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

Learning and exploring Life science through the EBI reosurces and tools BIOQUEST workshop_2011. Vicky Schneider, EMBL-EBI Training Programme Project leader vicky@ebi.ac.uk. Services. www.ebi.ac.uk/services. Principles of service provision. Accessibility. @ Patrick Hoesly. Compatibility.

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

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  1. Learning and exploring Life science through the EBI reosurces and tools BIOQUEST workshop_2011 Vicky Schneider, EMBL-EBI Training Programme Project leader vicky@ebi.ac.uk

  2. Services www.ebi.ac.uk/services

  3. Principles of service provision Accessibility @ Patrick Hoesly Compatibility Comprehensive Portability Quality

  4. Databases: molecules to systems Literature and ontologies CiteXplore, GO Genomes EnsemblEnsembl 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.org 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 EBI’s 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 EBI’s core databases • NOT for bioinformaticians: does not provide programmatic access

  9. Quick databases tour

  10. Genomes 1: Ensembl Chromosomes Genes 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) The ENA has a three-tiered data architecture. It consolidates information from EMBL-Bank, the European Trace Archive (containing raw data from electrophoresis-based sequencing machines) and the Sequence Read Archive (containing raw data from next-generation sequencing platforms). 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. Manual curation • Literature-based annotation • Sequence analysis GO Functional info Protein identification data PRIDE Protein families and domains InterPro Molecular interactions IntAct IntEnz Enzymes • Automated annotation Microbial protein families HAMAP RESID Post-translational modifications Input sources for UniProtKB Some data sources for annotation InterPro classification Signal prediction UniProt Transmembrane prediction Other predictions Protein classification

  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. PRIDE: protein identifications from proteomics experiments Proteomics services IntAct: molecular interactions INTENZ: enzyme classification ChEBI: small molecules

  18. Structures: PDBe

  19. View mappings to other databases Chemical entities: ChEBI 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 Neglected Tropical Disease (NTD) archive ChEMBL database ChEMBL GPCR SARfari Browse targets Target search Kinase SARfari Search results Compound search

  21. Pathways: Reactome Compare events in different species View expression values overlaid on a pathway Link to source databases Export pathway to your favouritemodelling software Interaction overlay on a pathway diagram

  22. 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@ebi.ac.uk)

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