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Bioinformatics tools for biologists @ the EBI

Bioinformatics tools for biologists @ the EBI. An overview. Bioinformatics. The science of storing, retrieving and analyzing large amounts of biological information An interdisciplinary science, involving biologists, computer scientists and mathematicians At the heart of modern biology.

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Bioinformatics tools for biologists @ the EBI

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  1. Bioinformatics tools for biologists @ the EBI An overview

  2. Bioinformatics • The science of storing, retrieving and analyzing large amounts of biological information • An interdisciplinary science, involving biologists, computer scientists and mathematicians • At the heart of modern biology EBI Overview

  3. “Large-scale” focus • Data explosion and new types of data • High-throughput biology • Emphasis on systems, not reductionism • Large community of users with no training in bioinformatics • Growth of applied biology – molecular medicine, agriculture, food, environmental sciences… EBI Overview

  4. What is EMBL-EBI? • Based on the Wellcome Trust Genome Campus near Cambridge, UK • Part of the European Molecular Biology Laboratory • Non-profit organization 4 EBI Overview

  5. The 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 disseminatecutting-edge technologies to industry • Filler text EBI Overview

  6. Databases and tools www.ebi.ac.uk

  7. New types of data Literature and ontologies Genomes Protein sequence DNA & RNA sequence Protein structure Gene expression Chemical entities Protein families, motifs and domains Protein interactions Pathways Systems EBI Overview

  8. Databases: molecules to systems Literature and ontologies CiteXplore, GO Genomes EnsemblEnsembl Genomes EGA Protein families, motifs and domains InterPro Nucleotide sequence EMBL-Bank Microarray & gene expression data ArrayExpress Protein structure PDBe Protein interactions IntAct Pathways Reactome Proteomes UniProt, PRIDE Chemical entities ChEBI Systems BioModels 8 EBI Overview

  9. Database collaborations 9 EBI Overview

  10. 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 Microarray and Gene Expression Data (MGED) www.mged.org Cheminformatics www.ebi.ac.uk/chebi Pathways www.reactome.org www.biopax.org Systems modeling standards www.sbml.org Metabolomics Standards Initiative (MSI) www.metabolomicssociety.org Standards development – international collaborations 10 EBI Overview

  11. EBI website: www.ebi.ac.uk Databases Tools EBI Overview

  12. EBI search engine: EB-eye Search all main databases in one go EBI Overview

  13. Nucleotides: European Nucleotide Archive (ENA) • ENA provides a comprehensive, accessible and publicly available repository for nucleotide sequence data • Collaboration with GenBank and DDBJ for data sharing • 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) • Provides access to the whole scale of sequencing information: from raw data, through assembly and mapping information, through to high-level functional annotation (see figure). EBI Overview

  14. Nucleotides: ENA Download data Navigate to view related data, e.g. taxon-specific data Other type of data include SRA experiments EBI Overview

  15. Genomes: Ensembl & Ensembl Genomes • Genome browser providing free access to the complete sequences of higher and model organism • With Ensembl you can: • Retrieve all or part of a genome sequence • Perform sequence alignment using BLAST or BLAT • Link to genome annotation from microarray results • View expressed mRNA, protein, etc. in a chromosomal region • View variations such as SNPs across strains or populations • View all alternative splicing for a gene • Explore homologues and phylogenetic tree across > 30 species • View conserved regions across species • Ensembl Genomes extends to non-vertebrate genomes EBI Overview

  16. Genomes: Ensembl Chromosomes Genomic alignments Genes Pick a genome Synteny Gene families SNPs Across species Within species Orthology EBI Overview

  17. Genomes: Ensembl Genomes Using view options, you can select to view only the current gene or the entire expanded gene tree Ensembl-like genome browser for non-vertebrate species Ensembl Metazoa Ensembl Bacteria Select Orthologue view to see putative orthologues Across species View options EBI Overview

  18. Retrieving data with Biomart • BioMart is a search engine that can be used to download data into a table format • Many EBI databases are powered by Biomart • For example, you can use Ensembl Biomart to retrieve: • All the genes for one species • Or… only genes on one specific region of a chromosome • Or… genes on one region of a chromosome associated with an InterPro domain • Or…etc. EBI Overview

  19. Biomart – how it works First Step: Choose a dataset Second step: Add filters to define a gene set Third step: Add attributes to determine column output EBI Overview

  20. Biomart results EBI Overview

  21. www.biomart.org EBI Overview

  22. ArrayExpress & Atlas of Gene Expression • ArrayExpress Archive is a public repository of functional genomics experiments, including gene expression, supporting scientific publications • You can query it to retrieve experimental information and download functional genomics data • Atlas of Gene Expression contains a subset of curated and re-annotated Archive data • Can be queried for individual gene expression under different biological conditions across experiments EBI Overview

  23. Transcriptomes: ArrayExpress ArrayExpress Archive: browse experiments Expand results Search by keyword Spreadsheets describing the experiment, sample properties or array design EBI Overview

  24. Transcriptomes: Atlas of Gene Expression Search by gene name or biological condition Atlas interface Gene summary page Experiment page EBI Overview

  25. Protein sequence: UniProt • Provides the scientific community with a comprehensive, richly curated, high-quality and freely accessible resource of protein sequence and functional information • Users can perform simple and complex text-based queries, run sequence-based searches, perform multiple sequence alignments, etc. • Consists of: • UniProtKB/Swiss-prot, manually annotated • UniProtKB/TrEMBL, computationally analyzed records • Uniref, clustered by sequence identity • UniParc, most comprehensive publicly available non-redundant protein sequence db, un-annotated • UniMES, protein sequence from metagenomic and environmental data EBI Overview

  26. UniPort text search for Brca1 EBI Overview

  27. Protein families, motifs & domains: InterPro • Integrated documentation resource for protein families, domains and functional sites • Protein signatures from different member databases describing the same biological protein family or domain are united into a single InterPro entry containing information about the signature(s) and links to the protein in UniProt • Links to Gene Ontology indicate the biological function and process that the proteins are involved in EBI Overview

  28. Protein families, motifs and domains: InterPro Compare methods of protein signature prediction Visualize the taxonomic range for a protein signature View architectures of proteins containing a signature EBI Overview

  29. Molecular interaction database: Intact • IntAct provides a freely available, open source database system and analysis tools for protein interaction data. • All interactions are derived from literature curation or direct user submissions • With Intact you can: • Find molecules that interact with your protein of interest • Display interaction networks • Analyze interaction networks using GO terms, molecule type, role, etc. • Download data • Install IntAct system locally EBI Overview

  30. The Protein Data Bank in Europe (PDBe) • PDBe is a resource for the collection, organization and dissemination of data about biological macromolecular structures • A suite of web-based services allows you to: • PDBeView and PDBeLite provide a flexible and user-friendly query interface to the PDBe database • PDBeAnalysis provides searches and statistical analyses of macromolecular structure and residue information • PDBeFold allows performing pairwise or multiple comparisons as well as 3D alignments of structures • PDBeChem allows searching for and visualize any molecule in the PDB’s ligand dictionary • PDBePisa is an interactive tool for exploring macromolecular interfaces and surfaces, predicting probable quaternary structures (assemblies) and searching the PDB for structurally similar interfaces and assemblies • PDBeMotif allows complex searches of the PDB based on small 3D motifs, sequence motifs in conjunction with ligand environment, secondary structure patterns • Many more tools available EBI Overview

  31. Structures: PDBe Linking to domain data Sequence mapping Ligands Assemblies Electron density visualization Active sites Surface matching Fold matching EBI Overview

  32. PRoteomics IDEntifications database (PRIDE) • PRIDE is a centralized, standards compliant, public data repository for proteomics data • Provides the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications. • PRIDE is also able to capture details of post-translational modifications coordinated relative to the peptides in which they have been found. EBI Overview

  33. Enzymes: IntEnz • IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. • IntEnz contains the recommendations of the Nomenclature Committee of the IUBMB on the nomenclature and classification of enzyme-catalysed reactions. EBI Overview

  34. Chemical entities: ChEBI • ChEBI is a freely available, manually annotated database of small molecular entities • A molecular entity is any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, not directly encoded by the genome • With ChEBI you can: • Find the correct chemical terminolgy using name, formula or registry number • Visualize chemical structures • Perform similarity searches • View the relationship between molecules using the chEBI ontology • Bridge the gap between small molecules and the macromolecules they interact with (crosslink to UniProt and Reactome) • Downoload chemical structures • Submit new structures EBI Overview

  35. Chemical entities: ChEBI View mappings to other databases such as Reactome and Uniprot 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 EBI Overview

  36. Chemogenomics: ChEMBL • ChEMBL is a publicly available database of drugs, drug-like small molecules and their targets • The data includes information about how small molecules bind to their targets, how these compounds affect cells and whole organisms, and information on the molecules’ absorption, distribution, metabolism, excretion and toxicity. • ChEMBL holds two-dimensional structures, calculated molecular properties (e.g. logP, molecular weight, Lipinski ‘Rule of Five’ parameters) and bioactivity data (such as binding constants and pharmacology). • The bioactivity data is tagged to show links between molecular targets and published assays, with a set of varying confidence levels. • Additional data on the clinical progress of compounds is being integrated into ChEMBL. EBI Overview

  37. Chemogenomics: ChEMBL ChEMBL EBI Overview

  38. Pathways: Reactome • A free, online, open-source curated database of pathways and reactions in human biology • Information in the database is authored by expert biologist researchers, maintained by Reactome editorial staff • Used to infer orthologous events in 22 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast • Extensively cross-referenced to other resources e.g. NCBI, Ensembl, UCSC genome Browser, UniProt, PubMed, KEGG, ChEBI and GO. EBI Overview

  39. Pathways: Reactome View reactions and events in detail Select a pathway Compare events in different species Export pathway

  40. Pathways: Reactome Display expression data Link to source databases EBI Overview

  41. Biological ontologies: Gene Ontology (GO) • The GO project is a collaborative effort to address the need for consistent descriptions of gene products in different databases • GO develops ontologies that describe biological processes, cellular components and molecular functions in a species-independent manner • Also GO annotates several of the EBI’s databases with GO terms EBI Overview

  42. User support • 2Can bioinformatics user support – www.ebi.ac.uk/2Can • Online help pages – www.ebi.ac.uk/help • E-mail support – www.ebi.ac.uk/support EBI Overview

  43. http://www.ebi.ac.uk/Information/Brochures/ EBI Overview

  44. Research www.ebi.ac.uk/groups

  45. Key facts about research The EBI provides a unique environment for bioinformatics research Seven dedicated research groups aim to understand biology through new approaches to interpreting biological data Services teams also carry out R&D to enhance existing services and develop new ones Research program complements services and the two are mutually supportive 45 EBI Overview

  46. Literature analysis and semantic data integration in life science research Rebholz-Schuhmann Cheminformatics and metabolism Steinbeck Research Functional genomics and small RNA analysis Enright Vertebrate genome annotation Flicek Algorithmic methods for genome analysis Birney Transcriptome analysis on a genomic scale Brazma Analysis of protein structure, function and evolution Thornton Genome analysis using evolutionary tools Goldman Evolutionary biology Marioni Protein sequence analysis and functional annotation Apweiler Analysis and validation of protein structures; protein–ligand interactions Kleywegt Neurobiology networks and systems Le Novère Systems Biomedicine Saez-Rodriguez Genome-scale analysis of regulatory systems Luscombe Chemogenomics and drug discovery Overington Mammalian stem cell differentiation and development Bertone

  47. Training www.ebi.ac.uk/training

  48. A tripartite user-training programme Training any time, anywhere, at any pace www.ebi.ac.uk/training/elearning Training comes to you www.ebi.ac.uk/training/roadshow Hands-on user training on all our core data resources for researchers www.ebi.ac.uk/training/handson 48 48 EBI Overview

  49. Hands-on training for all levels of experience • Interactive training in our purpose-built IT training suite at EMBL-EBI, Hinxton, Cambridge • Learn from the EBI’s experts through a combination of talks and practical exercises • Take a tour of all our core data resources, or focus in on specific data types • Full programme at www.ebi.ac.uk/training/handson 49 EBI Overview

  50. eLearning project – pilot phase • Do you want to learn at your own pace at a time that suits you? • We are developing a new eLearning platform and need our users to help us test it • If you would like to get involved, contact: elearning@ebi.ac.uk 50 50 EBI Overview

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