TCMNP: A data processing and visualization database and R package for traditional Chinese medicine network pharmacology

Abstract

Background

Network pharmacology has become crucial for elucidating the mechanisms underlying traditional Chinese medicine (TCM). However, challenges persist in processing and visualizing complex data related to TCM network pharmacology (TCMNP). To address this, we developed ''TCMNP'', a specialized database and R package within the R environment, aimed at enhancing data processing and visualization capabilities for TCM research.

Methods

''TCMNP'' integrates data from prominent databases, including DrugBank, TCMSP, ETCM, DisGeNET, and OMIM, to establish a comprehensive relational framework connecting TCM prescriptions, medicinal materials, bioactive ingredients, therapeutic targets, and associated diseases. Leveraging packages such as ''dplyr'', ''clusterProfiler'', ''ggplot2'', and ''circlize'', we created a suite of functions that facilitate streamlined data analysis and advanced visualizations within R.

Results

''TCMNP'' supports comprehensive analysis and visualization workflows for TCM compounds, individual herbs, active ingredients, molecular targets, and biological pathways. The database comprises 571 TCM herbs, 17,118 unique ingredients, 10,013 diseases, and 15,956 targets, enabling automated processes from compound component screening to target and pathway enrichment analysis. Additional features include protein-protein interaction mapping and transcription factor-gene target analysis, complemented by a user-friendly interface for generating TCM network pharmacology visualizations. ''TCMNP'' is accessible at https://tcmlab.com.cn/tcmnp, and the package available at https://github.com/tcmlab/TCMNP.

Conclusion

''TCMNP'' database and package provide user-friendly visualization tools for analyzing the components of TCM formulas and their potential therapeutic effects on diseases. We anticipate that ''TCMNP'' will help to explore the mechanism of TCM to treat diseases.