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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 dati
Entry name e Accession Number
Informazioni associate
Ontologia: una formale descrizione
delle entità e delle relazioni
intercorrenti fra esse
Struttura delle Banche dati
Formato flat-file
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.
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 Library
Release 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 computerannotated 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 genomes
Ensembl 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
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UniProtKB

UniProt Knowledgebase:

1.
2.
Master headline
2 sections
UniProtKB/Swiss-Prot Non-redundant, highquality manual annotation - reviewed
UniProtKB/TrEMBL Redundant, automatically
annotated - unreviewed
www.uniprot.org
Manual annotation of UniProtKB/Swiss-Prot
Splice variants
Sequence
Sequence
features
UniProtKB
Ontologies
Annotations
Nomenclature
References
Splice variants

Master headline
Identification of amino acid variants
..and of PTMs
… and also

Master headline
Protein nomenclature

Master headline

Master headline
Annotation - >30 defined fields
Controlled vocabularies used whenever possible…

Master headline
Sequence evidence
Type of evidence that supports the existence of a protein
1 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)
2 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.
3 Inferred from homology
The existence of a protein is likely because orthologs exist in closely
related species
4 Predicted
5 Uncertain
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
Searching UniProt – Simple Search
• Text-based searching
• Logical operators ‘&’ (and), ‘|’

Master headline
Searching UniProt – Advanced Search

Master headline
Searching UniProt – Search Results
Each linked to the UniProt entry

Master headline
Searching UniProt – Search Results
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Master headline
Searching UniProt – Search Results

Master headline
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.