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Presentation on Chemical Entities of Biological Interest (ChEBI) for the Programmatic Access to Biological Databases (Perl) course22-26 February 2010 @ EBI
Citation preview
EBI is an Outstation of the European Molecular Biology Laboratory.
Accessing small molecule data using ChEBI
Janna Hastings, Duncan Hull and Nico Adams
Programmatic Access to Biological Databases (Perl)
22-26 February 2010 @ EBI
ChEBI – Chemical Entities of Biological Interest12.04.232
Overview
• Introduction to ChEBI
• Searching and browsing
• Understanding the ontology
• Downloads and programmatic access
EBI is an Outstation of the European Molecular Biology Laboratory.
Introduction to ChEBI
Block 1
Small Molecules within Bioinformatics
Literature
Nucleotide sequences
Genomes
Expressions
Protein sequencesProtein domains, families
3D structures
Enzymes
Small molecules
Pathways Systems
Literature
Nucleotide sequences
Genomes
Expressions
Protein sequencesProtein domains, families
3D structures
Enzymes
Small molecules
Pathways Systems
Small Molecules within Bioinformatics
Small moleculesSmall moleculesSmall moleculesSmall moleculesSmall molecules
Small molecules participate in all the processes of life
Signalingγ-aminobutyric acid
GABA: chief inhibitory neurotransmitter in the mammalian central nervous system.
In humans, also regulates muscle tone.
• synthesized by neurons
• found mostly as a zwitterion, that is, with the carboxyl group deprotonated and the amino group protonated (ChEBI:16865)
• conformational flexibility of GABA is important for its biological function, as it has been found to bind to different receptors with different conformations
• GABA deficiency linked to
• anxiety disorder, depression, alcoholism
• multiple sclerosis, action tremors, tardive dyskinesia
Metabolism
Adenosine 5’-triphosphate (ATP): the
"molecular unit of currency" of intracellular
energy transfer. (ChEBI:15422)
• generated in the cell by energy-consuming processes, broken down by energy-releasing processes
• proteins that bind ATP do so in a characteristic protein fold known as the Rossmann fold, which is a general nucleotide-binding structural domain that can also bind the cofactor NAD
Adenosine 5'-triphosphate
Enzymes
• Enzyme inhibitors are molecules that bind to enzymes and decrease their activity.
• Many drugs are enzyme inhibitors. They are also used as herbicides and pesticides.
• Enzyme activators bind to enzymes and increase their enzymatic activity.
• Enzyme activators are often involved in the allosteric regulation of enzymes in the control of metabolism.
clavulanic acid (ChEBI:48947)acts as a suicide inhibitor of bacterial β-lactamase
enzymes
Pathways
http://www.genome.jp/kegg-bin/highlight_pathway?scale=1.0&map=map00231&keyword=tryptophan
Systems biology
BioModels: quantitative models of biochemical and cellular systems
tryptophan
D-enantiomer: sweet L-enantiomer: bitter
Drug design
• Ligand-based: relies on knowledge of other molecules that bind to the biological target of interest.
• Structure-based: relies on knowledge of the 3D structure of the biological target.
• A lead has• evidence that modulation of the target will have therapeutic value: e.g. disease
linkage studies showing associations between mutations in the biological target and certain disease states.
• evidence that the target is druggable, i.e. capable of binding to a small molecule and that its activity can be modulated by the small molecule.
• Target is cloned and expressed, then libraries of potential drug compounds are screened using screening assays
Drug types 2003 - 2009
'Small molecules' in various shades of blue (http://chembl.blogspot.com/)
Getting the chemistry right
• Thalidomide a non-barbiturate hypnotic
• Thalidomide displays immunosuppresive and anti-angiogenic activity. It inhibits release of tumor necrosis factor-alpha from monocytes, and modulates other
cytokine action.
• Thalidomide is racemic — it contains both left and right handed isomers in equal amounts: one enantiomer is effective against morning sickness, and the other is teratogenic.
• Enantiomers are interconverted in vivo. That is, if a human is given D-thalidomide or L-thalidomide, both isomers can be found in the serum. Hence, administering
only one enantiomer does not prevent the teratogenic effect in humans.
http://www.drugbank.ca/drugs/DB01041
Small molecule data sources
Deposition-driven publicly available compound repository, containing more than 25 million unique structures.
http://pubchem.ncbi.nlm.nih.gov/
http://www.chemspider.com/
Automatic aggregation of publicly available chemistry data with crowdsourced annotation.
http://www.ebi.ac.uk/chebi/
Manually annotated database and ontology
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, …
Chemicals - ChEBI
Visualisation
caffeine1,3,7-trimethylxanthine methyltheobromine
Nomenclature
Formula: C8H10N4O2Charge: 0 Mass: 194.19
Chemical data
metaboliteCNS stimulanttrimethylxanthines
Ontology
MSDchem: CFFKEGG DRUG: D00528
Database Xrefs
Chemical Informatics
InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
SMILES CN1C(=O)N(C)c2ncn(C)c2C1=O
ChEBI – Chemical Entities of Biological Interest12.04.2318
What is ChEBI?
• 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• Provides chemical ontology
Access ChEBI at http://www.ebi.ac.uk/chebi/
ChEBI – Chemical Entities of Biological Interest12.04.2319
ChEBI home page
ChEBI – Chemical Entities of Biological Interest12.04.2320
How is ChEBI maintained?
• Automatic loading of preliminary data
• Automatic loading of 2 star annotated data (ChEMBL and others)
• Manual annotation
• User requests via Submission Tool
• Public release: First Wednesday of every month.
ChEBI – Chemical Entities of Biological Interest12.04.2321
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
ChEBI – Chemical Entities of Biological Interest12.04.2322
ChEBI entry view
ChEBI – Chemical Entities of Biological Interest12.04.2323
Automatic Cross-references
ChEBI – Chemical Entities of Biological Interest12.04.2324
Chemical Structures
• Chemical structure may be interactively exploredusing MarvinView applet
• Available in formats• Image• Molfile• InChI and InChIKey• SMILES
ChEBI – Chemical Entities of Biological Interest12.04.2325
Molfile format
EBI is an Outstation of the European Molecular Biology Laboratory.
Time for Exercises
EBI is an Outstation of the European Molecular Biology Laboratory.
Searching and browsing ChEBI
Block 2
• Simple text search
ChEBI – Chemical Entities of Biological Interest12.04.2328
Simple text search
Wildcard: *
Enter any text
Advanced text search
ChEBI – Chemical Entities of Biological Interest12.04.2329
Narrow to categoryAND, OR
and BUT NOT
ChEBI – Chemical Entities of Biological Interest12.04.2330
Structure searchSearch optionsStructure
drawing tools
ChEBI – Chemical Entities of Biological Interest12.04.2331
Search Results
Click to go to entry page
Hover-over for search menu
ChEBI – Chemical Entities of Biological Interest12.04.2332
Fingerprints
• Chemical substructure searching is computationally expensive…
ChEBI – Chemical Entities of Biological Interest12.04.2333
Fingerprints [2]
• … so heuristics must be used to decrease the number of search candidates
C8H9NO2
• Fingerprints are a generalized, abstract encoding of structural features which can be used as an effective screening device
cannot be a substructure of an entity which does not have at least 8 carbon atoms, 9 hydrogen atoms…
ChEBI – Chemical Entities of Biological Interest12.04.2334
Fingerprints [3]
• Encoding of structural patterns
water (HOH)0-bond paths H O H1-bond paths HO OH2-bond paths HOH
• Hashed to create bit strings, which are added together to give final fingerprint
Pattern Hashed bitmap H 0000010000O 0010000000HO 1010000000OH 0000100010HOH 0000000101Result: 1010110111
ChEBI – Chemical Entities of Biological Interest12.04.2335
Types of structure search
• Identity – based on InChI
• Substructure – uses fingerprints to narrow search range, then performs full substructure search algorithm
• Similarity – based on Tanimoto coefficient calculated between the fingerprints
InChI=1/H2O/h1H2
10101101110010110010
1010110111
0010110010Tanimoto(a,b)
= c / (a+b-c)
= 4 / (4+7-4) = 0.57
a
b
ChEBI – Chemical Entities of Biological Interest12.04.2336
Browse via Periodic Table
Molecular entities / Elements
ChEBI – Chemical Entities of Biological Interest12.04.2337
Navigate via links in ontology
Click to follow links
EBI is an Outstation of the European Molecular Biology Laboratory.
Time for Exercises
EBI is an Outstation of the European Molecular Biology Laboratory.
Understanding the ChEBI ontologyBlock 3
ChEBI – Chemical Entities of Biological Interest12.04.2340
Annotation of bioinformatics data
• Essential for capturing understanding and knowledge associated with core data
• Often captured in free text, which is easier to read and better for conveying understanding to a human audience, but…
• Difficult for computers to parse• Quality varies from database to database• Terminology used varies from annotator to annotator
• Towards annotation using standard vocabularies: ontologies within bioinformatics
ChEBI – Chemical Entities of Biological Interest12.04.2341
The ChEBI ontology
Organised into three sub-ontologies, namely• Molecular structure ontology
• Subatomic particle ontology
• Role ontology
(R)-adrenaline
ChEBI – Chemical Entities of Biological Interest12.04.2342
Molecular structure ontology
ChEBI – Chemical Entities of Biological Interest12.04.2343
Role ontology
ChEBI – Chemical Entities of Biological Interest12.04.2344
ChEBI ontology relationships
• Generic ontology relationships
• Chemistry-specific relationships
ChEBI – Chemical Entities of Biological Interest12.04.2345
Viewing ChEBI ontology
ChEBI – Chemical Entities of Biological Interest12.04.2346
Viewing ChEBI ontology [2]
Tree view
ChEBI – Chemical Entities of Biological Interest12.04.2347
Browsing ChEBI ontology (OLS)
Browse the ontology
Ontology Lookup Service (OLS): http://www.ebi.ac.uk/ontology-lookup/
ChEBI – Chemical Entities of Biological Interest12.04.2348
Ontology Lookup Service
• Provides a centralised query interface for ontology and controlled vocabulary lookup
• Can integrate any ontology available in OBO format• At last release, 58 ontologies integrated, including
• GO• ChEBI• Molecular interaction (PSI MI)• Pathway ontology (PW)• Human disease (DOID)• and many more…
• Provides a search and a browse facility, as well as displaying a graph of terms and relationships
“The OBO Foundry is a collaborative experiment involving developers of science-based ontologies
who are establishing a set of principles for ontology development with the goal of creating a suite of
orthogonal interoperable reference ontologies in the biomedical domain.”
OBO Foundry
ChEBI – Chemical Entities of Biological Interest12.04.2349
EBI is an Outstation of the European Molecular Biology Laboratory.
Time for Exercises
EBI is an Outstation of the European Molecular Biology Laboratory.
Download and programmatic access
Block 4
ChEBI – Chemical Entities of Biological Interest12.04.2352
ChEBI domain modelSelf-referencing -
merging
ChEBI – Chemical Entities of Biological Interest12.04.2353
Compound IDs and Merging
• Compound accessions are maintained after merging, but…
only the main accession of a merged group is displayed
Navigated accession: CHEBI:5585
Main accession: CHEBI:15377
ChEBI – Chemical Entities of Biological Interest12.04.2354
Compound IDs and Merging [2]
ID STATUS
CHEBI_ACCN SOURCE PARENT_ID NAME DEFINITION
15377 C CHEBI:15377 ChEBI null water null
5585 C CHEBI:5585 KEGG 15377 null null
Additional acc Parent ID
ID COMPOUND
ACCN_NUMBER
TYPE STATUS
SOURCE
URL_ABBR
16213 5585 C00001 KEGG accn C KEGG KEGG
17314 5585 7732-18-5 CAS Registry
C KEGG null
This compound ID = additional acc
Downloading ChEBI flavours
ChEBI – Chemical Entities of Biological Interest12.04.2355
• All downloads come in two flavours• 3 star only entries (manually annotated ChEBI
entries)• 2 and 3 star entries (manually annotated ChEBI,
ChEMBL and user submissions)
ChEBI – Chemical Entities of Biological Interest12.04.2356
Downloading ChEBI
• OBO file• Use on OBO-edit
• SDF File• Chemistry software compliant such as Bioclipse
• Flat file, tab delimited• Import all the data into Excel• Parse it into your own database structure
• Oracle binary dumps• Import into an oracle database
• Generic SQL insert statements• Import into MySQL or postgresql database
• File format defined specifically for capturing biological ontologies
• Why use this format?• Use it if you are primarily interested in the ontology.• Don’t use it if you are interested in chemical
structural information.• What can you do with it?
• Can parse it directly using parsers such as OBO-Edit• Can upload and browse the ontology using OBO-Edit
OBO File Format
ChEBI – Chemical Entities of Biological Interest12.04.2357
General header information
Synonym types used in terms
Root terms
Relationships to other terms
• Chemistry software compliant format• Why use this format?
• Use it to obtain the ChEBI entries with their chemical structural information.
• Don’t use it for the ontology.• What can I do with this format?
• Parse it using existing software libraries such as CDK.• Open it in standalone tools such as Bioclipse• Copy and paste individual structures into JChemPaint
SDF File Lite format
ChEBI – Chemical Entities of Biological Interest12.04.2358
Entries separated by $$$$
SDF File complete format
ChEBI – Chemical Entities of Biological Interest12.04.2359
Entries separated by
$$$$
Flat-file tab and comma delimited
ChEBI – Chemical Entities of Biological Interest12.04.2360
• Why use this format?• Use it to obtain the entire ChEBI database structure.
• What can I do with this format?• Open it using Excel• Import it into a relevant database such as Oracle
Table dumps
• Similar structure to the flat-file tab delimited files• Why use this format?• Use it to obtain the entire ChEBI database structure.
• Oracle binary dumps• Import into an oracle database
• Generic SQL insert statements• Import into MySQL or postgresql database
ChEBI – Chemical Entities of Biological Interest12.04.2361
ChEBI – Chemical Entities of Biological Interest12.04.2362
Web services
• Allow users to create their own applications to query data
User application
ChEBI – Chemical Entities of Biological Interest12.04.2363
The ChEBI web service
• Programmatic access to a ChEBI entry
• SOAP based Java implementation• Clients currently available in Java and perl
• Methods• getLiteEntity• getCompleteEntity and getCompleteEntityByList• getOntologyParents• getOntologyChildren and getAllOntologyChildrenInPath• getStructureSearch
• Documented at http://www.ebi.ac.uk/chebi/webServices.do.
ChEBI – Chemical Entities of Biological Interest12.04.2364
Web service client object model
getLiteEntity
getCompleteEntity
getOntology (Parents and
Children)
Methods and parameters (1)
ChEBI – Chemical Entities of Biological Interest12.04.2365
Methods and parameters (2)
ChEBI – Chemical Entities of Biological Interest12.04.2366
Methods and parameters (3)
ChEBI – Chemical Entities of Biological Interest12.04.2367
EBI is an Outstation of the European Molecular Biology Laboratory.
Time for Exercises
ChEBI – Chemical Entities of Biological Interest12.04.2369
For more information
• ftp://ftp.ebi.ac.uk/pub/software/webservices/Perl/WSChebiSOAPLite-2.0.zip
• Email: chebi-help@ebi.ac.uk
• SourceForge: https://sourceforge.net/projects/chebi/
• User Manual: http://www.ebi.ac.uk/chebi/userManualForward.do
• RSS Feed
ChEBI – Chemical Entities of Biological Interest12.04.2370
Acknowledgements
• The ChEBI teamNico Adams Paula de MatosAdriano Dekker Marcus EnnisJanna Hastings Duncan HullZara Josephs Steve TurnerChristoph Steinbeck
• Everyone @ the EBI and elsewhere who uses or contributes to ChEBI
ChEBI is funded by the European Commission under SLING, grant agreement number 226073 (Integrating Activity) within Research Infrastructures of the FP7 Capacities Specific Programme; and by the BBSRC, grant agreement number BB/G022747/1 within the "Bioinformatics and biological resources" fund.
EBI is an Outstation of the European Molecular Biology Laboratory.
Thank you
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