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List of biological databases
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.
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.[metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. The word metadatabase is an addition to the dictionary]. 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
- SubtiWiki: integrated database for the model bacterium Bacillus subtilis
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:
- 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.
Other databases
Gene expression databases (mostly microarray data)
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.
- ArrayExpress: archive of functional genomics data; stores data from high-throughput functional genomics experiments from EMBL
- Bioinformatic Harvester
- Cervical cancer gene database
- Ensembl: provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes
- Ensembl Genomes: provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform)
- FlyBase: genome of the model organism Drosophila melanogaster
- Gene Disease Database
- Gene Expression Omnibus (GEO): a public functional genomics data repository from the U.S. National Cancer Institute (NCI), which supports array- and sequence-based data. Tools for querying and downloading gene expression profiles are provided.
- Human Protein Atlas (HPA): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors.
- Legume Information System (LIS): genomic database for the legume family
- Personal Genome Project: human genomes of 100,000 volunteers from around the world
- RGD (Rat Genome Database): genomic and phenotype data for Rattus norvegicus
- Saccharomyces Genome Database: genome of the yeast model organism
- SNPedia
- SoyBase Database (SoyBase): USDA soybean genetics and genomic database (Soybean)
- UCSC Malaria Genome Browser: genome of malaria causing species (Plasmodium falciparum and others)
- Wormbase: genome of the model organism Caenorhabditis elegans and WormBase ParaSite for parasitic species
- Xenbase: genome of the model organism Xenopus tropicalis and Xenopus laevis
- Zebrafish Information Network: genome of this fish model organism
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
Amino acid / protein databases
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.
Database Short Name | Database Name |
---|---|
CCDS | The Consensus CDS protein set database |
DDBJ | DNA Data Bank of Japan |
ENA | European Nucleotide Archive |
GenBank | GenBank nucleotide sequence database |
Refseq | NCBI Reference Sequence Database |
UniGene | Database of computationally identifies transcripts from the same locus |
UniProtKB | Universal Protein Resource (UniProt) |
Database Short Name | Database Name |
---|---|
DisProt | Database of Protein Disorder |
MobiDB | Database of intrinsically disordered and mobile proteins |
ModBase | Database of Comparative Protein Structure Models |
PDBsum | Pictorial database of 3D structures in the Protein Data Bank |
ProteinModelPortal | Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase |
SMR | Database of annotated 3D protein structure models |
Protein sequence databases
- DisProt: database of experimental evidences of disorder in proteins (Indiana University School of Medicine, Temple University, University of Padua)
- InterPro: classifies proteins into families and predicts the presence of domains and sites
- MobiDB: database of intrinsic protein disorder annotation (University of Padua)
- neXtProt: a human protein-centric knowledge resource
- Pfam: protein families database of alignments and HMMs (Sanger Institute)
- PRINTS: a compendium of protein fingerprints from (Manchester University)
- PROSITE: database of protein families and domains
- Protein Information Resource (Georgetown University Medical Center [GUMC])
- SUPERFAMILY: library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms
- Swiss-Prot: protein knowledgebase (Swiss Institute of Bioinformatics)
- NCBI: protein sequence and knowledgebase (National Center for Biotechnology Information)
Protein structure databases
-
Protein Data Bank (PDB), comprising:
- Protein DataBank in Europe (PDBe)
- ProteinDatabank in Japan (PDBj)
- Research Collaboratory for Structural Bioinformatics (RCSB)
- Structural Classification of Proteins (SCOP)
- CATH : Protein Structure Classification database
For more protein structure databases, see also Protein structure database.
Protein model databases
- ModBase: database of comparative protein structure models (Sali Lab, UCSF)
- Similarity Matrix of Proteins (SIMAP): 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 and other molecular interactions
- BioGRID: general repository for interaction datasets (Samuel Lunenfeld Research Institute)
- RNA-binding protein database
- Database of Interacting Proteins (Univ. of California)
- IntAct: open-source database for molecular interactions (EMBL-EBI)
- String: an open source molecular interaction database to study interactions between proteins
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 (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory)
- WikiPathways
Metabolic pathway and protein function databases
- BioCyc Database Collection: includes EcoCyc and MetaCyc
- BRENDA: the comprehensive enzyme information system, including FRENDA, AMENDA, DRENDA, and KENDA
- HMDB: contains detailed information about small molecule metabolites found in the human body
- KEGG PATHWAY Database (Univ. of Kyoto)
- MANET database (University of Illinois)
- 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)
- SABIO-RK: database for biochemical reactions and their kinetic properties
- WikiPathways
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)
- Image Data Resource
- Morphobank
- Morphosource
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
- Biomodels Database: published mathematical models describing biological processes
Radiologic databases
Databases on antimicrobial resistance rates and antibiotic consumption
Databases on antimicrobial resistance mechanisms
- AMRFinderPlus
- Antimicrobial Drug Database (AMDD)
- ARDB (no longer maintained)
- ARGminer
- BacMet
- Beta-Lactamase Database (BLAD)
- Beta-Lactamase Database (BLDB)
- CBMAR
- The Comprehensive Antibiotic Resistance Database
- FARME
- INTEGRALL
- LacED
- MEGARes
- MUBII-TB-DB
- Mustard Database
- MvirDB
- PathoPhenoDB
- PATRIC database
- RAC: Repository of Antibiotic resistance Cassettes
- ResFinder
- TBDReaMDB
- u-CARE
- VFDB
Wiki-style databases
Specialized databases
- Barcode of Life Data Systems: database of DNA barcodes
- Bacterial Pesticidal Protein Database
- The Cancer Genome Atlas (TCGA): provides data from hundreds of cancer samples obtained using high-throughput techniques such as gene expression profiling, copy number variation profiling, SNP genotyping, genome-wide DNA methylation profiling, microRNA profiling, and exon sequencing of at least 1,200 genes
- Cellosaurus: a knowledge resource on cell lines
- CTD (Comparative Toxicogenomics Database): describes chemical-gene-disease interactions
- DiProDB: a database to collect and analyse thermodynamic, structural and other dinucleotide properties
- Housekeeping and Reference Transcript Atlas (HRT Atlas) web-based tool for searching cell specific candidate reference genes/transcripts suitable for qPCR experiment normalization. HRT Atlas also describes a complete list of human and mouse housekeeping genes and transcripts
- Dryad: repository of data underlying scientific publications in the basic and applied biosciences
- Edinburgh Mouse Atlas
- EPD Eukaryotic Promoter Database
- FINDbase (the Frequency of INherited Disorders database)
- GigaDB: repository of large scale datasets underlying scientific publications in the biological and biomedical research
- HGNC (HUGO Gene Nomenclature Committee): a resource for approved human gene nomenclature
- International Human Epigenome Consortium: integrates epigenomic reference data from well-known national endeavors such as the Canadian CEEHRC, European Blueprint, European Genome-phenome Archive (EGA), US ENCODE and NIH Roadmap, German DEEP, Japanese CREST, Korean KNIH, Singapore's GIS and China's EpiHK
- MethBase: database of DNA methylation data visualized on the UCSC Genome Browser
- Minimotif Miner: database of short contiguous functional peptide motifs
- Oncogenomic databases: a compilation of databases that serve for cancer research
- PubMed: references and abstracts on life sciences and biomedical topics
- RIKEN integrated database of mammals
- TDR Targets: a chemogenomics database focused on drug discovery in tropical diseases
- TRANSFAC: a database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles
- JASPAR: a database of manually curated, non-redundant transcription factor binding profiles.
- MetOSite: a database about methionine sulfoxidation sites and its functional roles in proteins
- Healthcare Cost and Utilization Project (HCUP) is the largest collection of hospital care data in the United States. It includes hundreds of millions of inpatient, outpatient, and emergency records.
- LEXAS curates descriptions of biological experiments from PMC articles.
- Bovine Metabolome Database is a free web database that lists known bovine metabolites
External links
- Nucleic Acid Research Molecular Biology Database Collection – over 1,600 databases
- Nucleic Acid Research (NAR) Database Summary Paper Category List