Biological databases are stores of biological information.^[1] The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. The 2018 issue has a list of about 180 such databases and updates to previously described databases.^[2] Omics Discovery Index can be used to browse and search several biological databases. Furthermore, the NIAID Data Ecosystem Discovery Portal developed by the National Institute of Allergy and Infectious Diseases (NIAID) enables searching across databases.

Meta databases

Meta databases are databases of databases that collect data about data to generate new data. They are capable of merging information from different sources and making it available in a new and more convenient form, or with an emphasis on a particular disease or organism.. originally, metadata was only common term referring simply to data about data such a tags, keywords, and markup headers.

• ConsensusPathDB: a molecular functional interaction database, integrating information from 12 others
• Entrez (National Center for Biotechnology Information)
• Neuroscience Information Framework (University of California, San Diego): integrates hundreds of neuroscience relevant resources; many are listed below

Model organism databases

Model organism databases provide in-depth biological data for intensively studied organisms.

• PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe^[3]
• SubtiWiki: integrated database for the model bacterium Bacillus subtilis^[4]
• TAIR: the knowledgebase for the plant Arabidopsis thaliana^[5]

Nucleic acid databases

DNA databases

The primary databases make up the International Nucleotide Sequence Database (INSD). The include:

• DNA Data Bank of Japan (National Institute of Genetics)
• EMBL (European Bioinformatics Institute)
• GenBank (National Center for Biotechnology Information)

DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. All three accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. These three databases are primary databases, as they house original sequence data. They collaborate with Sequence Read Archive (SRA), which archives raw reads from high-throughput sequencing instruments.

Secondary databases are:^{[clarification needed]}

• 23andMe's database
• HapMap
• OMIM (Online Mendelian Inheritance in Man): inherited diseases
• RefSeq
• 1000 Genomes Project: launched in January 2008. The genomes of more than a thousand anonymous participants from a number of different ethnic groups were analyzed and made publicly available.
• EggNOG Database: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. It provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation.^[6][7]

Other databases

• Nucleosome positioning region database

Gene expression databases

Generic gene expression databases

Microarray gene expression databases

Genome databases

These databases collect genome sequences, annotate and analyze them, and provide public access. Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism genome.

Phenotype databases

• PHI-base: pathogen-host interaction database. It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer-reviewed literature.
• RGD Rat Genome Database: genomic and phenotype data for Rattus norvegicus
• PomBase database: manually curated phenotypic data for the yeast Schizosaccharomyces pombe

RNA databases

• miRBase: the microRNA database
• PolymiRTS: a database of DNA variations in putative microRNA target sites
• PolyQ: database of polyglutamine repeats in disease and non-disease associated proteins
• Rfam: a database of RNA families
• IRESbase: A comprehensive database of experimentally validated internal ribosome entry sites.^[14]

Amino acid / protein databases

(See also: List of proteins in the human body)

Several publicly available data repositories and resources have been developed to support and manage protein related information, biological knowledge discovery and data-driven hypothesis generation.^[15] The databases in the table below are selected from the databases listed in the Nucleic Acids Research (NAR) databases issues and database collection and the databases cross-referenced in the UniProtKB. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other.^[15]

Proteins in human:

There are about ~20,000 protein coding genes in the standard human genome. (Roughly ~1200 already have Wikipedia articles - the Gene Wiki - about them) if we are Including splice variants, there could be as many as 500,000 unique human proteins^[16]

Different types of Protein databases

This section needs expansion. You can help by adding to it. (January 2015)