Cheminformatics and Metabolism
Chemical resources (structure, bioactivity and metabolomics): ChEBI,
MetaboLights and the Enzyme Portal
SME Bioinformatics Forum, Barcelona 8-9 October 2012
Pablo Conesa
EBI is an Outstation of the European Molecular Biology Laboratory.
Overview
• ChEBI
• Enzyme Portal
• MetaboLights
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ChEBI – Chemical Entities of Biological Interest
Enzyme
Portal
ChEBI
dictionary of „small‟ molecules
EBI is an Outstation of the European Molecular Biology Laboratory.
What is ChEBI?
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Chemical Entities of Biological Interest
Freely available
Focused on „small‟ chemical entities (no proteins or
nucleic acids)
Illustrated dictionary of chemical nomenclature
High quality, manually annotated database
Provides chemical ontology
Access ChEBI at http://www.ebi.ac.uk/chebi/
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ChEBI – Chemical Entities of Biological Interest
Chemicals - ChEBI
Nomenclature
Ontology
caffeine
1,3,7-trimethylxanthine
methyltheobromine
metabolite
CNS stimulant
trimethylxanthines
Chemical data
Database Xrefs
Formula: C8H10N4O2
Charge: 0
Mass: 194.19
MSDchem: CFF
KEGG DRUG: D00528
Chemical Informatics
InChI=1/C8H10N4O2/c1-10-4-9-65(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
SMILES CN1C(=O)N(C)c2ncn(C)c2C1=O
Visualisation
Small molecule annotations
• Often appear as free text in biological databases, in
which they are not the core data
• Are frequently referred to by common names which may
be chemically ambiguous
• eg. adrenaline
= (S)-adrenaline ? (R)-adrenaline ?
• May be referred to by several different names
• paracetamol, acetaminophen, 4-acetamidophenol,
N-(4-hydroxyphenyl)acetamide, …
ChEBI home page
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ChEBI – Chemical Entities of Biological Interest
ChEBI entries contain
• A unique, unambiguous, recommended ChEBI name and
an associated stable unique identifier
• An illustration where appropriate (compounds and
groups, but generally not classes)
• A definition where appropriate (mostly classes)
• A collection of synonyms, including the IUPAC
recommended name for the entity where appropriate
• A collection of cross-references to other databases
• Links to the ChEBI ontology
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ChEBI – Chemical Entities of Biological Interest
ChEBI entry view
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ChEBI – Chemical Entities of Biological Interest
Automatic Cross-references
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ChEBI – Chemical Entities of Biological Interest
Chemical Structures
• Chemical structure may be
interactively explored
using MarvinView applet
• Available in formats
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Image
Molfile
InChI and InChIKey
SMILES
ChEBI – Chemical Entities of Biological Interest
How is ChEBI maintained?
• Automatic loading of preliminary data
• Automatic loading of data annotated elsewhere
• Manual annotation
• User requests via Submission Tool
• Public release: First Monday of every month.
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ChEBI – Chemical Entities of Biological Interest
For more information
• Email: [email protected]
• SourceForge: https://sourceforge.net/projects/chebi/
• User Manual:
http://www.ebi.ac.uk/chebi/userManualForward.do
• RSS Feed
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ChEBI – Chemical Entities of Biological Interest
The EBI Enzyme Portal
Your portal to enzyme-related information at the EBI
EBI is an Outstation of the European Molecular Biology Laboratory.
The Enzyme Portal integrates EBI’s enzyme
resources into a single access point
MACiE
ChEMBL
Enzyme Portal
InterPro
Enzyme Portal home page
Enzyme Portal Results Page
Enzyme Portal Entry Summary
Enzyme Portal Protein Structure
Enzyme Portal Reactions/Pathways
Enzyme Portal Small Molecules
Enzyme Portal Small Molecules
Enzyme Portal Diseases
Enzyme Portal Literature
Online training – Quick Tour
• http://www.ebi.ac.uk/training/online/course/enzyme-portalquick-tour
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ChEBI – Chemical Entities of Biological Interest
MetaboLights
a repository for metabolomics experiments
and derived information
EBI is an Outstation of the European Molecular Biology Laboratory.
MetaboLights - Goal
Create the first open cross-species, crossplatform metabolomics repository
http://www.ebi.ac.uk/metabolights
(metabolights.org, metabolights.eu)
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MetaboLights – Main components
• Data Submission✔
• ISA creator
• Online data deposition
• Repository ✔
• Complete metabolomics experiments/studies
• Sharing Experiments
• Reference Layer
• Metabolite identification
• Curated
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MetaboLights – Data Submission Channels
• ISAcreator
• Bulk submission pipeline
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ISAcreator
Nature Genetics
doi:10.1038/ng.1054
Susanna-Assunta
Sansone,…... Haug,
Neumann, de Matos, Griffin,
Steinbeck, ….. and Hide
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ISAcreator - Study
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ISAcreator - Assays
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ISAcreator - Metabolite Identification plugin
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MetaboLights – Repository Website
http://www.ebi.ac.uk/metabolights
(metabolights.org, metabolights.eu)
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MetaboLights – Private data
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MetaboLights – Study Details
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MetaboLights - Search
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MetaboLights – Download page
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MetaboLights - Curation
NMR
GC
Species
Nomenclature
MS
LC
Reference
Spectroscopy
Structure
Crossrefs
Disease
Identifier
Reference
Chemistry
Publication
Experimental Repository
MetaboLights
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Tissues
Organs
Pathways
Cell Types
Reference
Biology
MetaboLights – The way forward
• Standards, MSI compliance
• Filling a gap, “First of a kind”
• Journals
• Stable identifiers
• High demand
• High quality curated data
• Listening to our users
• Open Data Access
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Thank you
Any questions?
EBI is an Outstation of the European Molecular Biology Laboratory.