10 Types of Biological Databases

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 Databases

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.

PubMed (nih.gov)

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

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 pathways.

KEGG: Kyoto Encyclopedia of Genes and Genomes


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

Home - OMIM

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

PubChem (nih.gov)

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 

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