FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases

Abstract

Abstract Motivation Metabolomics studies aim at reporting a metabolic signature (list of metabolites) related to a particular experimental condition. These signatures are instrumental in the identification of biomarkers or classification of individuals, however their biological and physiological interpretation remains a challenge. To support this task, we introduce FORUM: a Knowledge Graph (KG) providing a semantic representation of relations between chemicals and biomedical concepts, built from a federation of life science databases and scientific literature repositories. Results The use of a Semantic Web framework on biological data allows us to apply ontological-based reasoning to infer new relations between entities. We show that these new relations provide different levels of abstraction and could open the path to new hypotheses. We estimate the statistical relevance of each extracted relation, explicit or inferred, using an enrichment analysis, and instantiate them as new knowledge in the KG to support results interpretation/further inquiries. Availability and implementation A web interface to browse and download the extracted relations, as well as a SPARQL endpoint to directly probe the whole FORUM KG, are available at https://forum-webapp.semantic-metabolomics.fr. The code needed to reproduce the triplestore is available at https://github.com/eMetaboHUB/Forum-DiseasesChem. Supplementary information Supplementary data are available at Bioinformatics online.