Knowledge Graph Framework to Generate Hypotheses for Natural Product-Drug Interactions


NP-KG is a graph framework that creates a biomedical knowledge graph (KG) to identify and generate mechanistic hypotheses for pharmacokinetic natural product-drug interactions (NPDIs).

Github repository:

  • Taneja SB, Callahan TJ, Paine MF, Kane-Gill SL, Kilicoglu H, Joachimiak MP, Boyce RD. Developing a Knowledge Graph Framework for Pharmacokinetic Natural Product-Drug Interactions. Journal of Biomedical Informatics. 2023. DOI:
  • Taneja SB, Chapin MR, Li X, Kane-Gill SL, Boyce RD. Generating Mechanistic Hypotheses for Pharmacovigilance Signals using a Natural Products Knowledge Graph. Poster presentation, Advances in Pharmacovigilance for Herbal Medicines Conference; April 12-14, 2023.
  • Evaluation of Named Entity Recognition Systems to Improve Ontology Concept Annotation for Biomedical Knowledge Graphs. Presented at the Intelligent Systems for Molecular Biology (ISMB) Bio-ontologies Group, July 13, 2022,
  • Taneja SB, Ndungu PW, Paine MF, Kane-Gill SL, Boyce RD. Relation Extraction from Biomedical Literature on Pharmacokinetic Natural Product-Drug Interactions. Poster presentation, AMIA Informatics Summit 2022; March 21-24, 2022.
  • Taneja SB, Callahan TJ, Brochhausen M, Paine MF, Kane-Gill SL, Boyce RD. Designing potential extensions from G-SRS to ChEBI to identify natural product-drug interactions. Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB), 2021.

Funding: This work is funded by the National Institutes of Health National Center for Complementary and Integrative Health Grant U54 AT008909.