List of biological databases

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 (https://ww
w.omicsdi.org/) 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[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:

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: (http://eggnog5.embl.de/#/app/home) 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

Nucleosome positioning region database

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:[7] archive of functional genomics data; stores data Ensembl: provides automatic annotation databases for human,
from high-throughput functional genomics experiments from EMBL mouse, other vertebrate and eukaryote genomes
Bioinformatic Harvester
Cervical cancer gene database
 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

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.[13] 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.[13]

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[14]

Different types of Protein databases

Database Short
1 Database Name/link to website Provider Datasources Sources of revenue/sponsors Intergrates: Wiki article
Name

CATH-Gene3D,
cla
CDD, HAMAP,
pro
MobiDB,
European fam
ELIXIR PANTHER,
2 InterPro http://www.ebi.ac.uk/interpro/ Bioinformatics EMBL, The Welcome trust, BBSRC InterPro pre
infrastructure Pfam, SMART,
Institute pre
SUPERFAMILY,
dom
SFLD,
site
TIGRFAMs,

UniProt,
Cellosaurus,
Gnomad, IntAct,
ah
CALIPHO (is Swiss SRAA Atlas,
https://www.sib.swiss/about/funding- pro
3 NextProt https://www.nextprot.org/ a group at the Institute of Uniprot - GOA, neXtProt
sources kno
SIB) Bioinformatics BGEE,
res
COSMIC,
MassIVE,
Peptide atlas

http://severus.dbmi.pitt.edu/wiki- Madhavi K.
4 Wiki-pi
pi/ Ganapathiraju

Institute of
Human Protein Bioinformatics Human Protein
5 Reference (IOB), Reference
Database Bangalore, Database
India

pro
Sanger dat
6 Pfam
Institute alig
HM

Institute of
Bioinformatics
(IOB),
Human Human
7 Bangalore and
Proteinpedia Proteinpedia
Johns
Hopkins
University,

Human Protein Human Protein

8 The Swedish Government
Atlas Atlas

ac
Manchester
9 PRINTS of
University
fing

dat
10 PROSITE pro
and

Georgetown
University Protein
11 Medical Information
Center Resource
[GUMC]
12 SUPERFAMILY libr
HM
 rep
sup
and
of
and
ann
all
seq
org

Swiss
pro
13 Institute of Swiss-Prot
kno
Bioinformatics
pro
seq
kno
14 NCBI (Na
Ce
Bio
Info

Protein
DataBank in
Europe
(PDBe)[16],
ProteinDatabank
in Japan Protein Data
15 (PD
(PDBj)[17], Bank
Research
Collaboratory for
Structural
Bioinformatics
(RCSB)[18]
Structural
Classification
16
of Proteins
(SCOP)

Protein Structure
17 Classification CATH :
database
dat
com
Sali Lab,
18 ModBase pro
UCSF
str
mo

dat
pro
Similarity Matrix of
19 SIMAP sim
Proteins
com
usi

ser
rep
20 Swiss-model pro
str
mo
: da
am
ind
aci
21 AAindex
ma
pai
con
pot

Samuel gen
Lunenfeld rep
22 BioGRID
Research inte
Institute dat

RNA-binding
23
protein databas

Database of
Univ. of
24 Interacting
California
Proteins

ope
dat
25 (EMBL-EBI) IntAct:[19] mo
inte

26 String an
mo
inte
dat
stu
inte
 bet
pro

aim
ma
Human Protein hum
27
Atlas in c
tiss
org
Protein Model Portal of the PSI-
Nature Structural Biology
28 ProteinModelPortal ?? ??
Knowledgebase (http://www.prot
einmodelportal.org/)

Database of annotated 3D
protein structure models (http://s University of
29 SMR The Swiss goverment
wissmodel.expasy.org/repositor Basel
y/)

Indiana
University Swiss Prot/Uni
dat
School of Prot, CATH,
exp
Database of Protein Disorder (ht ELIXIR Medicine, funding from the European Union’s Pfam, Europe
30 DisProt DisProt evi
tp://www.disprot.org/) infrastructure Temple Horizon 2020 PMC, BITEM,
dis
University, ECO,
pro
University of Geneontology
Padua

John Moult,
dat
Database of intrinsically Christine
University of intr
31 MobiDB disordered and mobile proteins Orengo, Italian Goverment MobiDB
Padua dis
(http://mobidb.bio.unipd.it/) Predrag
ann
Radivojac

Ursula Pieper,
Database of Comparative Ben Webb,
Protein Structure Models (http:// Narayanan
32 ModBase UCSF, Sali Lab
modbase.compbio.ucsf.edu/mod Eswar, Andrej
base-cgi/index.cgi) Sali Roberto
Sanchez

Pictorial database of 3D
European
structures in the Protein Data
33 PDBsum Bioinformatics Wellcome Trust
Bank (http://www.ebi.ac.uk/pdbs
Institute 2013
um/)
The Consensus CDS protein set
34 CCDS database (https://www.ncbi.nlm. NCBI ??
nih.gov/CCDS/CcdsBrowse.cgi)

DNA Data Bank of Japan (http://

35 DDBJ ?? ??
www.ddbj.nig.ac.jp/)

European Nucleotide Archive (ht

36 ENA ?? ??
tp://www.ebi.ac.uk/ena)
GenBank nucleotide sequence
37 GenBank database (https://www.ncbi.nlm. ?? ??
nih.gov/genbank/)

NCBI Reference Sequence

38 Refseq Database (https://www.ncbi.nlm. ?? ??
nih.gov/refseq/)

Database of computationally
identifies transcripts from the
39 UniGene ?? ??
same locus (https://www.ncbi.nl
m.nih.gov/unigene/)
Universal Protein Resource
40 UniProtKB (UniProt) (http://www.uniprot.or ?? ??
g/)

SIB Swiss
Swiss Prot/Uni https://www.sib.swiss/swiss- European Bioinformatics Institute
41 Institute of
Prot prot,https://www.uniprot.org/ (EMBL-EBI)
Bioinformatics

See also: Protein structure database

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:[20]

Allen Brain Atlas

Digital Brain Bank[21]
Electron Microscopy Public Image Archive (EMPIAR)[22]
Image Data Resource[20]
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

Radiologic databases
The Cancer Imaging Archive (TCIA)
Neuroimaging Informatics Tools and Resources Clearinghouse

Databases on antimicrobial resistance rates and antibiotic consumption

CIPARS
EARS-Net
ESAC-Net

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
Wiki-style databases
Gene Wiki
WikiProfessional
Specialized databases
Barcode of Life Data Systems: database of DNA barcodes
Bacterial Pesticidal Protein Database[23][24]
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) (http://w
ww.housekeeping.unicamp.br) [25] 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
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S2CID 38996040 (https://api.semanticscholar.org/CorpusID:389960
40).
23. Crickmore, N.; Berry, C.; Panneerselvam, S.; Mishra, R.; Connor, T.
R.; Bonning, B. C. (November 2021). "A structure-based
nomenclature for Bacillus thuringiensis and other bacteria-derived
pesticidal proteins" (https://doi.org/10.1016%2Fj.jip.2020.107438).
Journal of Invertebrate Pathology. 186 (D1): 107438.
doi:10.1016/j.jip.2020.107438 (https://doi.org/10.1016%2Fj.jip.202
0.107438). PMID 32652083 (https://pubmed.ncbi.nlm.nih.gov/32652
083).
24. Panneerselvam S; Mishra R; Berry C; Crickmore N; Bonning BC
(2022). "BPPRC database: a web-based tool to access and
analyse bacterial pesticidal proteins" (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC9216523). Database (Oxford). 186 (D1): 107438.
doi:10.1093/database/baac022 (https://doi.org/10.1093%2Fdatabas
e%2Fbaac022). PMC 9216523 (https://www.ncbi.nlm.nih.gov/pmc/a
rticles/PMC9216523). PMID 35396594 (https://pubmed.ncbi.nlm.ni
h.gov/35396594).
25. Hounkpe BW, Chenou F, de Lima F, De Paula EV (January 2021).
"HRT Atlas v1.0 database: redefining human and mouse
housekeeping genes and candidate reference transcripts by mining
massive RNA-seq datasets" (https://www.ncbi.nlm.nih.gov/pmc/artic
les/PMC7778946). Nucleic Acids Research. 49 (D1): D947–D955.
doi:10.1093/nar/gkaa609 (https://doi.org/10.1093%2Fnar%2Fgkaa6
09). PMC 7778946 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC
7778946). PMID 32663312 (https://pubmed.ncbi.nlm.nih.gov/32663
312).
26. (IHEC) data portal (http://epigenomesportal.ca/ihec/index.html)
27. CEEHRC (http://www.epigenomes.ca/)
28. Blueprint (http://www.blueprint-epigenome.eu/)
29. EGA (https://www.ebi.ac.uk/ega/)
30. DEEP (http://www.deutsches-epigenom-programm.de)
31. CREST (http://crest-ihec.jp/english/database/index.html)
32. "Sharing epigenomes globally" (https://doi.org/10.1038%2Fnmeth.4
630). Nature Methods. 15 (3): 151. 2018. doi:10.1038/nmeth.4630
(https://doi.org/10.1038%2Fnmeth.4630). ISSN 1548-7105 (https://w
ww.worldcat.org/issn/1548-7105).
33. Valverde H, Cantón FR, Aledo JC (November 2019). "MetOSite: an
integrated resource for the study of methionine residues
sulfoxidation" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853
639). Bioinformatics. 35 (22): 4849–4850.
doi:10.1093/bioinformatics/btz462 (https://doi.org/10.1093%2Fbioinf
ormatics%2Fbtz462). PMC 6853639 (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC6853639). PMID 31197322 (https://pubmed.ncbi.n
lm.nih.gov/31197322).
External links
Nucleic Acid Research Molecular Biology Database Collection (https://web.archive.org/web/20060112045100/http://www.oxfordjournals.org/n
ar/database/c) – over 1,600 databases
Nucleic Acid Research (NAR) Database Summary Paper Category List (https://www.oxfordjournals.org/nar/database/c)

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