Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Contents Bioinformatics ! Examples of biological databases " " " ! Nucleic sequences: Genbank, EMBL, and DDBJ Protein sequences: UniProt The Gene Ontology (GO) project Issues and perspectives for biological databases Biomolecular databases Jacques van HeldenFORMER ADDRESS (1999-2011) Université Libre de Bruxelles, Belgique Bioinformatique des Génomes et des Réseaux (BiGRe lab) http://www.bigre.ulb.ac.be/ NEW ADDRESS (since Nov 1st, 2011) [email protected] Université d’Aix-Marseille, France Lab. Technological Advances for Genomics and Clinics (TAGC, INSERM Unit U1090) http://tagc.univ-mrs.fr/ B!GRe Bioinformatique des Génomes et Réseaux !"#$ Inserm U1090 !"#$%&'&()#*'+*,-*%#".+/&0+("%&1)#.+*%,+#')%)#. Examples of biomolecular databases Biomolecular Databases ! Sequence and structure databases " " " " " ! Genome sequences and annotations " Examples of biomolecular databases " ! Genome-specific databases (SGD, FlyBase, AceDB, PlasmoDB, !) Multiple genomes (Integr8, NCBI, KEGG, TIGR, !) Molecular functions " " " ! Protein sequences (UniProt) DNA sequences (EMBL, Genbank, DDBJ) 3D structures (PDB) Structural motifs (CATH) Sequence motifs (PROSITE, PRODOM) Transcriptional regulation (TRANSFAC, RegulonDB, InteractDB) Enzymatic catalysis (Expasy, LIGAND/KEGG, BRENDA) Transport (YTPdb) Biological processes " " " " Metabolic pathways (EcoCyc, LIGAND/KEGG, Biocatalysis/biodegradation) Signal transduction pathways (CSNdb, Transpath) Protein-protein interactions (DIP, BIND, MINT) Gene networks (GeneNet, FlyNets) [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ Databases of databases Biomolecular Databases ! ! There are hundreds of databases related to molecular biology and biochemistry. New databases are created every year. Every year, the first issue of Nucleic Acids Research is dedicated to biological databases " " ! The same journal maintains a database of databases: the Molecular Biology Database Collection " ! http://nar.oupjournals.org/ 2011 Issue: http://nar.oxfordjournals.org/content/39/suppl_1 http://www.oxfordjournals.org/nar/database/c/ Some bioinformatics centres maintain multiple database, with cross-links between them. The SRS server at EBI holds an impressive collection of databases. " Nucleic sequence databases: GenBank, EMBL, and DDBJ http://srs.ebi.ac.uk/ [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ Nucleic sequence databases ! ! ! To publish an article dealing with a sequence, scientific journals impose to have previously deposited this sequence in a reference database. There are 3 main repositories for nucleic acid sequences. Sequences deposited in any of these 3 databases are automatically synchronized in the 2 other ones. The sequencing pace ! Nucleic sequences " ! Entire genomes " " ! Genbank (April 2011) http://www.ncbi.nlm.nih.gov/genbank/ • 126,551,501,141 bases in 135,440,924 sequence records in the traditional GenBank divisions • 191,401,393,188 bases in 62,715,288 sequence records in the Whole Genome Ssequencing GOLD Release V.2 (Oct 2011) contains ~2000 completely sequenced genomes. http://www.genomesonline.org/gold_statistics.htm Protein sequences " Essentially obtained by translation of putative genes in nucleic sequences (almost no direct protein sequencing). UniProtKB/TrEMBL (2011) contains 17 millions of protein sequences. " http://www.ebi.ac.uk/swissprot/sptr_stats/index.html " Okubo et al. (2006) NAR 34: D6-D9 Size of the nucleotide database EMBL Nucleotide Sequence Database: Release Notes - Release 113 September 2012 http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.html ! Class entries nucleotides! ------------------------------------------------------------------! CON:Constructed 7,236,371 359,112,791,043! EST:Expressed Sequence Tag 73,715,376 40,997,082,803! GSS:Genome Sequence Scan 34,528,104 21,985,922,905! HTC:High Throughput CDNA sequencing 491,770 594,229,662! HTG:High Throughput Genome sequencing 152,599 25,159,746,658! PAT:Patents 24,364,832 12,117,896,594! STD:Standard 13,920,617 37,665,112,606! STS:Sequence Tagged Site 1,322,570 636,037,867! TSA:Transcriptome Shotgun Assembly 8,085,693 5,663,938,279! WGS:Whole Genome Shotgun 88,288,431 305,661,696,545! ----------- ---------------! Total 252,106,363 450,481,663,919! ! Division entries nucleotides! ------------------------------------------------------------------! ENV:Environmental Samples 30,908,230 14,420,391,278! FUN:Fungi 6,522,586 11,614,472,226! HUM:Human 32,094,500 38,072,362,804! INV:Invertebrates 31,907,138 52,527,673,643! MAM:Other Mammals 40,012,731 145,678,620,711! MUS:Mus musculus 11,745,671 19,701,637,499! PHG:Bacteriophage 8,511 85,549,111! PLN:Plants 52,428,994 55,570,452,118! PRO:Prokaryotes 2,808,489 28,807,572,238! ROD:Rodents 6,554,012 33,326,106,733! SYN:Synthetic 4,045,013 782,174,055! TGN:Transgenic 285,307 849,743,891! UNC:Unclassified 8,617,225 4,957,442,673! VRL:Viruses 1,358,528 1,518,575,082! VRT:Other Vertebrates 22,809,428 42,568,889,857! ----------- ---------------! Total 252,106,363 450,481,663,919! Adapted from Didier Gonze Genbank (NCBI - USA) http://www.ncbi.nlm.nih.gov/Genbank/ The EMBL Nucleotide Sequence Database (EBI - UK) DDBJ - DNA Data Bank of Japan http://www.ebi.ac.uk/embl/ http://www.ddbj.nig.ac.jp/ Size of the nucleic sequence databases Biomolecular Databases ! ! Summary of database contents for the 3 main databases of nucleic sequences. Source: NAR database issue January 2006. DDBJ EMBL GenBank URL http://www.ddbj.nig.ac.jp/ http://www.ebi.ac.uk/embl/ http://www.ncbi.nlm.nih.gov/ Sequences 2.0E+06 Bases (without shotgun) 1.7E+09 4.6E+07 5.1E+10 bases (including shotgun) Organisms 1.0E+11 1.0E+11 2.0E+05 2.1E+05 UniProt : protein sequences and functional annotations [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ UniProt - the Universal Protein Resource UniProt example - Human Pax-6 protein Header : name and synonyms http://www.uniprot.org/ ! ! ! Database content (Sept 2012) " UniProtKB: • 24,532,088 entries • Translation of EMBL coding sequences (non-redundant with Swiss-Prot) " UniProtKB/Swiss-Prot section (reviewed): • 537,505 entries • annotation by experts • high information content • many references to the literature • good reliability of the information " The rest (90% of the entries) • Automatic annotation by sequence similarity. Features " The most comprehensive protein database in the world. " A huge team: >100 annotators + developers. " Annotation by experts: annotators are specialized for different types of proteins or organisms. " World-wide recognized as an essential resource. References " Bairoch et al. The SWISS-PROT protein sequence data bank. Nucleic Acids Res (1991) vol. 19 Suppl pp. 2247-9 " The UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res (2008). Database Issue. Number of entries (polypeptides) in Swiss-Prot http://www.expasy.org/sprot/relnotes/relstat.html Taxonomic distribution of the sequences UniProt example - Human Pax-6 protein Human-based annotation by specialists Within Eukaryotes UniProt example - Human Pax-6 protein Structured annotation : keywords and Gene Ontology terms UniProt example - Human Pax-6 protein Protein interactions; Alternative products UniProt example - Human Pax-6 protein UniProt example - Human Pax-6 protein Peptidic sequence UniProt example - Human Pax-6 protein References to original publications Detailed description of regions, variations, and secondary structure UniProt example - Human Pax-6 protein Cross-references to many databases (fragment shown) 3D Structure of macromolecules [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ PDB - The Protein Data Bank http://www.rcsb.org/pdb/ Genome browsers [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ EnsEMBL Genome Browser (Sanger Institute + EBI) UCSC Genome Browser (University California Santa Cruz - USA) http://www.ensembl.org/ http://genome.ucsc.edu/ Human gene Pax6 aligned with Vertebrate genomes UCSC Genome Browser (University California Santa Cruz - USA) UCSC Genome Browser (University California Santa Cruz - USA) http://genome.ucsc.edu/ http://genome.ucsc.edu/ Drosophila gene eyeless (homolog to Pax6) aligned with Insect genomes Drosophila 120kb chromosomal region covering the Achaete-Scute Complex ECR Browser EnsEMBL - Example: Drosophila gene Pax6 http://ecrbrowser.dcode.org/ http://www.ensembl.org/ Integr8 - access to complete genomes and proteomes http://www.ebi.ac.uk/integr8/ Comparative genomics [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ Integr8 - genome summaries Integr8 - clusters of orthologous genes (COGs) http://www.ebi.ac.uk/integr8/ http://www.ebi.ac.uk/integr8/ Integr8 - clusters of paralogous genes http://www.ebi.ac.uk/integr8/ Databases of protein domains [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ Prosite - protein domains, families and functional sites Prosite - aligned sequences and logo http://www.expasy.ch/prosite/ http://www.expasy.ch/prosite/ ! ! ! Some of the sequences that were used to built the Prosite profile for the Zn(2)-C6 fungal-type DNAbinding domain (ZN2_CY6_FUNGAL_2, PS50048). The Sequence Logo (below) indicates the level of conservation of each residue in each column of the alignment. Note the 6 cysteines, characteristic of this domain. Prosite - Example of profile matrix Prosite - Example of sequence logo http://www.expasy.ch/prosite/ http://www.expasy.ch/prosite/ Prosite - Example of domain signature PFAM (Sanger Institute - UK) http://pfam.sanger.ac.uk/ http://www.expasy.ch/prosite/ Protein families represented by multiple sequence alignments and hidden Markov models (HMMs) ! The domain signature is a string-based pattern representing the residues that are characteristic of a domain. CATH - Protein Structure Classification CATH - Protein Structure Classification http://www.cathdb.info/ http://www.cathdb.info/ ! CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: " " " " ! ! Class (C), Architecture (A), Topology (T) Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis. References " " Orengo et al. The CATH Database provides insights into protein structure/ function relationships. Nucleic Acids Res (1999) vol. 27 (1) pp. 275-9 Cuff et al. The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res (2008) pp. InterPro (EBI - UK) http://www.ebi.ac.uk/interpro/ InterPro (EBI - UK) Antennapedia-like Homeobox (entry IPR001827) Ontology definition Biomolecular Databases ! ! Ontologie: partie de la métaphysique qui s'intéresse à l'être en tant qu'être, indépendamment de ses déterminations particulières Ontology: part of the metaphysics that focusses on the being as a beging, independently of its particular determinations Le Petit Robert - dictionnaire alphabétique et analogique de la langue française. 1993! The Gene Ontology (GO) database [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ The "bio-ontologies" ! Answer to the problem of inconsistencies in the annotations " " ! Gene ontology: processes Controlled vocabulary Hierarchical classification between the terms of the controlled vocabulary E.g.: The Gene Ontology " " " molecular function ontology process ontology cellular component ontology Gene ontology: molecular functions Gene ontology: cellular components Gene Ontology Database Gene Ontology Database (http://www.geneontology.org/) Example: methionine biosynthetic process http://www.geneontology.org/ Status of GO annotations (NAR DB issue 2006) ! Term definitions " " " " ! Genomes with annotation " ! Biological process terms Molecular function terms Cellular component terms Sequence Ontology terms QuickGO (http://www.ebi.ac.uk/QuickGO/) Web site http://www.ebi.ac.uk/QuickGO/ A user-friendly Web interface to the Gene Ontology. Graphical display of the hierarchical relationships between terms. Convenient browsing between classes. ! 9,805 7,076 1,574 963 30 ! ! ! Excludes annotations from UniProt, which represent 261 annotated proteomes. Annotated gene products " " " Total Electronic only Manually curated 1,618,739 1,460,632 158,107 Remarks on "bio-ontologies" ! Improvement compared to free text " " ! " e.g. compartment subtypes (plasma membrane is a membrane) e.g. compartment locations (nucleus is inside cytoplasm is inside plasma membrane) To be useful, should remain purpose-based " " ! A "bio-ontologies" is usually nothing more than a taxonomical classification of the terms of a controlled vocabulary Multiple possibilities of classification criteria " ! ! each biologist might wish to define his/her own classification based on his/her needs and scope of interest impossible to define a unifying standard for all biologists No representation of molecular interactions " " relationships between objects are only hierarchical, not horizontal or cyclic e.g. does not describe which genes are the target of a given transcription factor A general definition " controlled vocabulary (choice among synonyms) hierarchical relationships between the concepts Nothing to do with the philosophical concept of ontology " ! What is biological function ? " ! Fonction: action, rôle caractéristique d un élément, d un organe, dans un ensemble (souvent opposé à structure). Source: Le Petit Robert - dictionnaire alphabetique et analogique de la langue francaise. 1982. Function: characteristic action (role) of an element (organ) within an set (often opposed to structure) Function and gene ontology " " Understanding the function requires to establish the link between molecular activity and the context in which it takes place (process). Multifunctionality • Same activity can play different roles in different processes. ! Example: scute gene in Drosophila melanogaster: a transcription factor (activity) involved in sex determination, determination of neural precursors and malpighian tubules (3 processes). • Multiple activities of a same protein in a given process ! Example: aspatokinase PutA in Escherichia coli, contains 2 enzymatic domains (enzymatic activities) + a DNA-binding domain (DNA binding transcription factor) -> 3 molecular activities in the same process (proline utilization). LIGAND - Small compounds and metabolic reactions Biomolecular Databases Small compounds, reactions and metabolic pathways [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ KEGG - Kyoto Encycplopaedia of Genes and Genomes Biomolecular Databases Ecocyc, BioCyc and Metacyc - Metabolic pathways Biomolecular Databases Protein interaction networks and transduction pathways Microarray databases [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ HapMap http://www.hapmap.org/ ! ! Human genome resources The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Associations between genetic variations (SNPs, ...) and diseases + response to pharmaceuticals. [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ Issues for biological databases Biomolecular Databases ! ! Dealing with biological complexity Data content " " ! Issues for biomolecular databases Data quality " " ! ! " ! Data structure Consistency Query capabilities Interfaces " ! Coverage Information content User interfaces Programmatic interfaces Annotation Funding [email protected] Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/ Towards biological complexity ! ! ! The main databases currently available are focussed on one type of molecular entity : nucleic sequences, proteins, compounds, ! This type of organization is very convenient as far as the information to be represented is simple (e.g. DNA sequences, structures of small molecules and macromolecules). It becomes more difficult if we want to represent " " " the interactions between biological objects, the integration of various elements in a biological process (metabolic pathways, protein interaction networks, regulatory networks, !) complex concepts such as ”biological function” Data content ! Scope of the database ! Number of entries ! Information content ! References to the source of information " " " types of biological objects represented coverage of the current knowledge Level of detail in the description of the biological objects Data quality ! Query capabilities Data Consistency " " " " always use the same name to indicate the same object (this seems trivial, but its is unfortunately still not always the case) event better: define an ID for each objects, and allow to retrieve it by any of its synonyms spelling mistakes ! Data Structuration ! Reliability " " " " " " ! user-friendly convenient browsing intuitive query forms visualization (graphical output) communication with external programs: • other databases (concept of distributed database) • analysis tools Funding ! Public funding " ! Problem: easier to obtain public funds for creating a new database than for maintaining or expanding existing resources Private funding " ! More elaborate search ! Complex querying " " " select records with some constraints select specific fields of some records with constraints on some fields (~SQL SELECT) ability to return an answer that results from a "live" computation, and was not part of any record of the dabatase Annotation Programmatic interfaces " ! Evidences ? Level of confidence ? Assignation of function by similarity • recursive process ! propagation of errors User interfaces " Browsing (click and read) Simple search distinct fields for distinct attributes of the biological objects Interfaces ! ! ! Industrial companies are • ready to invest in good data and good query capabilities • interested by academic expertise Solutions " " All users pay (per query for example) • Note: academic users are anyway funded by public funds Hybrid solution • access is free for academic users, not for companies • companies can buy the whole database an install it in-house (+ add their own private data) • academia-industry interface is often ensured by a spinoff company ! Problem ! Strategies " " " " " The flow of available data is increasing exponentially internal curators selected external experts public submission computer-based extraction of information from biological texts