Learning and exploring Life science through the EBI reosurces and tools

1

• Learning and exploring Life science through the
  EBI reosurces and tools
• BIOQUEST workshop_2011

Vicky Schneider, EMBL-EBI Training Programme
Project leader vicky_at_ebi.ac.uk
2
Services

• www.ebi.ac.uk/services

3
Principles of service provision
Accessibility
Compatibility
Comprehensive
Portability
Quality
4
Databases molecules to systems
Literature and ontologies CiteXplore, GO
Genomes Ensembl Ensembl Genomes EGA
Protein families, motifs and domains InterPro
Functional genomics ArrayExpress Expression Atlas
Nucleotide sequence ENA
Macromolecular PDBe
Protein activity IntAct , PRIDE
Pathways Reactome
Protein Sequences UniProt
Chemical entities ChEBI
Systems BioModels BioSamples
Chemogenomics ChEMBL
5
Database collaborations
6
Standards development international
collaborations
Genomics Standards Consortium (GSC) http//gensc.o
rg
Genome annotation www.geneontology.org
Protein sequence www.uniprot.org
Nucleotide sequence www.insdc.org
Protein structure www.wwpdb.org
HUPO- Proteomics Standards Initiative
(PSI) www.psidev.info/
Functional Genomics Data Society www.fged.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
7
New search service
Access from the EBIs homepage
Species selector allows for easy comparison

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

Explore data, return easily to your results
8
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 EBIs core databases
• NOT for bioinformaticians does not provide
  programmatic access

9
Quick databases tour
10
Genomes 1 Ensembl
Genes
Chromosomes
Genomic alignments
Pick a genome
Synteny
Variations
Variation Effect Predictor
User Upload
Gene trees
Gene families
11
Genomes 2 Ensembl Genomes
Genome portals for the five kingdoms of life
Variation data for plant, metazoan and fungal
species
Interface uses Ensembl technology
Multi-way comparison of whole bacterial
chromosomes
Pan-taxonomic comparative analysis
12
Nucleotides European Nucleotide Archive (ENA)
Figure adapted from Cochrane, G. et al. Public
Data Resources as the Foundation for a Worldwide
Metagenomics Data Infrastructure. In
Metagenomics Theory, Methods and Applications
(Chapter 5), Caister Academic Press, Universidad
Nacional de Cordoba, Argentina. Ed. D. Marco
(2010).
13
Transcriptomes ArrayExpress
Expand results
ArrayExpress Archive browse experiments
Search by keyword
Spreadsheets describing the sample properties
14
Transcriptomes Gene Expression Atlas
Atlas browse changes in gene expression
Search by gene or biological condition
Gene page
Experiment page
15
Input sources for UniProtKB
UniProt
16
Protein families, motifs and domains InterPro
Compare methods of protein signature prediction
Powerful tool for protein classification,
integrating several methods into one resource
Visualise the taxonomic range for a protein
signature
View architectures of proteins containing a
signature
17
Proteomics services
PRIDE protein identifications from proteomics
experiments
IntAct molecular interactions
INTENZ enzyme classification
ChEBI small molecules
18
Structures PDBe
19
Chemical entities ChEBI
View mappings to other databases
Download flat files, database dumps and the ChEBI
Ontology for local installation
View relationships in the ChEBI Ontology
View structure, nomenclature, formula and more
Link to other databases
20
Chemogenomics ChEMBL
ChEMBL
21
Pathways Reactome
Compare events in different species
View expression values overlaid on a pathway
Link to source databases
Export pathway to your favourite modelling
software
Interaction overlay on a pathway diagram
22
Data management

• Over 4M web requests per day over 4.6M if
  Ensembl is included
• Over 280,000 unique hosts served per month,
  excluding Ensembl
• Total disk space 10 petabytes in 2010.

• Leased two new data centres (with 11.4M from UK
  Research Councils)
• Over 800 million cross-references in the
  databases we serve

23
User support

• E-mail support  www.ebi.ac.uk/support
• Online help pages  www.ebi.ac.uk/help
• 2Can bioinformatics user support
  www.ebi.ac.uk/2Can
• eLearning Portal coming soon (elearning_at_ebi.ac.u
  k)