AIC Seminar Series

Biochemical ‘small molecules’ are involved in all living processes across all biological domains. Chemical ontologies provide structured chemical data and thereby support cross-disciplinary and integrative research across systems biology, chemogenomics and metabolomics. ChEBI (Chemical Entities of Biological Interest) is an ontology of molecular entities such as molecules, groups, rings and atoms, apart from those that have been directly encoded by the genome such as proteins. These chemical entities are active in biological systems in several different ways, including as inhibitors or activators of enzymatic activity, as drugs, as nutrients and as the by-products of metabolic reactions. These and other 'roles' of chemical entities are organised in the ChEBI role ontology, linked to the chemical entities by the 'has role' relationship. In this talk, I will discuss the several different types of roles that chemical entities can take in biological systems and methods to define and distinguish between them, touching on some issues surrounding the embedding of a chemical perspective into biological knowledge bases, and the challenges raised by differing levels of granularity in whole-systems description.

Janna Hastings is a bioinformatician and ontologist at the European Bioinformatics Institute in the Chemoinformatics and Metabolism group led by Dr. Christoph Steinbeck, and a PhD student at the University of Geneva. Her research centres around the computational representation of knowledge in the life sciences and machine reasoning based on such knowledge. She has worked on research problems in structured object representation and reasoning, knowledge representation using hybrid logical and probabilistic formalisms, good ontology design and engineering, and integrated reasoning across ontologies from different domains. She studied Mathematics and Computer Science at the Universities of Cape Town (UCT) and South Africa (UNISA), and has worked as a software engineer and analyst in areas including distribution warehouse management and automated reconciliation in telecommunications before taking a position at the EBI in 2006 and entering the intriguing domain of scientific ontologies.

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