List of biological databases

Biological databases
information.[1]

biological

4. ConsensusPathDB - A molecular functional interaction database, integrating information from 12 other

databases.

sequence

5. Entrez (National Center for Biotechnology Information)

International Nucleotide Sequence Database (INSD) consists of the following databases.

6. Enzyme Portal Integrates enzyme information such

as small-molecule chemistry, biochemical pathways
and drug compounds. (European Bioinformatics Institute)

are

stores

Primary nucleotide
databases

of

7. euGenes (Indiana University)

1. DNA Data Bank of Japan (National Institute of Genetics)

8. GeneCards (Weizmann Inst.)

2. EMBL (European Bioinformatics Institute)

9. MetaBase (KOBIC) - A user contributed database

of biological databases.

3. GenBank (National Center for Biotechnology Information)

10. mGen containing four of the world biggest databases

GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction

The three databases, DDBJ (Japan), GenBank (USA)

and European Nucleotide Archive (Europe), are repositories for nucleotide sequence data from all organisms.
All three databases 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.

11. MOPED (Seattle Childrens Research Institute) - A

multi-omics expression proling database providing
integrated proteomics and transcriptomics data from
human, mouse, worm, and yeast.
12. PathogenPortal A repository linking to the
Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and
Infectious Diseases (NIAID)
13. SOURCE (Stanford University) encapsulates the genetics and molecular biology of genes from the
genomes of Homo sapiens, Mus musculus, and Rattus
norvegicus into easy to navigate GeneReports

Meta databases

These databases of databases collect data from dierent

sources and make them available in a new and more convenient form, or with an emphasis on a particular disease
or organism.

14. iRefIndex: provides an index of protein interactions available in a number of primary interaction
databases including BIND, BioGRID, CORUM,
DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT,
MPact, MPIDB, MPPI and OPHID.

1. BioGraph (University of Antwerp, Vlaams Instituut

voor Biotechnologie) A knowledge discovery service based on the integration of more than 20 heterogeneous databases

15. Pathway Commons (Memorial Sloan-Kettering

Cancer Center and University of Toronto)
16. Nowomics Tracks changes in several biological
databases, users 'follow' genes and keywords to see
a news feed of new data and papers.

2. Bioinformatic Harvester (Karlsruhe Institute of

Technology) - Integrating 26 major protein/gene resources.

17. BioGPS (The Scripps Research Institute) An extensible Gene Portal System. Plugin library extends
BioGPS beyond the Gene Expression Visualizer and
the links to Gene Wiki to a huge number of other
databases and services

3. Neuroscience Information Framework (University

of California, San Diego) - Integrates hundreds of
neuroscience relevant resources, many are listed below.
1

18. The Encyclopedia of DNA Elements (ENCODE)

Consortium is an international collaboration of research groups to build a comprehensive parts list of
functional elements in the human genome. The corresponding data is available for download and analysis from UCSC Genome Browser.
19. Human Epigenome Atlas, a collection of normal epigenomes of dierent tissues produced by
Roadmap Epigenomics Project. Data types include
histone modications, DNA methylation, chromatin
accessibility, gene expression, and small RNA expression.

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.
1. Bioinformatic Harvester
2. Gene Disease Database
3. SNPedia
4. CAMERA Resource for microbial genomics and
metagenomics
5. Corn, the Maize Genetics and Genomics Database
6. EcoCyc a database that describes the genome and
the biochemical machinery of the model organism
E. coli K-12
7. Ensembl provides automatic annotation databases
for human, mouse, other vertebrate and eukaryote
genomes.
8. Ensembl Genomes provides genome-scale data for
bacteria, protists, fungi, plants and invertebrate
metazoa, through a unied set of interactive and programmatic interfaces (using the Ensembl software
platform).
9. PATRIC, the PathoSystems Resource Integration
Center
10. Flybase, genome of the model organism Drosophila
melanogaster
11. MGI Mouse Genome (Jackson Lab.)
12. JGI Genomes of the DOE-Joint Genome Institute
provides databases of many eukaryote and microbial
genomes.

GENOME DATABASES

13. National Microbial Pathogen Data Resource.

A manually curated database of annotated
genome data for the pathogens Campylobacter,
Chlamydia,
Chlamydophila,
Haemophilus,
Listeria, Mycoplasma, Neisseria, Staphylococcus,
Streptococcus, Treponema, Ureaplasma, and
Vibrio.
14. RegulonDB RegulonDB is a model of the complex
regulation of transcription initiation or regulatory
network of the cell E. coli K-12.
15. Repbase Repbase is the most commonly used
database for repetitive elements (transposons).
16. Saccharomyces Genome Database, genome of the
yeast model organism.
17. Viral Bioinformatics Resource Center Curated
database containing annotated genome data for
eleven virus families.
18. The SEED platform for microbial genome analysis
includes all complete microbial genomes, and most
partial genomes. The platform is used to annotate
microbial genomes using subsystems.
19. Xenbase, genome of the model organism Xenopus
tropicalis and Xenopus laevis
20. Wormbase, genome of the model organism
Caenorhabditis elegans and WormBase ParaSite for
parasitic species
21. Zebrash Information Network, genome of this sh
model organism.
22. TAIR, The Arabidopsis Information Resource.
23. UCSC Malaria Genome Browser, genome of
malaria causing species (Plasmodium falciparum
and others)
24. RGD Rat Genome Database: Genomic and phenotype data for Rattus norvegicus
25. INTEGRALL: Database dedicated to integrons,
bacterial genetic elements involved in the antibiotic
resistance
26. Fourmidable ant genome database provides ant
genome blast search and sequence download.
27. VectorBase The NIAID Bioinformatics Resource Center for Invertebrate Vectors of Human
Pathogens
28. EzGenome, comprehensive information about manually curated genome projects of prokaryotes (archaea and bacteria) [2]
29. Banana Genome Hub, The Banana Genome
database.

3
30. GeneDB for Apicomplexan Protozoa, Kinetoplastid Protozoa, Parasitic Helminths, Parasite Vectors
+ several bacteria and viruses

14. ProteomeScout - Includes a graphics exports of

protein annotations including domains, secondary
structure, and post-translational modications

31. EuPathDB Eukaryotic pathogen database resources

includes amoeba, fungi, plamodium, trypanosomatids etc.

32. SNiPhunter SNP search engine: search for SNPs in

Pubmed open access literature using SNP IDs.

1. Proteomics Identications Database (PRIDE) A

public repository for proteomics data, containing
protein and peptide identications and their associated supporting evidence as well as details of posttranslational modications. (European Bioinformatics Institute)

33. The 1000 Genomes Project was launched in January

2008. The genomes of more than a thousand anonymous participants from a number of dierent ethnic
groups were analyzed and made publicly available.

2. ProteomeScout - A public repository of processed

proteomics datasets concerning post-translational
modications, includes quantication across conditions (if applicable). Also includes a graphics exports of protein annotations.

34. Personal Genome Project: human genomes

Proteomics databases

Protein sequence databases

3. MitoMiner - A mitochondrial proteomics database

integrating large-scale experimental datasets from
mass spectrometry and GFP studies for 12 species.
(MRC Mitochondrial Biology Unit)

1. UniProt Universal Pesource (EBI, Swiss Institute of

Bioinformatics, PIR)
2. Protein Information Resource (Georgetown University Medical Center (GUMC))
3. Swiss-Prot Protein Knowledgebase (Swiss Institute
of Bioinformatics)

4. GelMap - A public database of proteins identied

on 2D gels (University of Hanover Proteomics Department)

4. PEDANT Protein Extraction, Description and

ANalysis Tool (Forschungszentrum f. Umwelt &
Gesundheit)

5. OWL - A public non-redundant database for protein

search, derived from : SWISS PROT, PIR, GenBank(translation) and NRL-3D

5. PROSITE Database of Protein Families and

Domains

6. ProteomeXchange provides a coordinated submission of mass spectrometry proteomics data to the

main existing proteomics repositories. It includes
datasets such as PRIDE, Tranche, and PeptideAtlas.

6. Database of Interacting Proteins (Univ. of California)

7. Pfam Protein families database of alignments and
HMMs (Sanger Institute)

Protein structure databases

8. PRINTS a compendium of protein ngerprints from Protein Data Bank (PDB) comprising:
(Manchester University)
9. ProDom Comprehensive set of Protein Domain
Families (INRA/CNRS)
10. SignalP 3.0 Server for signal peptide prediction (including cleavage site prediction), based on articial
neural networks and HMMs

Protein DataBank in Europe (PDBe)

ProteinDatabank in Japan (PDBj)
Research Collaboratory for Structural Bioinformatics (RCSB)

11. SUPERFAMILY Library of HMMs representing Secondary databases

superfamilies and database of (superfamily and fam1. SCOP Structural Classication of Proteins
ily) annotations for all completely sequenced organisms
2. CATH Protein Structure Classication
12. Annotation Clearing House a project from the
3. PDBsum
National Microbial Pathogen Data Resource
13. InterPro Classies proteins into families and pre- For more protein structure databases, see also Protein
dicts the presence of domains and sites.
structure database

11 SIGNAL TRANSDUCTION PATHWAY DATABASES

Protein model databases

1. Swiss-model Server and Repository for Protein
Structure Models
2. ModBase Database of Comparative Protein Structure Models (Sali Lab, UCSF)
3. Protein Model Portal (PMP) Meta database that
combines several databases of protein structure
models (Biozentrum, Basel, Switzerland)
4. Similarity Matrix of Proteins (SIMAP) is a database
of protein similarities computed using FASTA.

RNA databases

Carbohydrate
databases

structure

1. EuroCarbDB, A repository for both carbohydrate

sequences/structures and experimental data.

10 Protein-protein and
molecular interactions

other

1. BIND Biomolecular Interaction Network Database

2. BioGRID A General Repository for Interaction
Datasets (Samuel Lunenfeld Research Institute)
3. CCSB Interactome
4. DIP Database of Interacting Proteins

1. LncRNAWiki , a wiki-based database for community curation of human long non-coding RNAs
2. Rfam , a database of RNA families
3. miRBase , the microRNA database
4. snoRNAdb, a database of snoRNAs
5. lncRNAdb, a database of lncRNAs
6. DASHR The DAtabase of Small Human non-coding
RNAs: integrated annotation and sequencing-based
expression data for all major classes of human small
non-coding RNAs (sncRNAs) for both full sncRNA
transcripts and mature sncRNA products derived
from these larger RNAs.
7. MONOCLdb The MOuse NOnCode Lung
database: Annotations and expression proles of
mouse long non-coding RNAs (lncRNAs) involved
in Inuenza and SARS-CoV infections.

5. IntAct molecular interaction database: a central,

standards-compliant repository of molecular interactions, including proteinprotein, proteinsmall
molecule and proteinnucleic acid interactions.
6. NetPro
7. STRING: STRING is a database of known and predicted protein-protein interactions. (EMBL)
8. The Cell Collective
9. MINT: Molecular INTeraction database
10. iRefIndex: provides an index of protein interactions available in a number of primary interaction
databases including BIND, BioGRID, CORUM,
DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT,
MPact, MPIDB, MPPI and OPHID.
11. RNA-binding protein database
12. BioLiP: Protein-ligand binding database

8. piRNAbank, a database of piRNAs

9. GtRNAdb, a database of genomic tRNAs
10. SILVA, a database of ribosomal RNAs

11 Signal transduction pathway

databases

11. RDP, the Ribosomal Database Project

1. Cancer Cell Map

12. tmRDB, a database of tmRNAs

2. Netpath - A curated resource of signal transduction

pathways in humans

13. SRPDB, a database of signal recognition particle

RNAs

3. NCI-Nature Pathway Interaction Database

14. yeast snoRNA database

4. Reactome - Navigable map of human biological

pathways, ranging from metabolic processes to hormonal signalling.

15. Sno/scaRNAbase, a database of snoRNA and scaRNAs

16. snoRNA-LBME-db, a snoRNA database

5. SignaLink Database
6. WikiPathways

5
7. The Cell Collective
8. Literature-curated human signaling network, the
largest human signaling network database

12 Metabolic pathway and Protein

Function databases
1. BioCyc Database Collection including EcoCyc and
MetaCyc
2. BRENDA The Comprehensive Enzyme Information System, including FRENDA, AMENDA,
DRENDA, and KENDA,
3. KEGG PATHWAY Database (Univ. of Kyoto)
4. MANET database (University of Illinois)
5. MetaboLights Metabolomics experiments and derived information: metabolite structures, reference
spectra, biological roles, locations and concentrations. (European Bioinformatics Institute)
6. MetaNetX Automated Model Construction and
Genome Annotation for Large-Scale Metabolic Networks
7. Reactome Navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling. (Cold Spring Harbor Laboratory,
European Bioinformatics Institute, Gene Ontology
Consortium)
8. Small Molecule Pathway Database (SMPDB)
9. WikiPathways

13

Microarray databases

Main article: Microarray databases

7. Bgee Bgee is a database to retrieve and compare

gene expression patterns between species. It only
contains wild-type and manually curated microarray/RNASeq/in situ experiments.
8. BioGPS (The Scripps Research Institute) A Gene
Portal System with a Gene Expression Visualizer
9. The European Genome-phenome Archive (EGA)

14 Exosomal databases
ExoCarta

15 Mathematical model databases

1. Biomodels Database: published mathematical models describing biological processes.
2. CellML
3. The Cell Collective: build and simulate large-scale
models in real-time and in a highly collaborative
fashion

16 PCR and quantitative PCR

primer databases
1. PathoOligoDB: A free QPCR oligo database for
pathogens
2. RTPrimerDB - a public primers and probes database
for real-time PCR reactions

17 Phenotype databases
1. PhenCode linking human mutations with phenotype
2. PhenomicDB multi-organism database linking
genotype to phenotype

1. ArrayExpress (European Bioinformatics Institute)

2. Gene Expression Omnibus (GEO, National Center
for Biotechnology Information)
3. GPX(Scottish Centre for Genomic Technology and
Informatics)
4. maxd (Univ. of Manchester)
5. Stanford Microarray Database (SMD) (Stanford
University)
6. Genevestigator - Expression Search Engine (Nebion
AG)

3. 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.
4. RGD Rat Genome Database: Genomic and phenotype data for Rattus norvegicus
5. Planform:
planarian formalized-experiments
database, linking surgical, genetic, and pharmacological perturbations to morphological phenotypic
outcomes from published planarian regeneration
experiments.

18
6. Limbform: limb formalized-experiments database,
linking surgical, genetic, and pharmacological perturbations to morphological phenotypic outcomes
from published multi-organism limb regeneration
experiments.

SPECIALIZED DATABASES

Eukaryotic Linear Motif Database (ELM) Database

of short linear motifs.
EpimiRBase A comprehensive
microRNA-epilepsy associations.

database

of

FunSecKB The fungal secretome knowledgebase.

18

Specialized databases

FunSecKB2 The fungal secretome and subcellular

proteome knowledgebase (version 2)

Antibody Central Antibody information database

and search resource.

GreenPhylDB (A phylogenomic database for plant

comparative genomics)

AntibodyRegistry.org assigns unique identiers

used to track antibody reagents in published
literature.

GDB Hum. Genome Db (Human Genome Organisation)

Bgee Bgee is a database to retrieve and compare

gene expression patterns between species.
BIOMOVIE (ETH Zurich) movies related to biology and biotechnology
BioNumbers a database of useful biological numbers
Barcode of Life Data Systems, a database of DNA
barcodes
CGAP Cancer Genes (National Cancer Institute)
Clone Registry Clone Collections (National Center
for Biotechnology Information)
Colorectal Cancer Atlas catalogs multiple genomic
and proteomic data types from 13,711 tissue samples to identify sequence variants in more than 165
colorectal cancer cell lines.
Connectivity map Transcriptional expression data
and correlation tools for drugs
CTD The Comparative Toxicogenomics Database
describes chemical-gene-disease interactions
DBGET H.sapiens (Univ. of Kyoto)
DisGeNET DisGeNET is database that integrates
information on gene-disease associations

HGMD disease-causing mutations (HGMD Human

Gene Mutation Database)
HUGO (Ocial Human Genome Database: HUGO
Gene Nomenclature Committee)
HvrBase++ Human and primate mitochondrial
DNA
INTERFEROME The Database of Interferon Regulated Genes
List with SNP-Databases
MetazSecKB The metazoa [human/animal] secretome and subcellular proteome knowledgebase
Minimotif Miner -Database of short contiguous
functional peptide motifs
NCBI-UniGene (National Center for Biotechnology
Information)
Oncogenomic databases A compilation of databases
that serve for cancer research.
OMIM Inherited Diseases (Online Mendelian Inheritance in Man)
OrthoMaM (A database of Orthologous Mammalian Markers)
OrthoMCL Ortholog Groups of Protein Sequences
from Multiple Genomes including Archaea, Bacteria and Eukaryotes.

DiProDB A database to collect and analyse thermodynamic, structural and other dinucleotide properties.

p53 The p53 Knowledgebase

Drug2Gene Provides integrated information

for identied and reported relations between
genes/proteins and drugs/compounds

PlantSecKB The plant secretome and subcullular

proteome knowledgebase

Dryad a repository of data underlying scientic publications in the basic and applied biosciences.
Edinburgh Mouse Atlas
EPD Eukaryotic Promoter Database

PASD The plant alternative splicing database

Plasma Proteome Database Human plasma proteins

along with their isoforms
SABIO-RK SABIO-RK is a curated database that
contains information about biochemical reactions,
their kinetic rate equations with parameters and experimental conditions.

7
SciClyc An Open-access database to shared antibodies, cell cultures, and documents for biomedical
research.
Selectome Selectome is a database of positive selection based on a rigorous branch-site specic likelihood test. Positive selection is detected using
CODEML on all branches of animal gene trees.
SHMPD The Singapore Human Mutation and Polymorphism Database
SNPSTR database A database of SNPSTRs - compound genetic markers consisting of a microsatellite (STR) and one tightly linked SNP - in human,
mouse, rat, dog and chicken.

20 Wiki-style databases
1. CHDwiki
2. EcoliWiki
3. Gene Wiki
4. GyDB
5. NeuroLex
6. OpenWetWare
7. PDBWiki
8. Proteopedia
9. RiceWiki
10. LncRNAWiki

The Cancer Genome Atlas (TCGA) provides data

from hundreds of cancer samples obtained using
high-throughput techniques such as gene expression proling, copy number variation proling, SNP
genotyping, genome wide DNA methylation proling, microRNA proling, and exon sequencing of at
least 1,200 genes.
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 proles.

11. Topsan
12. WikiGenes
13. WikiPathways
14. WikiProfessional
15. YTPdb

21 Metabolomic Databases
1. MetaboLights
2. Human Metabolome Database (HMDB)

TreeBASE An open-access database of phylogenetic trees and the data behind them

3. Yeast Metabolome Database (YMDB)

Treefam TreeFam (Tree families database) is a

database of phylogenetic trees of animal genes

5. DrugBank

[XTractor] Discovering Newer Scientic Relations

Across PubMed Abstracts. A tool to obtain manually annotated relationships for Proteins, Diseases,
Drugs and Biological Processes as they get published
in PubMed.

7. BioMagResBank

4. E. coli Metabolome Database (ECMDB)

6. ChEBI

8. Golm Metabolome Database

9. MassBank

22 Unsorted
19

Taxonomic databases

1. Catalogue of Life source databases (a list of taxonomic databases that contribute to the Catalogue of
Life)
2. Encyclopedia of Life
3. Integrated Taxonomic Information System
4. EzTaxon-e, database for the identication of
prokaryotes based on 16S ribosomal RNA gene sequences

FINDbase (the Frequency of INherited Disorders

database)
RIKEN integrated database of mammals

23 References
[1] Wren JD, Bateman A (2008). Databases, data tombs
and dust in the wind.. Bioinformatics 24 (19): 21278.
doi:10.1093/bioinformatics/btn464. PMID 18819940.
[2] http://ezgenome.ezbiocloud.net/

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24.1

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List of biological databases Source: https://en.wikipedia.org/wiki/List_of_biological_databases?oldid=699399751 Contributors: Topbanana, Aliekens, Kaldari, Egonw, Rjwilmsi, Vossman, Bgwhite, Wavelength, Cache22, Rockpocket, CmdrObot, Ppgardne, Gmadey,
Erxnmedia, Magioladitis, Tiagoantao, DGG, Plindenbaum, Yannickwurm, Guillaume2303, Alexbateman, Doc James, Mishael sp, Denisarona, Peteruetz, Anchiguo, Apicoplast, Invention, FrescoBot, Egalegal, Zimmerph, My very best wishes, Mcrosenstein, Manuelcorpas, Amkilpatrick, Jesse V., RjwilmsiBot, IgorRodchenkov, MartinRSchiller, AvicBot, Jside, Bandrow, Sarahburge, Eastewart2010,
Michipanero, Pisaadvocate, Snotbot, Inocinnamon83, Habil zare, Biotechp, Vneveu, Augustulus2, Rnanfe, Latimeria iv ka, Holgerdinkel,
BattyBot, Biosthmors, Themarytodd, Josiasseb, Adiecoly, Jitan007, Hatagalow, Delnut, Kapagel, Pramit57, Gtsulab, Rnsmith100,
Waddink, Dokkam, Rdreos, Janis3 14159, Worldofworms and Anonymous: 46

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