ChEBI: An Open Bioinformatics and Cheminformatics Resource
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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
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PDF or HTML at Wiley Online LibraryTable 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
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PDF or HTML at Wiley Online LibraryFigures
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Figure 14.9.1 The ChEBI home page. View Image -
Figure 14.9.2 The main page of a sample ChEBI entry. View Image -
Figure 14.9.3 The Automatic Xrefs page of a sample ChEBI entry. View Image -
Figure 14.9.4 The MarvinView applet. View Image -
Figure 14.9.5 The Advanced Search page. View Image -
Figure 14.9.6 An Advanced Search result page. View Image -
Figure 14.9.7 Java code illustrating the construction of the ChEBI Web Service client. View Image -
Figure 14.9.8 Java code illustrating the Web Service search capabilities. View Image -
Figure 14.9.9 Java code illustrating the full retrieval of a ChEBI entry. View Image -
Figure 14.9.10 Java code illustrating the navigation of the ChEBI ontology. View Image
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. |
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