An ontological approach to represent molecular structure information

Authors:
Eva Armengol;Enric Plaza
Affiliations:
IIIA – Artificial Intelligence Research Institute, CSIC – Spanish Council for Scientific Research, Campus UAB, Bellaterra, Catalonia, Spain;IIIA – Artificial Intelligence Research Institute, CSIC – Spanish Council for Scientific Research, Campus UAB, Bellaterra, Catalonia, Spain
Venue:
ISBMDA'05 Proceedings of the 6th International conference on Biological and Medical Data Analysis
Year:
2005

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Abstract

Current approaches using Artificial Intelligence techniques applied to chemistry use representations inherited from existing tools. These tools describe chemical compounds with a set of structure-activity relationship (SAR) descriptors because they were developed mainly for the task of drug design. We propose an ontology based on the chemical nomenclature as a way to capture the concepts commonly used by chemists in describing molecular structure of the compounds. In this paper we formally specify the concepts and relationships of the chemical nomenclature in a comprehensive ontology using a form of relational representation called feature terms. We also provide several examples of describing chemical compounds using this ontology and compare our proposal with other SAR based approaches.