Using ChEBI to explore the underlying biology in metabolomics studies

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ChEBI is a chemical database and ontology that is widely used to annotate biological data. Here, we show a tool that is currently in development that allows exploration of the biological annotations for metabolites that are found to be enriched in metabolomics investigations. This tool will be made available online soon.

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  • C
  • ChEBI is manually curated. Chemicals are given a structure-based classification and assigned with the has_role relationship to the role ontology.
  • List one: List two: CHEBI:16004 CHEBI:35804 CHEBI:30779 CHEBI:15708 CHEBI:16199 CHEBI:33568 CHEBI:18243 CHEBI:18089 CHEBI:26271 CHEBI:16958
  • Using ChEBI to explore the underlying biology in metabolomics studies

    1. 1. Exploring the biological impact of chemicalswith the ChEBI Ontology Janna Hastings EBI Cheminformatics and Metabolism
    2. 2. ChEBI – a database and ontologyfor chemical entities of biological interest Names, synonyms oxytocin Cross-references Structures Chemical data Classification Citations
    3. 3. Thursday, November 1, 2012 3
    4. 4. All ChEBI entries are classified ChEBI Ontology chemical entity role chemical substance biological role molecular entity application group chemical role carbonyl compound pharmaceutical solventcarboxy group carboxylic acid antibacterial drug cyclooxygenase has part inhibitor has role cefpodoxime (CHEBI:606443) Thursday, November 1, 2012 6
    5. 5. ChEBI ontology relationships• Generic ontology relationships• Chemistry-specific relationshipsChEBI – Chemical Entities of 01.11.12 8Biological Interest
    6. 6. Recent addition: ‘Metabolite of Species’
    7. 7. MetaboLights – a repository formetabolomics experiments
    8. 8. Metabolites identified in study linked to ChEBI
    9. 9. Messerli: Chocolate consumption, cognitive function, and Nobel laureates 01/11/1212
    10. 10. How does chocolate lead to Nobel prizes?
    11. 11. Ontology enrichment analysis for chemicals inmetabolomics result based on ChEBI roles
    12. 12. Chemical—GO enrichment (uses GO-ChEBI XPs)
    13. 13. Chemical role enrichment for metabolites identifiedin bipolar disorder metabolomics study Annotation density increases quality of enrichment results ChEBI cross-references can be adapted to be used as sources of annotations
    14. 14. Coming Soon: BinChe – a web-based tool forenrichment analysis based on ChEBI Ontology Based on BinGO plugin for CytoScape Structure- based Role- based
    15. 15. THANKS Christoph Steinbeck Bhavana Harsha, Pablo Moreno, Stephan Beisken Venkatesh Muthukrishnan, Adriano Dekker Marcus Ennis, Gareth Owen, Steve Turner Reza Salek, Kenneth Haug, Mark Williams Funding: BBSRC, EMBL, EU 1 November 201218

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