Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses

This repository contains code and data described in detail in our paper, "Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses" (Domingo-Fernández et al., 2023).

Table of Contents

• Citation
• Reproducibility
• Data
• References

Citation

If you have found our manuscript useful in your work, please consider citing:

Domingo-Fernandez, D.†, Gadiya, Y.†, Mubeen, S., Bollerman, T.J., Chanana, S., Gura, R., Healey, D., Colluru, V. (2023). Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses. iScience, Volume 26, Issue 9, 107729 DOI.

Reproducibility

Set up the environment (python)

Install requirements

python -m venv .venv && source ./.venv/bin/activate
pip install -r requirements.txt

Rerun the notebooks

Run the notebooks located in the notebooks corresponding to each analysis. The prefix of the notebooks indicates the section of the manuscript (e.g., 2_1_data_processing.ipynb corresponds to processing the data described in section 2.1, 3_2_geography_influence.ipynb corresponds to the analysis described in section 3.2. For more information about each notebook, see the README inside the notebooks directory.

Set up the environment (R)

To re-create the circular plot with heat-map, make sure to have R v4.2.2 navigate to notebooks/phylogenetic-viz and run the notebook color_figure_red_circle.R. Please install the libraries listed at the top of the script using the command install.packages("package_name")

Data

The manuscript is based on publicly available data from the following resources:

• BERN2 [1]
• LOTUS [2]
• COCONUT [3]
• VietHerb [4]
• Ewé [5]
• IMPPAT 2.0 [6]
• ETM-DB [7]
• Korean Traditional Knowledge Portal (KTKP) [8]
• Trefle

Furthermore, the directory data contains all the figures of the manuscript (generated by the notebooks), mapping files, and raw and intermediary files (also generated by the notebooks). The only file not included in the repo is the full dump of trefle, which available here. The file has to be located under ./data/raw/trefle_species_dump.csv to run the two notebooks relevant to section 3.2.

References

1. Sung, M., Jeong, M., Choi, Y., Kim, D., Lee, J., & Kang, J. (2022). BERN2: an advanced neural biomedical named entity recognition and normalization tool. arXiv preprint arXiv:2201.02080.
2. Rutz, A., Sorokina, M., Galgonek, J., Mietchen, D., Willighagen, E., Gaudry, A., ... & Allard, P. M. (2022). The LOTUS initiative for open knowledge management in natural products research. Elife, 11, e70780.
3. Sorokina, M., Merseburger, P., Rajan, K., Yirik, M. A., & Steinbeck, C. (2021). COCONUT online: collection of open natural products database. Journal of Cheminformatics, 13(1), 1-13.
4. Nguyen-Vo, T. H., Le, T., Pham, D., Nguyen, T., Le, P., Nguyen, A., ... & Le, L. (2018). VIETHERB: a database for Vietnamese herbal species. Journal of chemical information and modeling, 59(1), 1-9.
5. Souza, E. D. N. F., & Hawkins, J. A. (2020). Ewé: a web-based ethnobotanical database for storing and analysing data. Database, 2020.
6. Vivek-Ananth, R. P., Mohanraj, K., Sahoo, A. K., & Samal, A. (2022). IMPPAT 2.0: an enhanced and expanded phytochemical atlas of Indian medicinal plants. bioRxiv.
7. Bultum, L. E., Woyessa, A. M., & Lee, D. (2019). ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database. BMC complementary and alternative medicine, 19(1), 1-11.
8. Shin, J. S., Lee, Y. S., & Lee, M. S. (2010). Protection and utilization of traditional knowledge resources through Korean traditional knowledge portal (KTKP). The Journal of the Korea Contents Association, 10(5), 422-426.