Hypothesizing mechanistic links between microbes and disease using knowledge graphs.

ABSTRACT: Knowledge graphs have been a useful tool for many biomedical applications because of their effective representation of biological concepts. Plentiful evidence exists linking the gut microbiome to disease in a correlative context, but uncovering the mechanistic explanation for those associations remains a challenge. Here we demonstrate the potential of knowledge graphs to hypothesize plausible mechanistic accounts of host-microbe interactions in disease. We have constructed a knowledge graph of linked microbes, genes and metabolites called MGMLink, and, using a shortest path or template-based search through the graph and a novel path-prioritization methodology based on the structure of the knowledge graph, we show that this knowledge supports inference of mechanistic hypotheses that explain

SUBMITTER: Santangelo BE 

PROVIDER: S-EPMC11865272 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature