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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]
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.[5][6]
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.
- ArrayExpress:[7] 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[8]): 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[9]): 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[10]
- 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:[11] genome of the yeast model organism
- SNPedia
- SoyBase Database[12] (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
- IRESbase: A comprehensive database of experimentally validated internal ribosome entry sites.[13]
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.[14] 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.[14]
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[15]
Different types of Protein databases
 | This section needs expansion. You can help by adding to it. (January 2015) |
| DB name | DB website | Provider | Data sources | Revenue/Sponsors sources | Integrates | Wiki article | Desc. | Size | DB type | Actively maintained | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| InterPro | http://www.ebi.ac.uk/interpro/ | ELIXIR infrastructure | European Bioinformatics Institute | EMBL, The Welcome trust, BBSRC | CATH-Gene3D, CDD, HAMAP, MobiDB, PANTHER, Pfam, SMART, SUPERFAMILY, SFLD, TIGRFAMs, | InterPro | classifies proteins into families and predicts the presence of domains and sites | Protein sequence databases | Yes | ||
| NextProt | https://www.nextprot.org/ | CALIPHO (is a group at the SIB) | Swiss Institute of Bioinformatics | https://www.sib.swiss/about/funding-sources | UniProt, Cellosaurus, Gnomad, IntAct, SRAA Atlas, Uniprot - GOA, BGEE, COSMIC, MassIVE, Peptide atlas | neXtProt | a human protein-centric knowledge resource | Protein sequence databases | Yes | ||
| Wiki-pi | http://severus.dbmi.pitt.edu/wiki-pi/ | Madhavi K. Ganapathiraju | At present Wiki-Pi contains 48,419 unique interactions among 10,492 proteins. However it is not clear if this is unique proteins | Protein interactoin Database | ?? | ||||||
| Human Protein Reference Database | Institute of Bioinformatics (IOB), Bangalore, India | Human Protein Reference Database | One source claims 15000 [16] proteins. But it is unclear how many of these are unique | ||||||||
| Sanger Institute | Pfam | protein families database of alignments and HMMs | Protein sequence databases | ||||||||
| Human Proteinpedia | Institute of Bioinformatics (IOB), Bangalore and Johns Hopkins University, | Human Proteinpedia | 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 Atlas | The Swedish Government | Human Protein Atlas | It 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 | ||||||||
| Manchester University | PRINTS | a compendium of protein fingerprints | Protein sequence databases | ||||||||
| PROSITE | database of protein families and domains | Protein sequence databases | |||||||||
| Georgetown University Medical Center | Protein Information Resource | Protein sequence databases | |||||||||
| SUPERFAMILY | library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms | Protein sequence databases | |||||||||
| Swiss Institute of Bioinformatics | Swiss-Prot | protein knowledgebase | Protein sequence databases | ||||||||
| NCBI | protein sequence and knowledgebase (National Center for Biotechnology Information) | Protein sequence databases | |||||||||
| Protein DataBank in Europe (PDBe),[17] ProteinDatabank in Japan (PDBj),[18] Research Collaboratory for Structural Bioinformatics (RCSB)[19] | Protein Data Bank | (PDB) | Protein structure databases | ||||||||
| Structural Classification of Proteins (SCOP) | Protein structure databases | ||||||||||
| Protein Structure Classification database | CATH : | Protein structure databases | |||||||||
| Sali Lab, UCSF | ModBase | database of comparative protein structure models | Protein model databases | ||||||||
| Similarity Matrix of Proteins | SIMAP | database of protein similarities computed using FASTA | Protein model databases | ||||||||
| Swiss-model | server and repository for protein structure models | Protein model databases | |||||||||
| AAindex | : database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials | Protein model databases | |||||||||
| Samuel Lunenfeld Research Institute | BioGRID | general repository for interaction datasets | Protein-protein and other molecular interactions | ||||||||
| RNA-binding protein databas | Protein-protein and other molecular interactions | ||||||||||
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