A
biological database is an organized collection of related biological data, that
can be easily stored, accessed and managed.
Let’s
take a simple example to understand database;
Student
database in a school or college; it is a related information of student data
like name, address, roll number etc. that is saved, that can be modified or
accessed based on our need.
10
Types of biological database based on data type.
1.
Bibliographic Database
Contains
research article and research papers of different journals.
Example:
Pubmed is a biomedical literature database.
2.
Sequence database
Contains
protein and nucleotide sequence. Example: GenBank, DDBJ, PIR
- GenBank: world’s largest annotated collection of all publicly available DNA sequences
- maintained by NCBI (National Center for Biotechnology Information)
- GenBank Overview (nih.gov)
DDBJ (DNA Data Bank of Japan):
- Nucleotide Sequence database
- DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia
- maintained by National Institute of Genetics (NIG) in Mishima.
PIR
(Protein Information Resource): protein
sequences databases
- Contains protein sequences and functional information submitted globally
- by the National Biomedical Research Foundation (NBRF)
- Welcome to PIR [Protein Information Resource]
3.
Structure Database
Contains
3D structure of proteins and nucleic acids. Example:PDB
PDB (Protein Data Bank)
- primary protein structure database
- Include information about the 3D structures of large biological molecules, including proteins and nucleic acids.
- Structure determined by X-ray crystallography, NMR experiments, and molecular modeling.
- The PDB was established in 1971 at Brookhaven National Laboratory
- RCSB PDB: Homepage
4.Metabolic
Database
Contains
data about various biological
KEGG:
Kyoto Encyclopedia of Genes and Genomes
https://www.kegg.jp/
MetaCyc:
MetaCyc is a curated database of
experimentally elucidated metabolic pathways from all domains of life.
This video is a summary of 10 databases.
5. Model organism Database
Contains
in-depth biological data of studied model organism.
Flybase:
A Database of Drosophila Genes & Genomes FlyBase Homepage
EcoCyc
is a scientific database for the bacterium Escherichia coli K-12 MG1655.
6.
Enzyme Database
Contains
data about structure and function of various enzymes.
BRENDA: collection of enzyme functional data available to the scientific
community
BRENDA Enzyme Database
(brenda-enzymes.org)
7.
Disease Database
Disease
related information
OMIM
(Online Mendelian Inheritance in Man): An Online Catalog of Human Genes and Genetic
Disorders
8.
Chemical Database
Data
on several small organic molecules.
PubChem:
PubChem is the world's largest
collection of freely accessible chemical information.
Maintained
by NCBI
9.
Microarray Database
Gene
expression data from microarray experiments.
Gene
Expression Omnibus (GEO): a database
for gene expression profiling and RNA methylation profiling managed by the
National Center for Biotechnology Information (NCBI). Home - GEO - NCBI (nih.gov)
10.
Taxonomic Database
Database
that provides information on earths species of animals, plants.
Catalogue of life: The most complete authoritative list of the world's species - maintained by hundreds of global taxonomists. COL | The Catalogue of Life
