Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.
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DOI：
10.1186/1471-2105-10-s2-s6
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发表时间：
2009-02-05
影响因子：
3
通讯作者：
Altman RB
中科院分区：
文献类型：
--
作者：
Garten Y;Altman RB
药物基因组学研究遗传变异与药物反应表型变异之间的关系。该领域正迅速变得越来越重要：它承诺根据遗传背景针对特定亚群的药物。药物基因组学文献迅速扩展，但分散在许多期刊上。因此，确定药物和分子实体（特别是基因和基因变体）之间的重要联系是具有挑战性的，因此这些关键联系往往会丢失。文本挖掘技术可以使我们将自由风格的文本转换为可计算的、可搜索的格式，在该格式中，药物基因组学概念（如基因、药物、多态性和疾病）被识别，并且这些概念之间的重要联系被记录。作为文本挖掘引擎输入的全文文章的可用性是关键，因为文献摘要通常不包含足够的信息来识别这些药物基因组学关联。因此，在一个名为Textbook的工具的基础上，我们创建了Pharmspresso工具，以帮助识别全文文章中的重要药物基因组学事实。Pharmspresso解析文本以查找人类基因、多态性、药物和疾病及其关系的参考资料。它以一系列有标记的文本片段的形式呈现这些内容，其中关键概念在视觉上突出显示。为了评估Pharmspresso，我们使用了45篇人类策划文章的金标准。Pharmspresso分别确定了78%，61%和74%的靶基因，多态性和药物概念。Pharmspresso是一个文本分析工具，可以自动从文献中提取药物基因组学概念，从而以可计算的形式捕获我们目前对基因-药物相互作用的理解。我们已将Pharmspresso提供给。
Pharmacogenomics studies the relationship between genetic variation and the variation in drug response phenotypes. The field is rapidly gaining importance: it promises drugs targeted to particular subpopulations based on genetic background. The pharmacogenomics literature has expanded rapidly, but is dispersed in many journals. It is challenging, therefore, to identify important associations between drugs and molecular entities – particularly genes and gene variants, and thus these critical connections are often lost. Text mining techniques can allow us to convert the free-style text to a computable, searchable format in which pharmacogenomic concepts (such as genes, drugs, polymorphisms, and diseases) are identified, and important links between these concepts are recorded. Availability of full text articles as input into text mining engines is key, as literature abstracts often do not contain sufficient information to identify these pharmacogenomic associations. Thus, building on a tool called Textpresso, we have created the Pharmspresso tool to assist in identifying important pharmacogenomic facts in full text articles. Pharmspresso parses text to find references to human genes, polymorphisms, drugs and diseases and their relationships. It presents these as a series of marked-up text fragments, in which key concepts are visually highlighted. To evaluate Pharmspresso, we used a gold standard of 45 human-curated articles. Pharmspresso identified 78%, 61%, and 74% of target gene, polymorphism, and drug concepts, respectively. Pharmspresso is a text analysis tool that extracts pharmacogenomic concepts from the literature automatically and thus captures our current understanding of gene-drug interactions in a computable form. We have made Pharmspresso available at .