Abstract: Disclosed is a method and system of predictive toxicology in the form of a multigenome knowledge base incorporating gene and protein molecular expression analysis, gene/protein functional annotation, domain specific ontologies, and literature mapping. The knowledge base can be globally queried by means of local sequence alignment as well as by any other knowledge base object. This sequence linkage enables continuous refinement of data quality, information documentation, and integration of new knowledge across species. Any molecular expression profile derived experimentally or in the clinic, representing expressed genes, proteins, or partial sequences known to the knowledge base, can be used to globally query the knowledge base to find common concordant expression profiles reflecting specific clinical observations and measurements that have been indexed and context documented in terms of dose, treatment time and phenotypic severity.