Databases & Data banks

1. Databases & Data banks “It is a capital mistake to theorize before one has data”. Sir Arthur Conan Doyle (1859-1930), A scandal in Bohemia

2. Banche Dati Biologiche  informazioni e dati di letteratura, sperimentali e in silico.

3. Banche Dati Biologiche Struttura delle Banche Dati Banche Dati Primarie Banche Dati Specializzate e Risorse Genomiche Interoperabilità fra le Banche Dati Sistemi di Retrieval

4. Struttura delle Banche dati elemento biologico centrale "entry" della banca dati

5. Struttura delle Banche dati Entry name e Accession Number Informazioni associate Ontologia: una formale descrizione delle entità e delle relazioni intercorrenti fra esse

6. Struttura delle Banche dati Formatoflat-file

7. Colonna =attributi Riga=record o k--tupla Tabella relazioni Fig.2.3. Relational database. A table (relation) is a set and the three basic table operations shown here are extensions of the standard set operations.

8. DB deduttivi Fig.2.4. Deductive database. The data in the family tree is represented and manipulated in a deductive database, which consists of a relational database and a logic programming

9. Object oriented Fig. 2.5. Object-oriented database. The concept of similarity is implemented in an object-oriented database wich incorporates many different aspects of genes.

10. Banche Dati DNA e RNA Le Banche Dati di sequenze di acidi nucleici sono spesso Banche Dati Primarie in quanto contengono solo informazioni generiche con un minimo di informazione da associare alla sequenza per identificarla dal punto di vista specie-funzione.

11. Banche Dati Primarie(DNA) 1980  EMBL 1982  GenBank 1986  DDBJ

12. EMBL Data LibraryRelease 110 – Dec 2011 • 230,021,806 Entries • 376,471,768,435Nucleotides

20. Banche Dati Primarie(Proteine) SWISS-PROT TrEMBL PIR

22. Importance of reference protein sequence databases • Completeness and minimal redundancy A non redundant protein sequence database, with maximal coverage including splice isoforms, disease variant and PTMs. Low degree of redundancy for facilitating peptide assignments • Stabilityand consistency Stable identifiers and consistent nomenclature Databases are in constant change due to a substantial amount of work to improve their completeness and the quality of sequence annotation • High quality protein annotation Detailed information on protein function, biological processes, molecular interactions and pathways cross-referenced to external source

23. Summary of protein sequence databases • Updated from Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics. 4,1419–1440l

24. UniProtKB • UniProt Knowledgebase: • 2 sections • UniProtKB/Swiss-Prot Non-redundant, high-quality manual annotation - reviewed • UniProtKB/TrEMBL Redundant, automatically annotated - unreviewed www.uniprot.org Master headline

27. Manual annotation of UniProtKB/Swiss-Prot Splice variants Sequence Sequence features UniProtKB Ontologies Annotations References Nomenclature

28. Splice variants Master headline

29. Identification of amino acid variants ..and of PTMs … and also Master headline

30. Protein nomenclature Master headline

31. Master headline

32. Annotation - >30 defined fields Controlled vocabularies used whenever possible… Master headline

33. Evidence at protein level There is experimental evidence of the existence of a protein (e.g. Edman sequencing, MS, X-ray/NMR structure, good quality protein-protein interaction , detection by antibodies) Evidence at transcript level The existence of a protein has not been proven but there is expression data (e.g. existence of cDNAs, RT-PCR or Northern blots) that indicates the existence of a transcript. Inferred from homology The existence of a protein is likely because orthologs exist in closely related species 4 Predicted 5 Uncertain Sequence evidence Type of evidence that supports the existence of a protein

35. Manual annotation of the human proteome(UniProtKB/Swiss-Prot) A draft of the complete human proteome has been available in UniProtKB/Swiss-Prot since 2008 Manually annotated representation of 20,242 protein coding genes with ~ 36,000 protein sequences - an additional 38,484 UniProtKB/TrEMBL form the complete proteome set Approximately 63,000 single amino acid polymorphisms (SAPs), mostly disease-linked 80,000 post-translational modifications (PTMs) Close collaboration with NCBI, Ensembl, Sanger Institute and UCSC to provide the authoritative set to the user community

36. Text-based searching • Logical operators ‘&’ (and), ‘|’ Searching UniProt – Simple Search Master headline

37. Searching UniProt – Advanced Search Master headline

38. Each linked to the UniProt entry Searching UniProt – Search Results Master headline

39. Searching UniProt – Search Results Master headline

40. Searching UniProt – Search Results Master headline

41. Inter-operabilità fra le Banche dati Di fondamentale importanza e’ introdurre nel disegno delle banche dati i meccanismi di cross-referencing che consentono di navigare fra i database anche se dislocati su siti tra di loro remoti

42. A link-based integration of molecular biology databases in the DBGET/LinkDB system at GenomeNet (http://www.genome.ad.jp/). The lines indicate thet the cross-references are given by the original databases.