Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature

Dalton Schutte; Jake Vasilakes; Anu Bompelli; Yuqi Zhou; Marcelo Fiszman; Hua Xu; Halil Kilicoglu; Jeffrey R. Bishop; Terrence Adam; Rui Zhang

arXiv · 2106.12741

Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature

Dalton Schutte·Jake Vasilakes·Anu Bompelli·Yuqi Zhou·Marcelo Fiszman·Hua Xu·Halil Kilicoglu·Jeffrey R. Bishop·Terrence Adam·Rui Zhang

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Abstract

OBJECTIVE: Leverage existing biomedical NLP tools and DS domain terminology to produce a novel and comprehensive knowledge graph containing dietary supplement (DS) information for discovering interactions between DS and drugs, or Drug-Supplement Interactions (DSI). MATERIALS AND METHODS: We created SemRepDS (an extension of SemRep), capable of extracting semantic relations from abstracts by leveraging a DS-specific terminology (iDISK) containing 28,884 DS terms not found in the UMLS. PubMed abstracts were processed using SemRepDS to generate semantic relations, which were then filtered using a PubMedBERT-based model to remove incorrect relations before generating our knowledge graph (SuppKG). Two pathways are used to identify potential DS-Drug interactions which are then evaluated by medical professionals for mechanistic plausibility. RESULTS: Comparison analysis found that SemRepDS returned 206.9% more DS relations and 158.5% more DS entities than SemRep. The fine-tuned BERT model obtained an F1 score of 0.8605 and removed 43.86% of the relations, improving the precision of the relations by 26.4% compared to pre-filtering. SuppKG consists of 2,928 DS-specific nodes. Manual review of findings identified 44 (88%) proposed DS-Gene-Drug and 32 (64%) proposed DS-Gene1-Function-Gene2-Drug pathways to be mechanistically plausible. DISCUSSION: The additional relations extracted using SemRepDS generated SuppKG that was used to find plausible DSI not found in the current literature. By the nature of the SuppKG, these interactions are unlikely to have been found using SemRep without the expanded DS terminology. CONCLUSION: We successfully extend SemRep to include DS information and produce SuppKG which can be used to find potential DS-Drug interactions.

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Dalton Schutte, Jake Vasilakes, Anu Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang. 2021-06-24. Discovering novel drug-supplement interactions using a dietary supplements knowledge graph generated from the biomedical literature. https://arxiv.org/abs/2106.12741

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