EBIMed - text crunching to gather facts for proteins from Medline
EBIMed - text crunching to gather facts for proteins from Medline
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DOI：
10.1093/bioinformatics/btl302
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发表时间：
2007-01-15
期刊：
影响因子：
5.8
通讯作者：
Stoehr, Peter
中科院分区：
文献类型：
--
作者：
Rebholz-Schuhmann, Dietrich;Kirsch, Harald;Stoehr, Peter
为了能够高效、系统地检索 Medline 中的语句，我们开发了 EBIMed，这是一项将文档检索与基于共现的 Medline 摘要分析相结合的服务。根据关键字查询，EBIMed 会从 EMBL-EBI 安装的 Medline 中检索摘要，并筛选出包含公共生物信息学资源中维护的生物医学术语的句子。提取的句子和术语用于生成相同生物学背景下使用的蛋白质、基因本体（GO）注释、药物和物种的概述表。检索到的摘要和提取的句子中的所有术语都链接到生物医学数据库中的条目。我们评估了检索到的句子中术语和关系的识别质量。超过 90% 的蛋白质名称确实代表了一种蛋白质。根据对 Wnt 通路中的四个蛋白质-蛋白质对的分析，我们估计包含此类对的陈述中有 37% 提到了有意义的相互作用，并阐明了 Dkk 与 LRP 的相互作用。我们的结论是，EBIMed 改善了对蛋白质和药物参与同一生物过程的信息的获取，例如。带有蛋白质 GO 注释、蛋白质-蛋白质相互作用以及药物对蛋白质的影响的语句。
To allow efficient and systematic retrieval of statements from Medline we have developed EBIMed, a service that combines document retrieval with co-occurrence-based analysis of Medline abstracts. Upon keyword query, EBIMed retrieves the abstracts from EMBL-EBI's installation of Medline and filters for sentences that contain biomedical terminology maintained in public bioinformatics resources. The extracted sentences and terminology are used to generate an overview table on proteins, Gene Ontology (GO) annotations, drugs and species used in the same biological context. All terms in retrieved abstracts and extracted sentences are linked to their entries in biomedical databases. We assessed the quality of the identification of terms and relations in the retrieved sentences. More than 90% of the protein names found indeed represented a protein. According to the analysis of four protein-protein pairs from the Wnt pathway we estimated that 37% of the statements containing such a pair mentioned a meaningful interaction and clarified the interaction of Dkk with LRP. We conclude that EBIMed improves access to information where proteins and drugs are involved in the same biological process, e.g. statements with GO annotations of proteins, protein-protein interactions and effects of drugs on proteins.