Exploring the biological impact of chemicals

with the ChEBI Ontology

Janna HastingsEBI Cheminformatics and Metabolism

ChEBI – a database and ontologyfor chemical entities of biological interest

Names, synonyms

Structures

Chemical data

Cross-references

Classification

Citations

oxytocin

Wednesday, April 12, 2023 3

All ChEBI entries are classified

Wednesday, April 12, 2023 6

ChEBI Ontology

chemical entity role

carboxylic acid

application

antibacterial drug

cefpodoxime (CHEBI:606443)

pharmaceutical

biological role

chemical role

chemical substance

molecular entitygroup

carbonyl compoundsolvent

has role

cyclooxygenaseinhibitor

carboxy group

has part

ChEBI – Chemical Entities of Biological Interest

12.04.23 8

ChEBI ontology relationships

• Generic ontology relationships

• Chemistry-specific relationships

Recent addition: ‘Metabolite of Species’

MetaboLights – a repository for metabolomics experiments

Metabolites identified in study linked to ChEBI

12/04/2312

Messerli: Chocolate consumption, cognitive function, and Nobel laureates

How does chocolate lead to Nobel prizes?

Ontology enrichment analysis for chemicals in metabolomics result based on ChEBI roles

Chemical—GO enrichment (uses GO-ChEBI XPs)

Chemical role enrichment for metabolites identified in bipolar disorder metabolomics study

Annotation density increases quality of enrichment results

ChEBI cross-referencescan be adapted tobe used as sources ofannotations

Coming Soon: BinChe – a web-based tool for enrichment analysis based on ChEBI Ontology

Structure-based

Role-based

Based on BinGOplugin for CytoScape

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

12 April 202318

Funding: BBSRC, EMBL, EU