Bioinformatics Databases

Bioinformatics

The acquisition, archiving and interpretation (analysis) of molecular biology information.

Biological Databases

A large, persistent collection of systemically organised data, managed by a software that can retrieve and update records.

Types of biological data

• Genomic, transcriptomic, and protein sequences.

• Genomic annotation, e.g. genes, transcription factors binding sites, gene function, pathways

• Phenotypes and more..

Key concepts of biological databases

• Unique identifier aka accession number

• Fixed format/vocab

In molecular biology what are the two sequence formats frequently used?

GENBANK and FASTA

FASTA

de facto standard for any raw sequence. FASTA is a machine interpretable format.

• a ‘>’ symbol for every new entry, with a unique identifier (name) and the sequence on the following line

Biological System

• Cell lines

• Animal model

• Human

Organisation

• Organelles

• Single cells

• Tissues

Scope and Coverage

1. biased or partial (candidate gene)

2. comprehensive (omics data)

Genesis

1. Computational predictions

2. experimental data

Curation

1. Raw/archival data (SRA)

2. Curated data (RefSeq)

Types of Curation

1. computationally curated (UniProt)

2. community curated (GO)

3. Expert reviewed (RefSeq)

Primary Sources

Data derived from experiments (GenBank, DDBJ, PDB)

Secondary sources

Curated/ derived from analysis of primary data/ literature (Pfam, InterPro, PROSITE, OMIM)

Composite or hybrid sources

Characteristics of both primary and secondary data (Uniprot, Entrez)

Pubmed

Most popular free database, good support for structured queries.

Web of Science

Oldest paid access database and provides a reputable collection of journals with impact factors and number of citations.

Medline

Updated frequently, focus on life and medical sciences, access freely from Pubmed.

Scopus

Paid access database owned by Elsevier, an academic journals publisher.

GenBank

• Archival in nature

• Subjective

• Multiple copies

• Human readable format

• part of NCBI nucleotide

• Flat file format

Entrez Gene (NCBI gene)

• Information about genes, unique identifiers and associated info

• While GenBank is a primary database containing sequences Entrez Gene is another database containing many kinds of info.

UniProt

• Protein focused database consisting of the combined databases SwissProt, TrEMBL

• SwissProt is manually annotated and reviewed

• TrEMBL are automatically annotated and not reviewed

Gene Ontology

Species-independent vocab that describes gene function in a systemic way using fixed terms- GO terms.

How are genes GO terms assigned?

Based on the literature about the function of the gene.

KEGG Pathway Database

Repository of species- independent metabolic pathways.

KEGG Orthology Database

Repository of species-independent molecular functions extracted from KEGG Pathways.

How are genes assigned molecular functions?

On the basis of their involvement on a particular KEGG pathway.