Detailed Beginners Guide to Bioinformatics Databases

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.[citation needed] They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics.

Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.

Biological databases can be broadly classified into sequence, structure and functional databases. Nucleic acid and protein sequences are stored in sequence databases and structure databases store solved structures of RNA and proteins. Functional databases provide information on the physiological role of gene products, for example enzyme activities, mutant phenotypes, or biological pathways.

There are three to four main types of biological databases

• Primary database

• Secondary Databases

• Derived database

• Literature Databases

Primary databases

In bioinformatics, and indeed in other data intensive research fields, databases are often categorised as primary or secondary. Primary databases are populated with experimentally derived data such as nucleotide sequence, protein sequence or macromolecular structure. Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature. Once given a database accession number, the data in primary databases are never changed: they form part of the scientific record.

Secondary databases

By contrast, secondary databases comprise data derived from the results of analysing primary data. They are often referred to as curated databases but this is a bit of a misnomer because primary databases are also curated to ensure that the data in them is consistent and accurate.

Secondary databases often draw upon information from numerous sources, including other databases (primary and secondary), controlled vocabularies and the scientific literature. They are highly curated, often using a complex combination of computational algorithms and manual analysis and interpretation to derive new knowledge from the public record of science.

Secondary databases have become the molecular biologist’s reference library over the past decade or so, providing a wealth of (often daunting) information on just about any gene or gene product that has been investigated by the research community. The potential for mining this information to make new discoveries is vast. It’s our job in this course to reduce your activation energy to make more of these resources for your research.

International Nucleotide Sequence Database (INSD) consists of the following databases.

DNA Data Bank of Japan (National Institute of Genetics)

EMBL (European Bioinformatics Institute)

GenBank (National Center for Biotechnology Information)

A few popular databases are GenBank from NCBI (National Center for Biotechnology Information), UNIProt from the Swiss Institute of Bioinformatics.

Explained the different primary databases

GenBank

EMBL

UniProt

DDBJ

Explained primary Databases

Array Express and BioStudies:

GEO

Explained Secondary Databases

REACTOME

Broad Institute of Harvard and MIT

Genome Analysis Toolkit - Broad Institute

Firebrowse

KEGG: Kyoto Encyclopedia of Genes and Genomes

TCGA Computational Tools - National Cancer Institute

Secondary databases make use of publicly available sequence data in primary databases to to provide layers of information to DNA or protein sequence data. ... Secondary databases comprise data derived from analysing entries in primary databases.

Explained Secondary Databases

1000 Genomes Browser

BLAST

ClinVar

Explained Secondary Databases

dbSNP

dbVar

dbGaP

Explained Secondary Databases

Gene

Genome

MedGen

Explained secondary databases

NCBI Develop

E-Utilities API for NCBI

ENCODE