207
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发表时间：
2004-09-01
期刊：
影响因子：
5.8
通讯作者：
Andrade, MA
中科院分区：
文献类型：
--
作者：
Pérez, AJ;Perez-Iratxeta, C;Andrade, MA
动机：通过关键词描述数据库中的基因有助于非专业人员快速掌握基因的特性，并提高应用于基因数据的计算工具的效率（例如，在基因数据库中搜索与特定生物过程相关的序列）。然而，关联的关键字的基因或蛋白质序列是一个困难的过程，最终意味着检查的文献相关的基因。结果：为了支持这一任务，我们提出了一个程序来获得关键字从一组科学摘要相关的基因。我们的系统是基于从不同的数据库中使用的模糊关联，可以适用于所有的一般性的任何一对链接的数据库模型的相关术语之间的映射的自动提取。我们测试了系统的注释基因的SWISS-PROT数据库与关键字来自摘要链接到他们的条目（存储在MEDLINE数据库的科学参考）。的注释过程的性能是更好的SWISS-PROT关键字（召回率为47%，精度为68%）比基因本体论术语（召回率为8%，精度为67%）。
Motivation: The description of genes in databases by keywords helps the non-specialist to quickly grasp the properties of a gene and increases the efficiency of computational tools that are applied to gene data (e.g. searching a gene database for sequences related to a particular biological process). However, the association of keywords to genes or protein sequences is a difficult process that ultimately implies examination of the literature related to a gene.Results: To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene. Our system is based on the automated extraction of mappings between related terms from different databases using a model of fuzzy associations that can be applied with all generality to any pair of linked databases. We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references). The performance of the annotation procedure was much better for SWISS-PROT keywords (recall of 47%, precision of 68%) than for Gene Ontology terms (recall of 8%, precision of 67%).