A novel semantic framework for toxicogenomics

Abstract

Complex biological data stored in bioinformatics databases often require additional knowledge to specify and constrain the values held in a particular database. One method of capturing knowledge within bioinformatics applications and databases is the use of ontologies. Existing ontologies can model components of environmental risk and corresponding events, but cannot synthesize them or describe the broader framework of ideas used to conceptualize and study environmental risk. Environmental Risk Ontology (ERO) aims to synthesize and describe a framework for investigating environmental risk. ERO is intended as a metadata framework for data and literature curation and data mining. In this review, we summarize and describe the basic public databases available for toxicogenomics and present a novel approach that uses a semantic knowledge base — which also organizes the literature in a growing, comprehensive bibliographic database — concerning environmental risk and toxicogenomics.