Scientists have long been driven by the desire to describe, organize, classify and compare objects or observables. Biology was one of the first fields to use ontologies and taxonomies, permitting the representation of biological data in a structured and accessible manner. Geology, medicine, physics and many other scientific disciplines followed suit and have also developed their own standard taxonomies and ontologies. Unfortunately, in the world of chemistry, such a standard ontology is lacking. Moreover, the size (millions of compounds) and complexity of chemical structures is such that the manual development of chemical or biochemical ontologies and taxonomies would be a truly daunting task. In a recent project, we proposed a first attempt at a standard, computable, and comprehensive, structure-based ontology, with the development of the Chemical Ontology, ChemOnt. The first publicly available version of ChemOnt provided a structure-based ontology, with mappings to some of the controlled vocabularies mostly used by chemists. With the ever-increasing amount of publicly available data, computers are also needed to integrate various types of data, find links between concepts (e.g. a gene and a disease), and suggest biologically meaningful hypotheses. In recent years, the use of semantic technologies in Life Sciences has shown to be an efficient and productive way to complete such tasks. However, such semantic technologies rely on comprehensive, comprehensive, well-structured ontologies that cover several areas of interest (biology, chemistry, health and safety, environmental sciences), in order to fully explore the chemical space. Here, we present an extended version of ChemOnt, which combines structural, as well as functional sub-ontologies, and allows to represent and integrated types of data, including structural classification, chemical, biological, toxicology, industrial, safety, and metabolomic data, among others. Furthermore, ChemOnt is backed by a semantic infrastructure, which allows easy data integration, and helps linking chemistry data with other data types in queryable ways.

ChemOnt: A semantic-based ontology for chemical and biological data integration

256th National Meeting (2018)

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