List of 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.
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.- ConsensusPathDB: a molecular functional interaction database, integrating information from 12 other
- Entrez
- Neuroscience Information Framework : integrates hundreds of neuroscience relevant resources; many are listed below
Model organism databases
- PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe
Nucleic acid databases
DNA databases
Primary databasesInternational Nucleotide Sequence Database consists of the following databases.
DDBJ, GenBank and European Nucleotide Archive 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, which archives raw reads from high-throughput sequencing instruments.
Secondary databases
- 23andMe's database
- HapMap
- OMIM : 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.
- 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.
Gene expression databases (mostly microarray data)
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
- Rfam: a database of RNA families
Amino acid / protein databases
[Protein sequence] databases
[Protein structure] databases
- Protein Data Bank, comprising:
- * Protein DataBank in Europe
- * ProteinDatabank in Japan
- * Research Collaboratory for Structural Bioinformatics
- Structural Classification of Proteins
Protein model">Protein structure prediction">Protein model databases
- ModBase: database of comparative protein structure models
- Similarity Matrix of Proteins : database of protein similarities computed using FASTA
- Swiss-model: server and repository for protein structure models
- AAindex: database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials
Protein-protein">Protein-protein interaction">Protein-protein and other molecular interactions
- BioGRID: general repository for interaction datasets
- RNA-binding protein database
Protein expression">Protein production">Protein expression databases
- Human Protein Atlas: aims at mapping all the human proteins in cells, tissues and organs
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
- WikiPathways
Metabolic pathway and protein function 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
- Biomodels Database: published mathematical models describing biological processes
Taxonomic databases
- BacDive: bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity, including taxonomy information
- EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
Radiologic databases
- The Cancer Imaging Archive
- Neuroimaging Informatics Tools and Resources Clearinghouse
[Antimicrobial resistance] databases
Wiki-style databases
- Gene Wiki
- WikiProfessional
Specialized databases