Biological databases are stores of biological information. 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. 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.
bio.tools: a community-driven registry of bioinformatics software and data resources ConsensusPathDB: a molecular functional interaction database, integrating information from 12 others Entrez search system at the National Center for Biotechnology Information (NCBI) link Expert Protein Analysis System (ExPASy) link Neuroscience Information Framework (University of California, San Diego): integrates hundreds of neuroscience relevant resources; many are listed below Resources at the Health Sciences Library System (HSLS) of the University of Pittsburgh MolBio Information Service OBRC: Online Bioinformatics Resources Collection HSLS MolBio Available Software Databases A-Z
Model organism databases Model organism databases provide in-depth biological data for intensively studied organisms.
PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe SubtiWiki: integrated database for the model bacterium Bacillus subtilis TAIR: the knowledgebase for the plant Arabidopsis thaliana
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:
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. 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.
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. 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. 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
Different types of Protein databases
Other protein database links The Pfam (proteins families) database link The Worldwide Protein Data Bank (wwPDB) link and the related foundation link
Signal transduction pathway databases NCI-Nature Pathway Interaction Database Netpath: curated resource of signal transduction pathways in humans Reactome: navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory) WikiPathways
Metabolic pathway and protein function databases
Taxonomic 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:
Allen Brain Atlas Digital Brain Bank Electron Microscopy Public Image Archive (EMPIAR) FlyExpress Image Data Resource Morphobank Morphosource
Radiologic databases The Cancer Imaging Archive (TCIA) Neuroimaging Informatics Tools and Resources Clearinghouse
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 Biomodels Database: published mathematical models describing biological processes MorpheusML Model Repository: published, community-contributed, and educational multi-scale and multicellular models for systems biology
Databases on antimicrobial resistance rates and antibiotic consumption CIPARS EARS-Net ESAC-Net
Databases on antimicrobial resistance mechanisms
Wiki-style databases Gene Wiki WikiSpecies WikiProfessional
Specialized databases
References
External links The Bioregistry database system link The Database of Molecular Motions link The ELIXIR coordination project link The National Center for Biotechnology Information (NCBI) link Nucleic Acid Research (NAR) Database Summary Paper Category List
Nucleic Acid Research Molecular Biology Database Collection – over 1,600 databases