List of resources, including tools and databases, for analyzing traditional chinese medicine (TCM) and herbal medicine. Contributions welcome...
Initial list provided by godkin1211, Wei-hung Chuang, and Chris Kuo.
Inspired by awesome-single-cell
ETCM - ETCM includes comprehensive and standardized information for the commonly used herbs and formulas of TCM, as well as their ingredients. To facilitate functional and mechanistic studies of TCM, ETCM provides predicted target genes of TCM ingredients, herbs, and formulas. A systematic analysis function is also developed in ETCM, which allows users to explore the relationships or build networks among TCM herbs, formulas, ingredients, gene targets, and related pathways or diseases. ETCM is free for academic use and the data can be conveniently exported.
KEGG - KEGG Plant is an interface to plant related datasets that are dispersed in PATHWAY, BRITE, GENOME, GENES, COMPOUND, DISEASE and DRUG databases. The following list shows plant-specific datasets, excluding those that are relevant to both plants and other organism groups, such as conserved pathways for metabolism, transport and genetic information processing.
Mapman -??? Good visualization tool, especially for rice research.
SymMap - SymMap integrates traditional Chinese medicine (TCM) with modern medicine (MM) through both internal molecular mechanism and external symptom mapping. It contains 499 herbs registered in the KEGG Plant is an interface to plant related datasets that are dispersed in PATHWAY, BRITE, GENOME, GENES, COMPOUND, DISEASE and DRUG databases. The following list shows plant-specific datasets, excluding those that are relevant to both plants and other organism groups, such as conserved pathways for metabolism, transport and genetic information processing.
Chinese pharmacopoeia with 19,595 ingredients, and 1,717 corresponding symptoms used in traditional Chinese medicine (TCM symtptom). Those TCM symptoms were rigorously mapped to 961 symptom terms used in modern medicine (MM symptom). Furthermore, SymMap collected associated targets (gene) and diseases for these herbs, either by symptom-disease associations, or by ingredient-target relationships. In total, 4,302 targets and 5,235 diseases were included in SymMap.
Currently, SymMap provides massive descriptive information on herbs, TCM symptoms, MM symptoms, ingredients, targets and diseases. It also provides pairwise relationships among all these six types of components through direct association or indirect statistical inference. In summary, it displayed a network for integrative relationships among all six components.
TCMGeneDIT - TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information collected from public databases are also available. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in deducing possible synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. TCMGeneDIT is a unique database of various association information about TCMs. The database integrating TCMs with life sciences and biomedical studies would facilitate the modern clinical research and the understanding of therapeutic mechanisms of TCMs and gene regulations.