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 a common term referring simply to data about data such as tags, keywords, and markup headers.

Model organism databases

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

Nucleic acid databases

DNA databases

For DNA barcoding databases with a taxonomic focus, see Taxonomic databases.

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

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]

  • 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

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

RNA databases

For rRNA databases with a taxonomic focus, see Taxonomic databases.

Amino acid and 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.[16] 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.[16]

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[17]

Different types of Protein databases

See also: Protein structure database
DB nameDB websiteProviderData sourcesRevenue/Sponsors sourcesIntegratesDesc.SizeDB typeActively maintained
InterProInterProELIXIR infrastructureEuropean Bioinformatics InstituteEMBL, The Welcome trust, BBSRCCATH-Gene3D, CDD, HAMAP, MobiDB, PANTHER, Pfam, SMART, SUPERFAMILY, SFLD, TIGRFAMs,classifies proteins into families and predicts the presence of domains and sitesProtein sequence databasesYes
NeXtProtNextProtCALIPHO (is a group at the SIB)Swiss Institute of BioinformaticsFunding sourcesUniProt, Cellosaurus, Gnomad, IntAct, SRAA Atlas, Uniprot - GOA, BGEE, COSMIC, MassIVE, Peptide atlasa human protein-centric knowledge resourceProtein sequence databasesYes
Wiki-PiWiki-PiMadhavi K. GanapathirajuAt present Wiki-Pi contains 48,419 unique interactions among 10,492 proteins. However it is not clear if this is unique proteins[13][clarification needed]Protein interaction Database??
Human Protein Reference DatabaseInstitute of Bioinformatics (IOB), Bangalore, IndiaOne source claims 15000 [18] proteins. But it is unclear how many of these are unique
PfamSanger Instituteprotein families database of alignments and HMMsProtein sequence databases
Human ProteinpediaInstitute of Bioinformatics (IOB), Bangalore and Johns Hopkins University,The human Proteinpedia is based on HPRD (Human protein reference database)which is a repository hosting over 30,000 human proteins. However it is unclear how many of these are unique proteins
Human Protein AtlasThe Swedish GovernmentIt contains roughly 10 million IHC images of a bit less than 25,000 antibodies. But once again it is unclear how many of these are unique
PRINTSManchester Universitya compendium of protein fingerprintsProtein sequence databases
PROSITEPrositedatabase of protein domains, families and functional sitesProtein sequence databases
Protein Information ResourceGeorgetown University Medical Center [GUMC]Protein sequence databases
SUPERFAMILYlibrary of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organismsProtein sequence databases
Swiss-ProtSwiss Institute of Bioinformaticsprotein knowledgebaseProtein sequence databases
Protein Data BankRCSB PDB (Research Collaboratory for Structural Bioinformatics - Protein Data Bank)Protein DataBank in Europe (PDBe),[19] ProteinDatabank in Japan (PDBj),[20] and RCSB[21](PDB)Protein structure databases
Structural Classification of Proteins (SCOP)Protein structure databases
CATH databaseProtein structure databases
ModBaseSali Lab, UCSFdatabase of comparative protein structure modelsProtein model databases
SIMAPdatabase of protein similarities computed using FASTAProtein model databases
Swiss-modelserver and repository for protein structure modelsProtein model databases
AAindexdatabase of amino acid indices, amino acid mutation matrices, and pair-wise contact potentialsProtein model databases
BioGRIDSamuel Lunenfeld Research Institutegeneral repository for interaction datasetsProtein-protein and other molecular interactions
RNA-binding protein databaseProtein-protein and other molecular interactions
Database of Interacting ProteinsUniv. of CaliforniaProtein-protein and other molecular interactions
IntAct[22]EMBL-EBIopen-source database for molecular interactionsProtein-protein and other molecular interactions
Stringan open source molecular interaction database to study interactions between proteinsProtein-protein and other molecular interactions
Human Protein AtlasHuman Protein Atlasaims at mapping all the human proteins in cells, tissues and organsProtein expression databases
ProteinModelPortalProtein Model Portal of the PSI-Nature Structural Biology Knowledgebase????3D structure protein databases
SWISS-MODEL RepositoryDatabase of annotated 3D protein structure modelsUniversity of BaselThe Swiss government3D structure protein databases
DisProtDatabase of Protein DisorderELIXIR infrastructureIndiana University School of Medicine, Temple University, University of Paduafunding from the European Union's Horizon 2020Swiss Prot/Uni Prot, CATH, Pfam, Europe PMC, BITEM, ECO, Geneontologydatabase of experimental evidences of disorder in proteins3D structure protein databases, Protein sequence databases
MobiDBDatabase of intrinsically disordered and mobile proteinsJohn Moult, Christine Orengo, Predrag RadivojacUniversity of PaduaItalian Governmentdatabase of intrinsic protein disorder annotation3D structure protein databases, Protein sequence databases
ModBaseDatabase of Comparative Protein Structure ModelsUrsula Pieper, Ben Webb, Narayanan Eswar, Andrej Sali Roberto SanchezUCSF, Sali Lab3D structure protein databases
PDBsumPictorial database of 3D structures in the Protein Data BankEuropean Bioinformatics Institute 2013Wellcome Trust3D structure protein databases
CCDSThe Consensus CDS protein set databaseNCBI??Sequence databases
UniProtKBUniversal Protein Resource (UniProt)????Sequence databases
Swiss Prot/Uni ProtSwiss Prot and Uni ProtSIB Swiss Institute of BioinformaticsEuropean Bioinformatics Institute (EMBL-EBI)Swiss-Prot has collected over 81 000 variants in roughly 13,000 human protein sequence records from peer-reviewed literature. It is unclear how many unique proteins types are present in the database.

Signal transduction pathway databases

Metabolic pathway and protein function databases

Taxonomic databases

Main article: List of biodiversity databases

Numerous databases collect information about species and other taxonomic categories. The Catalogue of Life is a special case as it is a meta-database of about 150 specialized "global species databases" (GSDs) that have collected the names and other information on (almost) all described and thus "known" species.

  • BacDive: bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity, including taxonomy information
  • Catalogue of Life: a meta-database of all species on earth
  • EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
  • NCBI Taxonomy: a taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank, another database operated by NCBI).

Image databases

Images play a critical role in biomedicine, ranging from images of anthropological specimens to zoology. However, there are relatively few databases dedicated to image collection, although some projects such as iNaturalist collect photos as a main part of their data. A special case of "images" are 3-dimensional images such as protein structures or 3D-reconstructions of anatomical structures. Image databases include, among others:[23]

Radiologic databases

Additional databases

Exosomal databases

  • ExoCarta
  • Extracellular RNA Atlas: a repository of small RNA-seq and qPCR-derived exRNA profiles from human and mouse biofluids

Mathematical model databases

Databases on antimicrobial resistance rates and antibiotic consumption

Databases on antimicrobial resistance mechanisms

Wiki-style databases

Specialized databases

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