Research Article
Towards inference of a biochemical ontology from a metabolic database
Article first published online: 14 FEB 2006
DOI: 10.1002/cfg.500
Copyright © 2006 John Wiley & Sons, Ltd.
Issue
1532-6268/asset/cover.gif?v=1&s=83f2425dd7a3beba42173ff4176aeb965520570a "Comparative and Functional Genomics")
Comparative and Functional Genomics
Volume 6, Issue 7-8, pages 398–406, October - December 2005
Additional Information
How to Cite
McShan, D. C. (2005), Towards inference of a biochemical ontology from a metabolic database. Comp Funct Genom, 6: 398–406. doi: 10.1002/cfg.500
Publication History
- Issue published online: 14 FEB 2006
- Article first published online: 14 FEB 2006
- Manuscript Accepted: 5 DEC 2005
- Manuscript Revised: 1 DEC 2005
- Manuscript Received: 28 SEP 2005
Funded by
- US National Library of Medicine. Grant Number: LM007885
- Abstract
- Article
- References
- Cited By
Keywords:
- Ontology;
- classification;
- molecular structure;
- substructure search
Abstract
In order to predict the metabolic fate of an arbitrary compound based solely on structure, it is useful to be able to identify substructural ‘functional groups’ that are biochemically reactive. These functional groups are the substructural elements that can be removed and replaced to transform one compound into another. This problem of identifying functional groups is related to the problem of classifying compounds. The research presented here discusses the state of the art in biochemical databases and how these sources may be applied to the problem of classifying compounds based solely on structure. We describe a biochemical informatics system for processing molecular data and describe how 100 255 compositional (hasA) relationships are inferred between 835 abstractions and 9500 metabolites from the KEGG Ligand database. Specifically, we focus on the identification of amino acids and consider ways in which the inference of biochemical ontologies for metabolites will be improved in the future. Copyright © 2006 John Wiley & Sons, Ltd.