HERB 2.0: an updated database integrating clinical and experimental evidence for traditional Chinese medicine.

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2024-11-18 DOI:10.1093/nar/gkae1037

Kai Gao, Liu Liu, Shuangshuang Lei, Zhinong Li, Peipei Huo, Zhihao Wang, Lei Dong, Wenxin Deng, Dechao Bu, Xiaoxi Zeng, Chun Li, Yi Zhao, Wei Zhang, Wei Wang, Yang Wu

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引用次数: 0

Abstract

Clinical trials and meta-analyses are considered high-level medical evidence with solid credibility. However, such clinical evidence for traditional Chinese medicine (TCM) is scattered, requiring a unified entrance to navigate all available evaluations on TCM therapies under modern standards. Besides, novel experimental evidence has continuously accumulated for TCM since the publication of HERB 1.0. Therefore, we updated the HERB database to integrate four types of evidence for TCM: (i) we curated 8558 clinical trials and 8032 meta-analyses information for TCM and extracted clear clinical conclusions for 1941 clinical trials and 593 meta-analyses with companion supporting papers. (ii) we updated experimental evidence for TCM, increased the number of high-throughput experiments to 2231, and curated references to 6 644. We newly added high-throughput experiments for 376 diseases and evaluated all pairwise similarities among TCM herbs/ingredients/formulae, modern drugs and diseases. (iii) we provide an automatic analyzing interface for users to upload their gene expression profiles and map them to our curated datasets. (iv) we built knowledge graph representations of HERB entities and relationships to retrieve TCM knowledge better. In summary, HERB 2.0 represents rich data type, content, utilization, and visualization improvements to support TCM research and guide modern drug discovery. It is accessible through http://herb.ac.cn/v2 or http://47.92.70.12.

查看原文本刊更多论文

HERB 2.0：整合中医临床和实验证据的最新数据库。

临床试验和荟萃分析被认为是具有可靠可信度的高级医学证据。然而，传统中医药（TCM）的这些临床证据比较分散，需要一个统一的入口，以现代标准浏览所有可用的中医药疗法评价。此外，自 HERB 1.0 发布以来，中医药的新实验证据不断积累。因此，我们更新了HERB数据库，整合了四类中医药证据：（i）我们整理了8558项中医药临床试验和8032项荟萃分析信息，提取了1941项临床试验和593项荟萃分析的明确临床结论，并附有相关支持论文。(ii) 我们更新了中药的实验证据，将高通量实验的数量增加到 2231 个，并将参考文献的数量增加到 6 644 个。我们新增了 376 种疾病的高通量实验，并评估了中草药/成分/方剂、现代药物和疾病之间的所有配对相似性。(iii) 我们提供了一个自动分析界面，用户可以上传他们的基因表达谱，并将其映射到我们策划的数据集。(iv) 我们建立了 HERB 实体和关系的知识图谱，以便更好地检索中医药知识。总之，HERB 2.0 代表了丰富的数据类型、内容、利用和可视化改进，以支持中医药研究和指导现代药物发现。它可通过 http://herb.ac.cn/v2 或 http://47.92.70.12 访问。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.