ChEBI: An Open Bioinformatics and Cheminformatics Resource

Kirill Degtyarenko1, Janna Hastings1, Paula de Matos1, Marcus Ennis1

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.9
DOI:  10.1002/0471250953.bi1409s26
Online Posting Date:  June, 2009
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on “small” chemical compounds. This unit provides a detailed guide to browsing, searching, downloading, and programmatic access to the ChEBI database. Curr. Protoc. Bioinform. 26:14.9.1‐14.9.20. © 2009 by John Wiley & Sons, Inc.

Keywords: chemical compound; chemical nomenclature; InChI; InChIKey; IUPAC; molecular entity; ontology; substructure search; similarity search; Web Services

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol 1: Navigation and Simple Search
  • Basic Protocol 2: Advanced Search
  • Basic Protocol 3: Accessing ChEBI Via Web Services
  • Basic Protocol 4: Downloading ChEBI
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

   Côté, R.G., Jones, P., Apweiler, R., and Hermjakob, H. 2006. The ontology lookup service, a lightweight cross‐platform tool for controlled vocabulary queries. BMC Bioinformatics 7:97.
   Degtyarenko, K., Ennis, M., and Garavelli, J. 2007. “Good annotation practice” for chemical data in biology. In Silico Biol. 7:S1, 06.
   Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M., and Ashburner, M. 2008. ChEBI: A database and ontology for chemical entities of biological interest. Nucl. Acids Res. 36:D344‐D350.
   Heller, S.R. and McNaught, A.D. 2009. The IUPAC International Chemical Identifier (InChI). Chem. Int. 31:7‐9.
   Kochev, N., Monev, V., and Bangov, I. 2003. Searching chemical structures. In Chemoinformatics (J. Gasteiger and T. Engel, eds.) pp. 291‐318. Wiley‐VCH, Weinheim, Germany.
   Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., and Willighagen, E.L. 2006. Recent developments of the Chemistry Development Kit (CDK): An open‐source java library for chemo‐ and bioinformatics. Curr. Pharm. Des. 12:2111‐2120.
Key References
   Degtyarenko et al., 2008. See above.
  Explains main principles of ChEBI. This paper should be used to cite ChEBI.
   Kochev et al., 2003. See above.
  An excellent introduction to the principles of substructure and structure similarity search.
Internet Resources
  http://www.ebi.ac.uk/chebi/
  The ChEBI home page.
  http://www.ebi.ac.uk/chebi/faqForward.do
  ChEBI Frequently Asked Questions.
  http://www.ebi.ac.uk/chebi/userManualForward.do
  ChEBI User Manual.
  http://www.ebi.ac.uk/chebi/tutorialForward.do
  ChEBI Tutorials.
  http://www.ebi.ac.uk/chebi/annotationManualForward.do
  ChEBI Annotation Manual. This manual is designed to enable an annotator (curator) to follow the sequence of steps involved in checking and amending entries in ChEBI.
  http://www.ebi.ac.uk/chebi/downloadsForward.do
  ChEBI Downloads. Contains the latest ChEBI release in several formats.
  http://sourceforge.net/projects/chebi/
  ChEBI project at SourceForge.
  http://cdk.sourceforge.net
  The Chemistry Development Kit project at SourceForge.
  http://www.chemaxon.com/marvin/
  ChemAxon Marvin documentation page.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library