• Machine Learning in drug discovery has greatly benefited the pharmaceutical industry. • Application of machine algorithms must entail a robust design in real clinical tasks. • Trending machine learning algorithms in drug design: NB, SVM, RF and ANN.

This article presents the authors' experience in building the Chemicals ontologies from scratch using a methodology called Methontology and the Ontology Design Environment. The ontology-development process includes specification, conceptualization of domain knowledge as a set of intermediate representations based on tabular and graphic notations that are independent of the formal languages used to formalize ontologies, domain knowledge acquisition using knowledge-based-system knowledge-acquisition techniques, integration with existing ontologies, evaluation of the conceptual model generated by the expert, and automatic implementation from the conceptual model into Ontolingua.