image: Database structure and GPGD webpages. view more
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Traditional medicines have been globally used to treat various diseases for thousands of years, and critically, still play important roles in modern-day healthcare. During the coronavirus disease 2019 (COVID-19) global pandemic, traditional medicines displayed encouraging effects in improving symptom management, reducing deterioration, mortality, and disease recurrence rates in China. With the assistance of “omics” data, the decomposition of medicinal compound biosynthetic pathways has reached an unprecedented level. Herb genomic data are growing rapidly; however, this growth is accompanied by several issues exemplified by the hosting of data by different research groups, various and non-uniform data formats, and unstable web services, which combined, create obstacles for data use.
Science China Life Sciences recently publishes an online research paper entitled “Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias” by Chen Shilin’s team from the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences. This paper described the Global Pharmacopoeia Genome Database (GPGD, http://www.gpgenome.com) developed by Chen Shilin’s team. The database contains records for herb species from eight global pharmacopoeias (Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s Herbal Medicines Compendium). Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. Besides, a set of convenient bioinformatics tools, such as BLAST and JBrowse, were embedded in the system.
The database contains 34,346 records for 903 herb species, including 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, and 55 whole genomes from 49 species. By providing genomics-related data and analysis tools of different levels of herb species, GPGD serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis.
This work was supported by the National Key Research and Development Program of China (2019YFC1711100), the National Natural Science Foundation of China and Karst Science Research Center of Guizhou Province (U1812403-1), the Special Foundation for National Science and Technology Basic Research Program of China (2018FY100701), the Fundamental Research Funds for the Central Public Welfare Research Institutes (ZXKT17027, ZXKT18014), the Open Research Fund of Chengdu University of Traditional Chinese Medicine Key Laboratory of Systematic Research of Distinctive Chinese Medicine Resources in Southwest China (2020GZ2011016), the Funds for Fostering Outstanding Scholars in Science and Technology (Innovation) (ZZ13-YQ-047), and Innovation Fund of China Academy of Chinese Medical Sciences.
See the article
Liao, B, Hu, H, Xiao, S, et al. (2021). Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias. Sci China Life Sci, https://doi.org/10.1007/s11427-021-1968-7.
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Science China Life Sciences