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Open Access Highly Accessed Commentary

Communication and re-use of chemical information in bioscience

Peter Murray-Rust1*, John BO Mitchell1 and Henry S Rzepa2

Author Affiliations

1 Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge. CB2 1EW, UK

2 Department of Chemistry, Imperial College London, SW7 2AY, UK

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BMC Bioinformatics 2005, 6:180  doi:10.1186/1471-2105-6-180

Published: 18 July 2005

Abstract

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.