AIC Seminar Series
A chemical view into biological systems
|Janna Hastings||European Bioinformatics Institute||[Home Page]|
Notice: Hosted by Vinay Chaudhri.
Date: 2011-09-20 at 10:00
Location: EJ228 (SRI E building) (Directions)
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.
Please arrive at least 10 minutes early as you will need to sign in by
following instructions by the lobby phone at Building E. SRI is located
at 333 Ravenswood Avenue in Menlo Park. Visitors may park in the parking
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available from the Visiting AIC web page.
There are two entrances to SRI International located on Ravenswood Ave.
Please check the Builing E entrance signage.
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