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Welcome to the NP-KG wiki!
NP-KG is a knowledge graph (KG) framework to generate hypotheses for pharmacokinetic natural product-drug interactions (NPDIs).
Natural products include herbal and other botanical products used for complementary health approaches. Traditional herbal medicines have been used for centuries and are now being used to supplement modern pharmacotherapy. Sale of herbal products continue to grow all over the world, however, botanical natural products sold as dietary supplements in the United States are regulated differently than pharmaceutical drugs. While many natural products have purported benefits and widespread usage, understanding the potential risks and benefits of use of natural products is important.
Botanical and other natural products are being increasingly used for complementary health and co-consumption of natural products (such as dietary supplements) is common with pharmaceutical drugs. This co-consumption can lead to pharmacokinetic NPDIs and unexpected drug responses. Pharmacokinetic NPDIs occur when a natural product alters the absorption, distribution, metabolism, and/or excretion of a co-consumed drug, potentially resulting in reduced treatment efficacy or adverse events. Many food items also interact with drugs (food-drug interactions) and co-consumption of dietary supplements and drugs can cause adverse events due to drug-supplement interactions.
NP-KG aims to generate mechanistic hypotheses for pharmacokinetic NPDIs concerning popular botanical natural products (such as green tea and kratom) to understand the mechanisms underlying the interactions and prevent adverse interactions. NP-KG contains biomedical ontologies, drug databases, linked open data, and triples extracted from biomedical literature related to 30 natural products. See list of natural products in NP-KG.
NP-KG is an integration of biomedical ontologies and databases from the PheKnowLator workflow and relation extraction from natural products-related scientific literature. The ontology-grounded KG and literature-based graph are then combined to create NP-KG. Details of each version are in separate wiki pages.
Current release
Previous releases
- Sanya B. Taneja
- Tiffany J. Callahan
- Richard D. Boyce [primary mentor]
- Mary F. Paine [research mentor]
- Marcin P. Joachimiak
- Halil Kilicoglu
- Sandra Kane-Gill
- NP-KG: Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions
- Poster related to generating hypotheses for pharmacovigilance signals using NP-KG presented at the Advances in Pharmacovigilance for Herbal Medicines Conference 2023.
- Talk and poster related to named entity recognition evaluation in NP-KG presented at the Intelligent Systems for Molecular Biology (ISMB) Bio-ontologies COSI 2022
- Poster on relation extraction evaluation presented at the AMIA Informatics Summit 2022.
- Talk and poster on the natural product ontology extensions presented at the Intelligent Systems for Molecular Biology (ISMB) Bio-ontologies COSI 2021
- NP-KG preliminary work presented at the Pitt-CMU Medical Informatics Colloquium (Recorded Talk)
This project is licensed under Apache License 2.0 - see the LICENSE.md file for details. If you intend to use any of the information on this Wiki, please cite:
Zenodo
@dataset{taneja_sanya_bathla_2024_12536780,
author = {Taneja, Sanya Bathla},
title = {{NP-KG: Knowledge Graph for Natural Product-Drug
Interactions}},
month = jun,
year = 2024,
publisher = {Zenodo},
version = {3.0.0},
doi = {10.5281/zenodo.12536780},
url = {https://doi.org/10.5281/zenodo.12536780}
}