Proceedings of the Workshop on Computation: Theory and Practice (WCTP 2024)

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PythoPharmVis: A Network Analysis tool to Identify Key Entities and Communities for Phytomedicine and Pharmacogenomics

Authors
Emmanuel Ednalan1, *, Geoffrey Solano1
1Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Ermita, Manila, Philippines
*Corresponding author. Email: edednalan@up.edu.ph
Corresponding Author
Emmanuel Ednalan
Available Online 30 April 2025.
DOI
10.2991/978-94-6463-684-0_15How to use a DOI?
Keywords
plants; phytochemicals; small-molecule drugs; genes; diseases; centrality; community detection; graph database
Abstract

Network science offers a powerful way of exploring and discovering on knowledge and insights. Making use of graphs as mathematical structures, it is able to model pair-wise relations between objects, thus, providing in-depth understanding of relationships of entities within and among networks and structures across various disciplines. The motivation of this study is to explore how it can be useful in the study of the relationships between plants, small-molecule drugs, genes and diseases, particularly in the identification of key entities and detection of communities. Data from open-source databases were used to derive the association networks, particularly, Dr. Duke’s Phytochemical and Ethnobotanical Databases for the plants and drugs datasets; BioGrid for the drugs and genes datasets; and PharmKB for the drugs and genes, as well as genes and diseases datasets. The networks were analyzes using the weighted degree centrality and the Leiden algorithm for community detection. A web application was also developed, which allows the users to view and analyze subnetworks based on certain plants, smds, genes or diseases of interest. It is hoped that the results of this study as well as the tool developed will help in phytomedical and pharmacogenomics research.

Copyright
© 2025 The Author(s)
Open Access
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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Volume Title
Proceedings of the Workshop on Computation: Theory and Practice (WCTP 2024)
Series
Atlantis Highlights in Computer Sciences
Publication Date
30 April 2025
ISBN
978-94-6463-684-0
ISSN
2589-4900
DOI
10.2991/978-94-6463-684-0_15How to use a DOI?
Copyright
© 2025 The Author(s)
Open Access
Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

Cite this article

risenwbib
TY  - CONF
AU  - Emmanuel Ednalan
AU  - Geoffrey Solano
PY  - 2025
DA  - 2025/04/30
TI  - PythoPharmVis: A Network Analysis tool to Identify Key Entities and Communities for Phytomedicine and Pharmacogenomics
BT  - Proceedings of the  Workshop on Computation: Theory and Practice (WCTP 2024)
PB  - Atlantis Press
SP  - 235
EP  - 249
SN  - 2589-4900
UR  - https://doi.org/10.2991/978-94-6463-684-0_15
DO  - 10.2991/978-94-6463-684-0_15
ID  - Ednalan2025
ER  -