ChemDIS: a chemical–disease inference system based on chemical–protein interactions

BACKGROUND: The characterization of toxicities associated with environmental and industrial chemicals is required for risk assessment. However, we lack the toxicological data for a large portion of chemicals due to the high cost of experiments for a huge number of chemicals. The development of computational methods for identifying potential risks associated with chemicals is desirable for generating testable hypothesis to accelerate the hazard identification process. RESULTS: A chemical–disease inference system named ChemDIS was developed to facilitate hazard identification for chemicals. The chemical–protein interactions from a large database STITCH and protein–disease relationship from disease ontology and disease ontology lite were utilized for chemical–protein–disease inferences. Tools with user-friendly interfaces for enrichment analysis of functions, pathways and diseases were implemented and integrated into ChemDIS. An analysis on maleic acid and sibutramine showed that ChemDIS could be a useful tool for the identification of potential functions, pathways and diseases affected by poorly characterized chemicals. CONCLUSIONS: ChemDIS is an integrated chemical–disease inference system for poorly characterized chemicals with potentially affected functions and pathways for experimental validation. ChemDIS server is freely accessible at http://cwtung.kmu.edu.tw/chemdis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-015-0077-3) contains supplementary material, which is available to authorized users.