Representing chemical structures using OWL and description graphs
Loading...
Authors
Hastings, Joanna Kathleen
Issue Date
2010-11
Type
Dissertation
Language
en
Keywords
Chemistry , Ontology , Description graphs , Chemical structures , Structured objects , Rules , OWL
Alternative Title
Abstract
Objects can be said to be structured when their representation also contains their parts.
While OWL in general can describe structured objects, description graphs are a recent,
decidable extension to OWL which support the description of classes of structured objects
whose parts are related in complex ways. Classes of chemical entities such as molecules,
ions and groups (parts of molecules) are often characterised by the way in which the
constituent atoms of their instances are connected via chemical bonds. For chemoinformatics
tools and applications, this internal structure is represented using chemical
graphs. We here present a chemical knowledge base based on the standard chemical graph
model using description graphs, OWL and rules. We include in our ontology chemical
classes, groups, and molecules, together with their structures encoded as description
graphs. We show how role-safe rules can be used to determine parthood between groups
and molecules based on the graph structures and to determine basic chemical properties.
Finally, we investigate the scalability of the technology used through the development
of an automatic utility to convert standard chemical graphs into description graphs, and
converting a large number of diverse graphs obtained from a publicly available chemical
database.
Description
Citation
Hastings, Joanna Kathleen (2010) Representing chemical structures using OWL and discriptions graphs, University of South Africa, Pretoria, <http://hdl.handle.net/10500/4695>