Services | Research | Training | Industry

Small Molecules

EBI Bioinformatics Roadshow

Gareth Owen, ChEBI group

The Jackson Laboratory October 18th 2012

Course Objectives

In this course you will learn…• How small molecules are stored in databases.• How data related to small molecules is stored in ChEBI

and ChEMBL and how to query these databases• Understand the ChEBI ontology• How to access and query enzyme resources at the EBI,

using the Enzyme Portal, with a closer look at individual resources such as IntEnz and Rhea

• How the Metabolights database can be used for storing information about metabolomics experiments

Exercises.

• Separate exercise sheets for each resource discussed.• Help reinforce learning.• Work alone or in teams.• Solutions will be shown in a run-through before the start

of the next session.

Questions

• Please feel free to ask questions at any time.• If you are confused, you are probably not alone.

• I am be happy to answer all questions, provided you will allow the following responses:• “We’ll be discussing that later”.• “I don’t know”

• Please do not deal with emails, etc. during the sessions• Please turn off mobiles, or set to vibrate.

EBI Metabolomics and Bioinformatics Resources training workshop The Jackson Laboratory Thursday 18th October 2012

Time Subject

09.00-09.30 Introduction to EBI and EBI search

09.30-10.30 Introduction to ChEBI

  Exercises

10.30-11.00 Tea & Coffee/ break

11.00-12.30 ChEBI: Searching and the ChEBI Ontology

  Exercises

12.30-13.15 Lunch

13.15-14.30 The Enzyme Portal, IntEnz and Rhea

14.30-15.00Exercises Introduction to MetaboLights

15.00-15.30 Tea & Coffee break

15.30-16.00 Small molecules and PDBe

16.00-17.00 Introduction to ChEMBL

  Exercises

  Course Feedback

Services | Research | Training | Industry

The EMBL-European Bioinformatics Institute

A whistlestop tour

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What is bioinformatics?

• The science of storing, retrieving and analysing large amounts of biological information

• An interdisciplinary science, involving biologists, computer scientists and mathematicians

• At the heart of modern biology

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Biology is changing

• Data explosion

• New types of data

• High-throughput biology

• Emphasis on systems, not reductionism

• Growth of applied biology

• molecular medicine

• agriculture

• food

• environmental sciences…

0

2000

4000

6000

8000

10000

12000

Dis

ks

(TB

)

Year

Growth of raw storage at EMBL-EBI(in terabytes)

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New types of data

GenomesGenomes

Nucleotide sequenceNucleotide sequence

Gene expressionGene expression

ProteomesProteomes

Protein families, domains and motifs

Protein families, domains and motifs

Protein structureProtein structure

Protein-protein interactions

Protein-protein interactions

Chemical entitiesChemical entities

PathwaysPathwaysSystemsSystems

LiteratureLiterature

Protein sequenceProtein sequence

What is EMBL-EBI?

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• Bioinformatics research and services institute

• Non-profit organisation

• ~ 500 staff

• Part of the European Molecular Biology Laboratory

The five branches of EMBL

Mouse biologyStructural biology

Bioinformatics

Hinxton

Structural biology

Hamburg

• Basic research in molecular biology

• Administration• EMBO

Heidelberg

• 1500 staff

• >60 nationalities

MonterotondoGrenoble

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EMBL member states

Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom

Associate member state: Australia

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EMBL-EBI

Cairns Pavilion(shared)

Sanger InstituteSulston building

Data centre

Sanger labs / informatics

The Wellcome Trust Genome Campus

© John Freebury

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EMBL-EBI’s Mission

• To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress

• To contribute to the advancement of biology through basic investigator-driven research in bioinformatics

• To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators

• To help disseminate cutting-edge technologies to industry

• To coordinate biological data provision across Europe

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EMBL-EBI external funding Sources of external funding for the year as of December 2010. The Wellcome Trust also supports us through provision of our buildings.

The UK’s Biotechnology and Biological Sciences Research Council (BBSRC) awarded a further €11.4m in August 2009 in support of EMBL-EBI’s planned role as the central hub of ELIXIR.

Services | Research | Training | Industry

Serviceswww.ebi.ac.uk/services

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Key facts about services

• European node for globally coordinated data collection and dissemination projects

• Core databases produced in collaboration with other world leaders, including NCBI (US), National Institute of Genetics (Japan), Swiss Institute of Bioinformatics, Cold Spring Harbor Laboratory (US)

• The world’s most comprehensive collection of molecular databases

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Principles of service provision

• Accessibility – all data and tools freely available without restriction, apart from information that could be used to identify individuals

• Compatibility – we develop and promote the use of standards in bioinformatics

• Comprehensive data sets – agreements with other data providers ensure that our resources contain comprehensive and up-to-date data; agreements with publishers ensure that published data are placed in a public repository at the earliest opportunity

• Portability – data and software can be downloaded and installed locally

• Quality – Our databases are enhanced through annotation and cross-referencing

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Databases: molecules to systemsGenomesEnsembl

Ensembl Genomes EGA

GenomesEnsembl

Ensembl Genomes EGA

Nucleotide sequenceENA

Nucleotide sequenceENA

Functional genomics

ArrayExpressExpression Atlas

Functional genomics

ArrayExpressExpression Atlas

Protein SequencesUniProt

Protein SequencesUniProt

Protein families, motifs and domains

InterPro

Protein families, motifs and domains

InterPro

Macromolecular PDBe

Macromolecular PDBe

Protein activityIntAct , PRIDE

Protein activityIntAct , PRIDE

Chemical entitiesChEBI

Chemical entitiesChEBI

PathwaysReactome

PathwaysReactome

SystemsBioModels

BioSamples

SystemsBioModels

BioSamples

Literature and ontologiesCiteXplore, GO

Literature and ontologiesCiteXplore, GO

ChemogenomicsChEMBL

ChemogenomicsChEMBL

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Database collaborations

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Standards development – international collaborations

Genome annotationwww.geneontology.org

Genome annotationwww.geneontology.org

Functional Genomics Data Society www.fged.org

Functional Genomics Data Society www.fged.org

Protein sequencewww.uniprot.org

Protein sequencewww.uniprot.org

HUPO- Proteomics Standards

Initiative (PSI)www.psidev.info/

HUPO- Proteomics Standards

Initiative (PSI)www.psidev.info/

Protein structurewww.wwpdb.org

Protein structurewww.wwpdb.org

Cheminformaticswww.ebi.ac.uk/chebi

Cheminformaticswww.ebi.ac.uk/chebi

Pathwayswww.reactome.org

www.biopax.org

Pathwayswww.reactome.org

www.biopax.org

Systems modelling standards

www.sbml.org

Systems modelling standards

www.sbml.orgMetabolomics Standards Initiative (MSI)www.metabolomicssociety.org

Metabolomics Standards Initiative (MSI)www.metabolomicssociety.org

Genomics Standards Consortium (GSC)http://gensc.org

Genomics Standards Consortium (GSC)http://gensc.org

Nucleotide sequencewww.insdc.org

Nucleotide sequencewww.insdc.org

New search service

Access from the EBI’s homepage

Access from the EBI’s homepage

Data organised according to: • gene• expression• protein• structure• literature

Data organised according to: • gene• expression• protein• structure• literature

Species selector allows for easy

comparison

Species selector allows for easy

comparison

Explore data, return easily to

your results

Explore data, return easily to

your results

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Goals of the new EBI Search

• Relevant to ‘wet-lab’ biologists

• Organises information based around a single gene (or a small number of genes)

• User-expectation centric (not database centric)

• Smooth transition to the detailed information in many of EBI’s core databases

• NOT for bioinformaticians: does not provide programmatic access

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User support

• E-mail support – www.ebi.ac.uk/support

• Online help pages – www.ebi.ac.uk/help

• eLearning Portal – coming soon

Services | Research | Training | Industry

Researchwww.ebi.ac.uk/groups

Key facts about research at EMBL-EBI

• A unique environment for bioinformatics research

• Nine dedicated research groups

• Seven services teams also carry out R&D

• Research and services are mutually supportive

Services | Research | Training | Industry

Trainingwww.ebi.ac.uk/training

Pre- and postdocs at EMBL-EBI

• EMBL International PhD Programme

• Postdoctoral fellowships:

• EIPOD – EMBL-sponsored interdisciplinary fellowships

• ESPOD – EBI–Sanger combined experimental and computational fellowships

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http://www.ebi.ac.uk/Information/Brochures/

EBI in a NutshellGuide to data resourcesResearch at a Glance 2012

For further information go to: