Introduction to databases at the EBI - European Bioinformatics Institute

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2 Οκτ 2013 (πριν από 3 χρόνια και 6 μήνες)

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Small Molecules

EBI Bioinformatics Roadshow


Gareth Owen, ChEBI group


The Jackson Laboratory October 18
th

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 18
th

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
-
15.00

Exercises

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

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The EMBL
-
European Bioinformatics Institute

A whistlestop tour

7

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


8

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…

Growth of raw storage

at EMBL
-
EBI

(in terabytes)

9

New types of data

Genomes

Nucleotide sequence

Gene expression

Proteomes

Protein families,
domains and motifs

Protein structure

Protein
-
protein
interactions

Chemical entities

Pathways

Systems

Literature

Protein sequence

What is EMBL
-
EBI?

10


Bioinformatics research and services institute


Non
-
profit
organisation


~ 500 staff


Part of the
E
uropean
M
olecular
B
iology
L
aboratory




The five branches of EMBL

Mouse biology



Structural biology


Bioinformatics


Hinxton

Structural biology


Hamburg


Basic research in
molecular biology


Administration


EMBO



Heidelberg


1500 staff


>60 nationalities

Monterotondo

Grenoble

12

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

13

EMBL
-
EBI

Cairns
Pavilion

(shared)

Sanger Institute

Sulston building

Data centre

Sanger
labs /
informatics

The Wellcome Trust Genome Campus

©
John Freebury

14

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

15

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.

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Services

www.ebi.ac.uk/services

17

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

18

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

19

Databases: molecules to systems

Genomes

Ensembl

Ensembl

Genomes
EGA

Nucleotide sequence

ENA

Functional
genomics

ArrayExpress

Expression Atlas

Protein Sequences

UniProt

Protein families,

motifs and domains

InterPro

Macromolecular

PDBe

Protein activity

IntAct

, PRIDE

Chemical entities

ChEBI

Pathways

Reactome

Systems

BioModels

BioSamples

Literature and ontologies

CiteXplore
, GO

Chemogenomics

ChEMBL

20

Database collaborations

21

Standards development


international collaborations

Genome annotation

www.geneontology.org

Functional Genomics
Data Society

www.fged.org

Protein sequence

www.uniprot.org

HUPO
-

Proteomics

Standards
Initiative (PSI)

www.psidev.info/

Protein structure

www.wwpdb.org

Cheminformatics

www.ebi.ac.uk/chebi

Pathways

www.reactome.org

www.biopax.org

Systems
modelling

standards

www.sbml.org

Metabolomics

Standards Initiative (
MSI
)

www.metabolomicssociety.org

Genomics Standards Consortium (
GSC
)

http://gensc.org

Nucleotide sequence

www.insdc.org

New search service

Access from the
EBI’s homepage

Data organised
according to:


gene


expression


protein


structure


literature

Species selector
allows for easy
comparison

Explore data,

return easily to

your results

22

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


23

24

User support


E
-
mail support


www.ebi.ac.uk/support


Online help pages


www.ebi.ac.uk/help


eLearning Portal


coming soon

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Research

www.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

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Training

www.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

3
1

32

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

EBI in a
Nutshell

Guide to data
resources

Research at a Glance
2012

For further information go to: