TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining
TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining
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DOI：
10.1186/1472-6882-8-58
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发表时间：
2008-10-14
影响因子：
--
通讯作者：
Juan, Hsueh-Fen
中科院分区：
文献类型：
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作者：
Fang, Yu-Ching;Huang, Hsuan-Cheng;Juan, Hsueh-Fen
背景资料：中医是西方国家的一种补充和替代医学体系，在东亚国家数千年来一直用于治疗各种疾病。近年来发现许多中草药通过调节多种基因表达或蛋白质活性而发挥多种作用。方法：从公共数据库中收集中医药信息、基因信息、疾病信息、生物学通路信息和蛋白质-蛋白质相互作用信息。为了发现关联，从PubMed获取文献语料，采用中药名、基因名、疾病名、中药成分和功效等进行标注。挖掘实体关联的概念是基于假设检验和搭配分析。利用自然语言处理工具对标注的语料库进行处理，并采用基于规则的方法对句子进行处理，以提取中药功效和功效之间的关系。结果：我们开发了一个数据库TCMGeneDIT，提供从大量生物医学文献中挖掘的关于中药、基因、疾病、中药功效和中药成分的关联信息。整合蛋白质相互作用和生物学通路信息也可用于探索与中医药疗效相关的基因调控。此外，通过共享的中间体可以推断基因、中药和疾病之间的传递关系。此外，TCMGeneDIT是有用的，通过基因调控了解可能的治疗机制的中药和推导的处方成分的整体治疗效果的协同或拮抗作用。该数据库现在可在http://tcm.lifescience.ntu.edu.tw/.Conclusion上获得：TCMGeneDIT是一个独特的数据库，提供有关TCM的各种关联信息。该数据库将中药与生物医学研究相结合，有助于临床研究，并阐明中药和基因调控的可能治疗机制。
Background: Traditional Chinese Medicine (TCM), a complementary and alternative medical system in Western countries, has been used to treat various diseases over thousands of years in East Asian countries. In recent years, many herbal medicines were found to exhibit a variety of effects through regulating a wide range of gene expressions or protein activities. As available TCM data continue to accumulate rapidly, an urgent need for exploring these resources systematically is imperative, so as to effectively utilize the large volume of literature.Methods: TCM, gene, disease, biological pathway and protein-protein interaction information were collected from public databases. For association discovery, the TCM names, gene names, disease names, TCM ingredients and effects were used to annotate the literature corpus obtained from PubMed. The concept to mine entity associations was based on hypothesis testing and collocation analysis. The annotated corpus was processed with natural language processing tools and rule-based approaches were applied to the sentences for extracting the relations between TCM effecters and effects.Results: We developed a database, TCMGeneDIT, to provide association information about TCMs, genes, diseases, TCM effects and TCM ingredients mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information are also available for exploring the regulations of genes associated with TCM curative effects. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in understanding the possible therapeutic mechanisms of TCMs via gene regulations and deducing synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. The database is now available at http://tcm.lifescience.ntu.edu.tw/.Conclusion: TCMGeneDIT is a unique database that offers diverse association information on TCMs. This database integrates TCMs with biomedical studies that would facilitate clinical research and elucidate the possible therapeutic mechanisms of TCMs and gene regulations.