Databases & Data banks
description
Transcript of Databases & Data banks
Databases & Data banks
“It is a capital mistake to theorize before one has data”.
Sir Arthur Conan Doyle (1859-1930),
A scandal in Bohemia
Banche Dati Biologiche
informazioni e dati di letteratura,
sperimentali e in silico.
Banche Dati Biologiche
Struttura delle Banche Dati Banche Dati Primarie Banche Dati Specializzate e Risorse
Genomiche Interoperabilità fra le Banche Dati Sistemi di Retrieval
Struttura delle Banche dati
elemento biologico centrale
"entry" della banca dati
Struttura delle Banche datiEntry name e Accession Number
Informazioni associate Ontologia: una formale descrizione delle entità e delle relazioni intercorrenti fra esse
Struttura delle Banche datiFormato flat-file
Tabella relazioni
Colonna =attributiRiga=record o k--tupla
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.
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
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.
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.
Banche Dati Primarie(DNA)
1980 EMBL 1982 GenBank
1986 DDBJ
EMBL Data LibraryRelease 110 – Dec 2011
230,021,806 Entries
376,471,768,435 Nucleotides
Banche Dati Primarie(Proteine)
SWISS-PROT
TrEMBL
PIR
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
• Stability and 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
Summary of protein sequence databases
Database Description Species
UniProtKB Expertly curated section (UniProtKB/Swiss-Prot) and computer-annotated section (UniProtKB/TrEMBL); minimum level of redundancy; high level of integration with other databases; stable identifiers; diversity of sources including large scale genomics, small scale cloning and sequencing, protein sequencing, PDB, predicted sequences from Ensembl and RefSeq
Many
UniRef100 Assembled from UniProtKB, Ensembl and RefSeq; merges 100% identical sequences; stable identifiers
Many
Ensembl Predictions using automated genome annotation pipeline; explicitly linked to nucleotide and protein sequences; stable reference; merge their annotations with Vega annotations at transcript level; extensive quality checks to remove erroneous gene models ; high level of integration with other databases
Over 50 Eukaryotic genomesEnsembl Genomes: Metazoa, Plants and Fungi, Protists, Bacteria and Archaea
RefSeq NCBI creates from existing data; ongoing curation; non-redundant; explicitly linked nucleotide and protein sequences; stable reference; high level of integration with other databases
Limited to fully sequenced organisms
Entrez protein (NCBInr) Assembled from GenBank and RefSeq coding sequence translations and UniProt KB ; annotations extracted from source curated databases; high degree of sequence redundancy
Many
Updated from Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics. 4,1419–1440l
UniProtKB
Master headline
UniProt Knowledgebase:
2 sections
1. UniProtKB/Swiss-Prot Non-redundant, high-quality manual annotation - reviewed
2. UniProtKB/TrEMBL Redundant, automatically annotated - unreviewed
www.uniprot.org
Sequence Sequence features
Ontologies
ReferencesNomenclature
Splice variants
Annotations
UniProtKB
Manual annotation of UniProtKB/Swiss-Prot
Master headline
Splice variants
Master headline
Identification of amino acid variants
..and of PTMs
… and also
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Protein nomenclature
Master headline
Master headline
Controlled vocabularies used whenever possible…
Annotation - >30 defined fields
1 Evidence at protein levelThere 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)
2 Evidence at transcript levelThe 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.
3 Inferred from homologyThe 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
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
Master headline
Searching UniProt – Simple Search
• Text-based searching• Logical operators ‘&’ (and), ‘|’
Master headline
Searching UniProt – Advanced Search
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Searching UniProt – Search Results
Each linked to the UniProt entry
Master headline
Searching UniProt – Search Results
Master headline
Searching UniProt – Search Results
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
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.