Microbiome knowledge graph as a tool to understand bacteria-host associations

Gut bacteria are well known to significantly influence human health and physiology. Knowledge Graph (KG) can effectively integrate the heterogenous factors modulating gut bacteria-host associations. Limited studies describe the construction and application of KGs capturing these associations for domain experts. This work outlines a methodology for constructing microbiome-centric KG and demonstrates how it enhances conventional microbiome data analysis workflows. Towards construction and deployment of this domain centric KG, methodologies involved in collection of data, selecting relevant entities and relationships, and preprocessing them are discussed. Key relevant entities include bacteria, host genetic and immune factors, chemicals and diseases. The KG construction in both RDF (Resource Description Framework) and LPG (Labeled Property Graph) models are demonstrated. Comparison of the querying techniques in both these models and applications of the KG using biologically relevant case studies are also presented. Overall, the work is intended to provide domain experts with a complete protocol for construction of a microbiome-centric KG starting from entity selection and schema design to utilizing the KG for microbiome data analysis and hypothesis generation.