Database Commons a catalog of biological databases

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Data type:

Database name Data type(s) Major organism(s) Location Citation* Status z-index
NCBI Gene - NCBI Gene United States 1802unstable55.45
euL1db - European database of L1HS retrotransposon insertions in humans France 2unstable0.60
Islander - Database of Genomic Islands United States 4alive1.33
MethBank - Methylation Bank China 6alive2.00
APASdb - Alternative PolyAdenylation Sites Database China 4unstable0.87
ChiTaRS - Chimeric Transcripts and RNA-Sequencing data Israel 48alive9.60
AnimalTFDB - Animal Transcription Factors Database China 82alive13.26
COXPRESdb - Coexpression Database Japan 230alive23.00
DBTSS - DataBase of Transcriptional Start Sites Japan 767alive47.94
EPD - Eukaryotic Promoter Database Switzerland 32unstable9.71
TFClass - Classification of Human Transcription Factors and Mouse Orthologs Germany 48unstable7.01
Gbshape - Genome Browser Database for DNA Shape Annotations United States 8alive2.67
TTSMI - triplex target DNA site Mapping and Integration database Singapore 1alive0.33
UniPROBE - Universal PBM Resource for Oligonucleotide Binding Evaluation United States 363alive40.33
RNAcentral United Kingdom 31alive10.13
Rfam - RNA Families
United Kingdom 3329alive221.93
The tmRNA website - The tmRNA website United States 300alive15.00
tRFdb - Transfer RNA related Fragments Database United States 4alive1.31
miRDB - miRNA target prediction and functional annotations database United States 465alive46.50
DIANA-TarBase - DIANA-TarBase Greece 1513alive126.08
DoRiNA - Database of RNA Interactions in Post-transcriptional Regulation Germany 115unstable17.44
lncRNAdb Australia 351alive49.64
LNCipedia - A comprehensive compendium of human long non-coding RNAs Belgium 168unstable20.16
lncRNASNP China 17unstable5.38
LncRNAWiki - a wiki-based platform for community curation of human lncRNAs China 15unstable4.20
LncRNA2Target - LncRNA-target association database China 12unstable1.32
MeT-DB - The MethylTranscriptome DataBase China 3alive0.96
UniProt - The Universal Protein Resource United Kingdom 13605alive962.07
InterPro - Protein sequence analysis & classification United Kingdom 5033alive279.61
CDD - Conserved Domain Database
United States 4407unstable195.87
SUPERFAMILY - SUPERFAMILY United Kingdom 976alive56.84
InParanoid - ortholog groups with inparalogs Sweden 1253alive95.42
OMA - The Orthologous Matrix project United Kingdom 153unstable16.39
OrthoDB - Orthologs Database Switzerland 468alive46.33
SMART - Simple Modular Architecture Research Tool
Germany 3106alive153.75
COG - Clusters of Orthologous Genes United States 11125unstable211.90
MBGD - Microbial Genome Database Japan 279alive18.23
MoonProt - Moonlighting Proteins Database United States 20alive6.53
TOPDB - Topology Database of Transmembrane Proteins
Hungary 57unstable3.76
TopFIND - Termini oriented protein Function Inferred Database Canada 98alive14.00
REBASE - The Restriction Enzyme Database United States 927alive61.80
NrichD - Remote Homology Detection using Enriched Databases
India 7alive1.75
KnotProt - A database of proteins with knots and slipknots
Poland 67alive11.17
MobiDB - A Database of Protein Disorder and Mobility Annotations Italy 80alive13.20
MatrixDB - The extracellular matrix interaction database France 4alive1.31
MiCroKiTS - Midbody,Centrosome,Kinetochore,Telomere and Spindle China 29alive3.63
RaftProt - Mammalian Lipid Raft Proteome Database Australia 0alive0.00
WDSPdb - WD40-repeat protein Structure Predictor China 8unstable2.45
RCSB PDB - RCSB Protein Data Bank United States 853unstable80.43
SASBDB - Small Angle Scattering Biological Data Bank Germany 0alive0.00
ValidatorDB - Database of validation
Czech Republic 0alive0.00
United Kingdom 1488alive97.22
Genome3D - Annotating Genomes with Structures United Kingdom 42unstable4.99
Platinum - Protein-ligand affinity change upon mutation United Kingdom 0unstable0.00
PoSSuM - Pocket Similarity Search using Multiple-Sketches Japan 24alive3.96
sc-PDB - An Annotated Database of Druggable Binding Sites from the Protein DataBank
France 165alive13.34
IMGT - Knowledge resource specialized in the immunoglobulins or antibodies France 22alive3.63
IPD - Immuno Polymorphism Database United Kingdom 323unstable18.63
BRENDA - The Comprehensive Enzyme Information System
Germany 706alive99.85
STRING - Known and Predicted Protein-Protein Interactions
Switzerland 9248alive513.78
EzCatDB - Database of Enzyme Catalytic Mechanisms
Japan 60unstable3.78
Switzerland 66unstable10.01
Binding MOAD - Binding Mother of All Databases
United States 148alive11.27
BioGRID - Biological General Repository for Interaction Datasets
Canada 4359unstable286.97
Complex Portal
United Kingdom 0unstable0.00
ComPPI - Compartmentalized Protein-Protein Interaction Database Hungary 0alive0.00
PTMcode Germany 56alive11.20
dbSNO - Database for Cysteine S-Nitrosylation Taiwan 52alive8.41
PhosphoSitePlus United States 653alive108.83
ProteomeScout United States 0unstable0.00
DEPOD - Human DEPhOsphorylation Database Germany 0unstable0.00
P2CS - Prokaryotic 2-Component Systems France 80alive8.80
United Kingdom 23alive7.67
CeCaFDB - Central Carbon Metabolic Flux Database China 0unstable0.00
Cfam - Chemical Families Database
Singapore 0dead0.00
HIV-1 Human Interaction Database United States 171unstable6.84
Viral Genomes - Viral Genomes United States 0unstable0.00
ViRBase - virus-host ncRna interaction database China 0alive0.00
VirHostNet - Virus-Host Network France 93unstable9.09
VirusMentha - VirusMentha Italy 0unstable0.00
rrnDB - Ribosomal RNA Operons Database United States 988unstable13.37
RefSeq genome - Reference Sequence Based on Genomes United States 211unstable28.13
GenoBase - Escherichia coli K-12 Resource Database Japan 5unstable0.58
MyMpn - The Mycoplasma pneumoniae database Spain 11unstable3.37
PAIDB - Pathogenicity Island Database Korea Rep. 110unstable7.53
DB-AT - Database of Apicomplexa Transcriptomes Germany 2alive0.67
TrypanoCyc - Trypanosoma brucei Database France 0alive0.00
PHI-base - Pathogen-Host Interactions database United Kingdom 340alive28.05
PomBase United Kingdom 131unstable16.81
Ensembl - Ensembl United Kingdom 12662alive775.55
UCSC Genome Browser - University of California, Santa Cruz Genome Browser United States 6429alive428.60
Genomicus - Genomes in Evolution France 182alive22.52
FlyBase - Database of Drosophila Genes & Genomes United States 3836alive159.83 United States 12alive4.00
VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens United States 382unstable7.99
i5k Workspace@NAL United States 10unstable2.87
iBeetle-Base - A database of Tribolium RNAi phenotypes Germany 0alive0.00
MGD - Mouse Genome Database United States 2658alive126.57
NHPRTR - Nonhuman Primate Reference Transcriptome Resource United States 31alive6.14
RGD - Rat Genome Database United States 60unstable17.60
SuperFly Spain 0alive0.00
Xenbase - Xenopus model organism database Canada 214alive21.40
neXtProt - Exploring the universe of human proteins Switzerland 237unstable11.06
DBTMEE - Database of Transcriptome in Mouse Early Embryos Japan 2alive0.67
DoGSD - Dog Genome SNP Database China 5alive1.63
AFND - Allele Frequency Net Database United Kingdom 39alive7.80
OMIM - Online Mendelian Inheritance in Man United States 3217unstable8.94
GRASP - Genome-Wide Repository of Associations between SNPs and Phenotypes United States 28unstable2.94
COSMIC - Catalogue of Somatic Mutations in Cancer United Kingdom 4018unstable261.17
The UCSC Cancer Genomics Browser United States 187unstable4.78
MTB - Mouse Tumor Biology System United States 105alive6.18
arrayMap Switzerland 0unstable0.00
BCCTBbp - Breast Cancer Campaign Tissue Bank Bioinformatics Portal United Kingdom 3alive0.97
India 0alive0.00
CCGD - Candidate Cancer Gene Database United States 8alive2.67
CMPD - Cancer Mutant Proteome Database Taiwan 0unstable0.00
Cancer3D United States 10alive3.30
MethHC - A database of DNA Methylation and gene expression in Human Cancer Taiwan 18alive5.88
YM500 - YM500 Taiwan 45alive8.82
VaDE - VarySysDB Disease Edition Japan 0unstable0.00
DAA - Digital Ageing Atlas United Kingdom 9alive3.00
DDMGD - database of diseases associated gene methylation in different species Saudi Arabia 2unstable0.53
Dr.VIS - Viral integration sites China 14unstable1.38
EpilepsyGene - EpilepsyGene database China 3unstable0.69
Organ system heterogeneity DB - A Database for the Visualization of Phenotypes at the Organ System Level Germany 0alive0.00
ADReCS - Adverse Drug Reaction Classification System China 3unstable0.93
Open TG-GATEs - Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System Japan 17dead0.00
T3DB - The Toxin and Toxin Target Database Canada 73alive9.13
Super Natural II
Germany 11alive3.67
NutriChem - A Systems Chemical Biology Resource to Explore the Medicinal Value of Plant-based Foods. Denmark 2alive0.65
EHFPI - Database of Essential Host Factors for Pathogenic Infection
China 1unstable0.23
AHTPDB - Database of Antihypertensive Peptides India 7alive2.33
PubAngioGen China 0alive0.00
PLAZA - An online platform for plant comparative genomics Belgium 196unstable15.90
PNRD - Plant Non-coding RNA Database China 10unstable3.03
Plastid-LCGbase - The Plastid Lineage-based Conserved Gene-pair Database China 2unstable0.38
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana Korea Rep. 0unstable0.00
Araport - Arabidopsis Information Portal United States 9unstable0.69
CATdb - Complete Arabidopsis Transcriptome database France 0alive0.00
RiceVarMap - Rice Variation Map China 9alive2.97
SNP-Seek database - SNP-Seek Database Philippines 53unstable11.13
CGH - Coffee Genome Hub France 3alive1.00
SGN - Sol Genomics Network United States 0unstable0.00
Europe PMC - Europe PubMed Central
United Kingdom 43alive6.14
GO - Gene Ontology Consortium Switzerland 5117alive301.00
GOA database - Gene Ontology Annotation (UniProt-GOA) Database
United Kingdom 229unstable28.63
HAMAP - High-quality Automated and Manual Annotation of Proteins Switzerland 161unstable15.74
DO - Disease Ontology United States 248alive40.92
HGNC - HUGO Gene Nomenclature Committee United Kingdom 612unstable45.90
NCBI Taxonomy Database - NCBI Taxonomy Database
United States 13unstable1.73
diArk - Database for Eukaryotic Genome Research Germany 16unstable1.37
United Kingdom 289unstable43.35
United Kingdom 13alive4.29
GeneFriends - GeneFriends:RNAseq United Kingdom 31alive5.17
ImmuCo - a database of gene Co-expression and Correlation in Immune cells China 4unstable1.16
Cyclebase - Cell-cycle Database Denmark 105unstable7.77
MOPED - Multi-Omics Profiling Expression Database United States 5dead0.03
VCGDB - Virtual Chinese Genome Database China 1alive0.25
United Kingdom 39unstable4.88
NGSmethDB - High-quality Methylation Maps Spain 52unstable5.13
uORFdb - upstream open reading frames database Germany 22unstable4.51
miRBase - microRNA dababase United Kingdom 11326alive792.82
miRNEST - miRNEST Poland 35alive5.78
miRTarBase - miRNA Target Database Taiwan 899alive128.43
PolymiRTS - Polymorphism in microRNAs and their TargetSites United States 264alive23.76
starBase - starBase China 491unstable54.01
NONCODE - Noncoding RNAs China 637unstable40.67
NPInter - ncRNA Interaction Database China 119unstable8.93
RADAR - Rigorously Annotated Database of A-to-I RNA editing United States 52alive12.87
NDB - Nucleic Acid Database
United States 28alive6.86
RNA Bricks
Poland 20alive4.95
SMMRNA - Small Molecule Modulators of RNA
India 5alive1.24
JASPAR Canada 2924alive204.68
TFBSshape - DNA shape features of transcription factor binding sites United States 39alive9.75
CollecTF - Database of Transcription Factor Binding Sites United States 31dead0.00
YEASTRACT - Yeast Search for Transcriptional Regulators And Consensus Tracking Portugal 793alive65.42
OnTheFly - TF and TFBS On The Fly United States 9unstable0.68
BloodChIP Australia 11unstable0.94
DPRP - Database of Phenotype-specific Regulatory Programs Taiwan 0alive0.00
Network portal - A Database for Storage, Analysis and Visualization of Biological Networks
United States 14alive3.50
KEGG - Kyoto Encyclopedia of Genes and Genomes Japan 25114alive1321.79
UniCarbKB - UniCarb KnowledgeBase Australia 85alive11.90
Pfam - Protein Families Database United Kingdom 19906alive947.90
eggNOG - Database of Orthologous Groups and Functional Annotation
Germany 107alive26.48
Gene3D - Gene3D United Kingdom 194alive19.40
LenVarDB - Database of length variant protein domains
India 2alive0.50
TCDB - Transporter Classification Database United States 87alive21.53
ELM - The Eukaryotic Linear Motif Resource Germany 325unstable9.21
FireDB - Database of Annotated Functionally Important Residues
Spain 59alive5.36
HRaP - Occurrence of HomoRepeats and Patterns in Eukaryotic and Bacterial Proteomes Russian Federation 6alive1.47
SIMAP - The Similarity Matrix of Proteins
Canada 7unstable1.14
SCOPe - Structural Classification of Proteins-extended
United States 83alive20.54
SCOP2 - Structural Classification of Proteins 2
United Kingdom 50alive12.38
Spain 84alive6.00
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature
Japan 43alive7.17
pE-DB - Protein Ensemble Database Belgium 55unstable12.93
ModBase - Database of Comparative Protein Structure Models
United States 990alive61.26
MP:PD - Packing Database of Membrane Proteins
Germany 5alive1.24
RepeatsDB - A Database of Tandem Repeat Protein Annotations
Italy 33alive8.17
iPfam - Catalog of Protein Family Interactions
United States 38unstable5.32
3did - 3-Dimensional Interacting Domains
Spain 399unstable22.71
FunCoup - Database of Genome-wide Functional Coupling Networks.
Sweden 73alive11.92
France 7unstable1.52
Negatome - The Negatome Database
Germany 109unstable12.94
STITCH - Search Tool for Interacting Chemicals
Germany 624alive62.40
UniHI - Unified Human Interactome Portugal 194alive17.64
GPCRDB - G Protein-coupled Receptor (GPCR) Database Denmark 964alive47.72
Laminin-database Brazil 4unstable0.94
CentrosomeDB Spain 58unstable6.12
Germany 43alive4.30
Hemolytik - Database of Hemolytic peptides India 13alive3.25
CR Cistrome - Chromatin Regulator Cistrome China 6unstable1.26
MetaCyc database - A database describing metabolic pathways and enzymes from all domains of life.
United States 199unstable20.89
Reactome - A Curated Pathway Database United States 615unstable119.92
SMPDB - The Small Molecule Pathway Database Canada 110alive13.48
CSA - Catalytic Site Atlas
United Kingdom 614unstable37.72
CAZy - Carbohydrate-active Enzymes Database
France 553alive138.25
EKPD - Database of Eukaryotic Protein Kinases China 12alive3.00
MEROPS - The peptidase Database United Kingdom 1760unstable79.20
ASD - Allosteric Database
China 94alive13.43
MultitaskProtDB - Multitasking Proteins DataBase
Spain 18alive4.37
SFLD - Structure Function Linkage Database
United States 231alive19.06
Ensembl Genomes - Ensembl Genome Annotation System United Kingdom 293alive36.63
IMG - Integrated Microbial Genomes United States 568unstable19.88
DEG - Database of Essential Genes China 573alive40.93
PATRIC - Pathosystems Resource Integration Center United States 279unstable28.60
BacDive - Bacterial Diversity Metadatabase Germany 8alive2.00
EBI Metagenomics - EBI Metagenomics
United Kingdom 32unstable5.76
GGBN - Global Genome Biodiversity Network Germany 28alive6.93
LPSN - List of Prokaryotic names with standing in nomenclature United States 129alive32.25
MetaRef - A pan-genomic database for microbial genomics Italy 9unstable1.89
POGO-DB - Database of Pairwise-comparisons Of Genomes and universal Orthologous genes United States 4alive0.98
RDP - Ribosomal Database Project United States 11954alive433.89
SILVA - High quality ribosomal RNA databases Germany 3927unstable96.39
COLOMBOS Belgium 35alive5.00
DOOR - Database of Prokaryotic Operons United States 218alive23.74
Virus Variation - Virus Variation United States 21unstable2.10
CyanoBase Japan 36alive9.00
RhizoBase Japan 19alive4.70
HoPaCI-DB - The Host-Pseudomonas and Coxiella Interaction database France 3unstable0.70
PortEco - potral for E. coli research United States 13alive3.15
SporeWeb Netherlands 11alive2.75
SubtiWiki - A community resource for the model organism Bacillus subtilis Germany 159alive17.49
MycoCosm - The fungal genomics resource United States 93unstable17.20
AspGD - Aspergillus Gene Database United States 117alive19.31
CGD - Candida Genome Database United States 167alive27.56
SGD - Saccharomyces Genome Database United States 772alive128.67
LoQAtE - The localization and quantitation atlas of the yeast proteome Israel 8alive1.96
YeastNet - Probabilistic Functional Gene Network of Saccharomyces cerevisiae Korea Rep. 17unstable3.87
BacMet - Antibacterial Biocide and Metal Resistance Genes Database Sweden 16unstable3.80
mVOC - Microbial volatile organic compound database Germany 38alive9.50
RefSeq - Reference Sequence Database United States 6794unstable150.98
VEGA - Vertebrate Genome Annotation United Kingdom 368unstable25.48
WormBase - WormBase Canada 2150alive126.47
WormQTLHD - A Web Database for Linking Human Disease to Natural Variation Data in C. elegans. Netherlands 27alive5.40
IMPC - International Mouse Phenotyping Consortium United Kingdom 44alive10.89
GXD - The mouse Gene Expression Database United States 479alive22.81
MPD - Mouse Phenome Database United States 201unstable12.61
EMAGE - Mouse Embryo Spatial Gene Expression Database United Kingdom 234alive18.92
TISdb - translation initiation site database United States 16alive4.00
GeneProf - GeneProf United Kingdom 44unstable6.31
CCDS - Consensus Coding Sequence United States 394unstable10.07
LRG - Locus Reference Genomic United Kingdom 155alive19.38
ExoLocator - ExoLocator Singapore 5unstable1.15
Manteia France 18alive4.50
AgeFactDB - Ageing Factor Database Germany 8alive2.00
PhylomeDB - Phylome DataBase Spain 241alive24.10
dbPSHP - Database of Positive Selection across Human Populations Hong Kong SAR China 16alive4.00
Selectome - A Database of Positive Selection Switzerland 43unstable4.54
TreeFam - database of phylogenetic trees United Kingdom 529alive44.08
Expression Atlas - Expression Atlas United Kingdom 90unstable16.65
GEISHA - Gallus Expression In Situ Hybridization Analysis United States 113alive7.83
The Gene Expression Barcode United States 15alive3.71
PED - Pancreatic Expression Database United Kingdom 75alive6.61
CellFinder Germany 5alive1.25
PPD - Plasma Proteome Database India 53unstable12.45
dbGaP - Database of Genotypes and Phenotypes United States 85unstable8.50
ClinVar - variation-phenotype relationships United States 944unstable94.40
DGV - Database of Genomic Variants Canada 233alive58.25
DECIPHER - Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. United Kingdom 41unstable2.36
NECTAR - Non-synonymous Enriched Coding muTation ARchive United Kingdom 0alive0.00
FINDbase - Frequency of Inherited Disorders Database Greece 111alive10.09
InvFEST - Human Polymorphic Inversion DataBase Spain 14alive3.50
rSNPBase - A Database for Curated Regulatory SNPs China 35alive8.75
canSAR United Kingdom 70alive11.20
DriverDB - database for cancer driver gene/mutation Taiwan 18alive4.41
Progenetix Switzerland 179unstable7.58
HbVar - Human Hemoglobin Variants and Thalassemias United States 510alive36.43
HMDD - Human MicroRNA Disease Database China 61alive15.25
United States 84unstable8.40
United Kingdom 1746unstable209.52
DrugBank - Open Data Drug and Drug Target Database
Canada 3839alive319.92
SuperPain Germany 3alive0.75
Transformer Germany 8alive2.00
TTD - Therapeutic target database Singapore 232alive37.89
VIOLIN - Vaccine investigation and online information network United States 20alive5.00
bNAber - Broadly Neutralizing Antibodies Electronic Resource
United States 22alive5.45
SAbDab - The Structural Antibody Database United Kingdom 23unstable5.06
India 16alive4.00
CAMP - Collection of Anti-Microbial Peptides
India 218alive26.70
GoMapMan - GoMapMan Slovenia 16alive3.92
P-MITE - Plant Miniature Inverted Transposable Element database China 24alive5.76
PlantTFDB - Plant Transcription Factor Database China 684unstable46.51
ppdb - plantpromoterdb Japan 19alive4.75
Gramene - A comparative resource for plants United States 79alive19.75
LSD - Leaf Senescence DataBase China 42unstable5.28
P3DB - Plant Protein Phosphorylation DataBase United States 129alive13.90
RiceWiki China 7alive1.73
CottonGen United States 42unstable9.66
GDR - Genome Database for Rosaceae United States 343unstable22.54
SoyKB - Soybean Knowledge Base United States 26alive6.37
MitoBreak - The mitochondrial DNA breakpoints database Portugal 4alive0.98
ENCODE - Encyclopedia of DNA Elements United States 2053unstable33.73
Dfam - Dfam United States 58unstable8.58
SINEBase - A Database and Tools for SINE Analysis Russian Federation 27alive5.29
DoriC - Database of oriC regions in Bacterial and Archaeal genomes China 111unstable9.08
Non-B DB - A Database for Integrated Annotations and Analysis of non-B DNA Forming Motifs United States 68dead0.00
UCNEbase - A database of ultraconserved non-coding elements and genomic regulatiory blocks Switzerland 20unstable3.64
APPRIS - Annotating Principal Splice Isoforms Spain 39alive7.80
HEXEvent - Human EXon splicing Events database United States 14alive2.72
SpliceAid-F Italy 20dead0.00
Spliceosome Database United States 20alive3.88
GeneTack database - GeneTack database United States 6unstable0.12
Factorbook - Factorbook United States 61unstable2.68
ChIPBase China 199unstable24.68
CTCFBSDB - CTCF Binding Sites and Genome Organization Database United States 118alive11.68
HOCOMOCO - Homo Sapiens Comprehensive Model Collection Russian Federation 62alive12.40
SwissRegulon - A Database of Genome-wide Annotations of Regulatory Sites Switzerland 118unstable6.01
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.68
BSRD - Bacteria Small Regulatory RNA Database Hong Kong SAR China 27alive5.29
DIANA-LncBase - Database on miRNA-lncRNA interactions Greece 98unstable17.25
miRGator - miRGator Korea Rep. 228alive22.12
Darned - DAtabase of RNa EDiting Ireland 128alive15.84
MODOMICS - A Database of RNA Modifications Poland 509alive41.99
RNApathwaysDB - RNA Pathways Database Poland 5alive0.99
PlantRNA France 13alive2.52
Voronoia4RNA - Voronoia for RNA
Germany 4unstable0.50
dbPTM - Database of Protein Post-Translational Modifications
Taiwan 205alive16.74
MetalPDB - Meta knowledge on Protein Data Bank
Italy 18alive3.60
eProS - Energy Profile Suite
Germany 4unstable0.25
SwissSidechain - A Molecular and Structural Database of Non-natural Sidechains
Switzerland 16unstable2.91
TOPPR - The Online Protein Processing Resource Belgium 9unstable1.40
ValidNESs - Validated NES-containing proteins, functional NES sites and NES predictions Taiwan 21unstable3.86
PROSITE - Database of protein domains, families and functional sites Switzerland 8754unstable285.32
KEGG OC - KEGG Ortholog Cluster Japan 37alive7.40
OrtholugeDB - A Bacterial and Archaeal Orthology Resource Canada 17alive3.37
PANTHER - Protein ANalysis THrough Evolutionary Relationships United States 854alive170.80
TIGRFAMs - TIGR defined protein families
United States 940unstable51.42
The Genome Properties database - The Genome Properties database United States 65unstable12.09
France 10alive1.92
ClusterMine360 Canada 26alive5.15
DoBISCUIT - Database of BIoSynthesis clusters CUrated and InTegrated
Japan 27alive5.40
EENdb - Database of Engineered EndoNucleases China 35unstable6.51
ESTHER - The database of ESTerases and alpha/beta-Hydrolase Enzymes and Relatives
France 47unstable3.38
KIDFamMap - Kinase-inhibitor-disease family map Taiwan 6alive1.20
PeroxiBase France 333alive27.75
UUCD - ubiquitin and ubiquitin-like conjugation database China 22alive4.40
ZiFDB - Zinc Finger Database United States 73dead0.00
ChEBI - Chemical Entities of Biological Interest
United Kingdom 187alive37.40
ChemProt - Chemical-protein Interaction Database
Denmark 97alive13.44
GFDB - Glycan Fragment Database
United States 10alive2.00
SIFTS - Structure Integration with Function, Taxonomy and Sequence
United Kingdom 50alive10.00
D2P2 - Database of Disordered Protein Prediction United Kingdom 80alive15.84
NPIDB - Nucleic acid-Protein Interaction DataBase
Russian Federation 46alive4.14
PDBTM - Protein Data Bank of Transmembrane Proteins Hungary 492alive35.14
dcGO - Database of Domain-centric Ontologies
United Kingdom 30alive6.00 - HGNC United Kingdom 785unstable58.88
DGA - Database of Disease and Gene Annotations China 23unstable4.19
United States 99alive19.80 - Gene Annotation Query as a Service
United States 99alive19.80
HBVdb - Hepatitis B Virus database France 16unstable1.38
PaVE - PapillomaVirus Episteme United States 83unstable5.31
ViralZone - ViralZone Switzerland 76unstable9.55
PR2 - Protist Ribosomal Reference Database France 80alive16.00
EcoCyc - BioCyc Database Collection United States 3517unstable67.14
EcoGene - The EcoGene Database of Escherichia coli Sequence and Function United States 312unstable15.25
ECMDB - Escherichia coli Metabolome Database Canada 32alive6.40
MicroScope - Microbial Genome Annotation & Analysis Platform France 195alive38.61
metaMicrobesOnline - Phylogenomic Analysis of Microbial Communities United States 5alive0.99
Quorumpeps database - Quorum Sensing Signalling Peptides Belgium 24alive4.75
SecReT4 - Type IV Secretion System Resource China 21unstable3.91
SEVA - Standard European Vector Architecture Spain 87alive17.40
dictyBase - Database for Dictyostelium Discoideum United States 128alive14.08
EuPathDB - The Eukaryotic Pathogen database United States 168unstable18.69
GenColors - GenColors Germany 17alive1.29
LAMP - Library of Apicomplexan Metabolic Pathways United Kingdom 19alive3.80
CFGP - Comparative Fungal Genomics Platform Korea Rep. 102unstable5.51
NetwoRx - Connecting Drugs to Networks and Phenotypes in Saccharomyces Cerevisiae Canada 6alive1.19
SchistoDB - Schistosoma Genomic Resources Brazil 94alive10.24
WDDD - Worm Developmental Dynamics Database Japan 4alive0.79
FlyAtlas - Drosophila gene expression atlas United Kingdom 983alive89.36
MonarchBase - The Monarch Butterfly Genome Database United States 23unstable4.37
enzyme portal - enzyme portal
United Kingdom 13unstable2.03
MetaboLights - A Repository for Metabolomics Studies and Associated Meta-data United Kingdom 161unstable19.86
WholeCellKB - WholeCellKB United States 16alive3.20
CPDB - Consensus Pathway Database Germany 368unstable26.99
HMDB - The Human Metabolome Database Canada 2615alive235.35
2P2IDB - Protein-Protein Interaction Inhibition Database
France 321alive39.72
PrePPI - A structure-informed database of protein-protein interactions United States 301unstable15.05
SynSysNet - Synaptic Proteins Database Germany 18alive3.60
TissueNet - The Database of Human Tissue Protein-Protein Interactions Israel 53alive10.39
OikoBase - A curated genome expression database of Oikopleura dioica Norway 16unstable3.04
ZFIN - Zebrafish Information Network United States 899alive42.38
ZInC - Zebrafish Insertional Collection United States 15unstable1.20
QTLdb - Animal QTL database United States 143unstable19.16
H2DB - Heritability Database Annotating with Trait-Associated Genomic Loci Japan 1unstable0.19
RhesusBase China 12unstable2.23
H-InvDB - H-Invitational Database Japan 109alive10.90
Atlas of Genetics and Cytogenetics in Oncology and Haematology - Atlas of Genetics and Cytogenetics in Oncology and Haematology France 1188alive66.00
GTR - National Institutes of Health Genetic Testing Registry United States 33unstable2.64
dbVar - Database of Genomic Structural Variation United States 41unstable3.28
DGVa - The Database of Genomic Variants archive
United Kingdom 41unstable6.15
CellLineNavigator Germany 9alive1.80
GDSC - Genomics of Drug Sensitivity in Cancer United Kingdom 114unstable20.75
TP53 mutation database France 30unstable4.80
TSGene - tumor suppressor gene database United States 89unstable3.56
SomamiR United States 27alive5.35
LncRNADisease - Database on lncRNA-disease associations China 267unstable30.44
GEO - Gene Expression Omnibus United States 9384unstable234.60
Allen Brain Atlas United States 67alive13.40
CircaDB - Circadian Database United States 61unstable5.25
GenomeRNAi - A Database for Cell-based and In Vivo RNAi Phenotypes Germany 45alive8.82
HAGR - Human Ageing Genomic Resources United Kingdom 595alive45.77
HemaExplorer Denmark 49unstable7.76
INTERFEROME Australia 224alive24.39
METscout - METscout
Germany 2alive0.40
SpermatogenesisOnline - Annotation of Genes/Proteins Involved in Spermatogenesis China 7dead0.00
PRIDE - PRoteomics IDEntifications United Kingdom 846unstable125.21
Clone DB
United States 6unstable0.48
LUCApedia - Last Universal Common Ancestor United States 10unstable1.46
IUPHAR-DB United Kingdom 144alive20.16
TCMID - Traditional Chinese Medicines Integrated Database
China 53alive10.18
United States 63alive12.60
G4LDB - G-quadruplex ligands database China 24unstable2.83
NPACT - Naturally occuring Plant based Anticancerous Compound-Activity-Target DataBase India 70alive5.00
StreptomeDB Germany 28unstable5.26
SwissBioisostere - A Database of Molecular Replacements for Ligand Design
Switzerland 30alive5.94
MIPS PlantsDB - Plant Genome and Systems Biology Germany 43alive8.60
PIECE - Plant Intron Exon Comparison and Evolution database United States 27unstable2.43
PRGdb Italy 98unstable2.94
TropGeneDB - tropical gene database France 34alive2.36
PhosPhAt - The Arabidopsis Protein Phosphorylation Site Database Germany 416alive41.60
SUBA - The SUBcellular localisation Database for Arabidopsis Proteins Australia 168alive33.60
OrysPSSP - A Comparative Platform for Small Secreted Proteins from Rice and Other Plants China 8unstable1.10
RGKbase - Rice Genome Knowledgebase China 9unstable1.03
RiceXPro - Rice Expression Profile Database Japan 189alive26.46
RiceFREND - Rice Functionally Related Gene Expression Network Database Japan 29alive5.68
IMGT/HLA United Kingdom 370unstable55.50
InnateDB Canada 339unstable29.15
CIL-CCDB - Cell Image Library United States 14alive2.72
NCBI Bookshelf - NCBI Bookshelf United States 8unstable0.64
DOR - DDBJ Omics Archive
Japan 35unstable5.19
DDBJ BioProject - The DNA Data Bank of Japan BioProject
Japan 35unstable5.19
SRA - Sequence Read Archive United States -unstable-
GeneDB - GeneDB United Kingdom 92alive15.18
IMG/M - Integrated Microbial Genomes and Metagenomes United States 605unstable13.92
MAPPER2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation United States 116unstable6.51
ScerTF - Saccharomyces cerevisia Transcription Factors Database United States 35unstable2.63
YeTFaSCo - Yeast Transcription Factor Specificity Compendium Canada 31alive5.17
DBG2I - Database for bacterial group II introns Canada 37unstable2.90
mirEX - MicroRNA Expression Database Poland 16unstable1.95
NAPP - Nucleic Acids Phylogenetic Profiling France 8unstable1.25
VIRsiRNAdb - database of viral siRNA/shRNA India 17alive2.83
CharProtDB - Characterized Protein Database
United States 21unstable2.87
MnM - Minimotif Miner
United States 231unstable13.28
MimoDB - Mimotope Database
China 76unstable8.93
SitEx Russian Federation 5alive0.81
ProtoNet Israel 187alive12.22
BYKdb - Bacteria Tyrosine Kinase Database
France 15unstable1.13
ConoServer - Database for Conopeptides Australia 205unstable17.63
DD - Database of Death Domain Korea Rep. 14alive2.33
Histome - The Histone Infobase India 49unstable7.68
MIPModDB - Major Intrinsic Protein Database
India 23alive3.83
OPM - Orientations of Proteins in Membranes Database
United States 142alive23.67
NucleaRDB - Information System for Nuclear Receptors
Netherlands 209unstable2.70
Polbase - Polymerase Database United States 8unstable0.31
ProGlycProt - Prokaryotic Glycoproteins India 13unstable2.06
ProRepeat Netherlands 10unstable0.32
Israel 57alive9.50
COD - Crystallography Open Database
Lithuania 263alive28.93
Canada 7alive1.16
MINAS - Metal Ions in Nucleic Acids
Switzerland 15alive2.50
RNA CoSSMos - RNA Characterization of Secondary Structure Motifs Database
United States 18alive3.00
MMDB - Macromolecular Database
United States 79unstable5.27
AH-DB - Apo and Holo Structures DataBase
Taiwan 9alive1.50
United Kingdom 7alive1.17
ccPDB - Compilation and Creation of datasets from PDB
India 12alive2.00
Cube-DB - Cube-DB Singapore 3alive0.49
the DARC site - The Database for Aligned Ribosomal Complexes site Germany 4unstable0.61
DOMMINO - Database of MacroMolecular Interactions
United States 14unstable1.05
IndelFR - Indel Flanking Region Database
China 12unstable0.26
NRG-CING - NMR Restraints Grid -Common Interface for NMR structure Generation
Netherlands 29unstable0.82
Korea Rep. 11alive1.82
PASS2 - Protein Alignments organised as Structural Superfamilies India 70alive4.38
Pocketome United States 54alive8.73
ProtChemSI - protein-chemical structural interactions Germany 9alive1.49
PSCDB - Protein Structural Change DataBase Japan 35alive5.00
GOLD - Genomes On Line Database United States 1646unstable30.18
United Kingdom 97alive16.17
MIRIAM Registry - MIRIAM Registry
United Kingdom 97unstable12.13
HFV - Hemorrhagic Fever Viruses (HFV) Database United States 9alive1.49
ViPR - virus pathogene resourse United States 57alive9.50
BacMap Canada 47alive3.62
BµG@Sbase United Kingdom 5unstable0.28
CoryneRegNet - Corynebacterial Transcription Factors and Gene Regulatory Networks Germany 202unstable8.75
DBETH - Database of Bacterial ExoToxins India 20alive3.20
ICEberg - ICEberg is a web-based resource for integrative and conjugative elements found in Bacteria. China 52unstable8.06
ProOpDB - Prokaryotic Operon DataBase Mexico 61alive9.86
ProPortal - Prochlorococcus Portal United States 18alive2.94
VFDB - Virulence Factor Database China 448alive34.46
CADRE - Central Aspergillus Resource United Kingdom 92unstable5.39
FungiDB - FungiDB United States 47alive7.75
OriDB - DNA Replication Origin Database United Kingdom 159alive14.45
PhenoM - Phenomics of yeast Mutants Canada 196unstable21.81
FlyRNAi - Drosophila RNAi screening center database United States 104unstable6.33
Nematode - United States 163alive11.64
UniPathway - UniPathway Switzerland 54unstable6.48
eQuilibrator - Biochemical Thermodynamics Calculator
Israel 65alive10.72
FunTree - FunTree
United Kingdom 23alive3.72
MACiE - Mechanism, Annotation and Classification in Enzymes
United Kingdom 45unstable6.45
Germany 128alive11.64
hiPathDB - human integrated Pathway DB with facile visualization Korea Rep. 24alive4.00
IPAVS - Integrated Pathway Resources,Analysis and Visualization System
Korea Rep. 11unstable1.58
MMMDB - Mouse Multiple tissue Metabolome DataBase Japan 17alive2.83
YMDB - Yeast Metabolome Database Canada 88alive14.37
HotRegion Turkey 23alive3.83
IBIS - Inferred Biomolecular Interactions Server
United States 33alive5.45
IntAct United Kingdom 499unstable62.38
France 15alive2.48
MINT - Molecular Interaction Database
Italy 312unstable39.52
PINA - Protein Interaction Network Analysis Australia 281unstable23.10
Predictive networks United States 24unstable3.48
Newt-omics - A Comprehensive Repository for Omics Data from the Newt notophthalmus viridescens Germany 20alive3.33
OGEE - Online GEne Essentiality database China 77alive12.83
zfishbook - zebrafish book United States 3alive0.49
HGPD - Human Gene and Protein Database Japan 36alive4.00
HaploReg United States 457unstable54.84
SNPeffect - Single Nucleotide Variants Belgium 261alive20.08
DPSC-Cancer - Donnelly - Princess Margaret Screening Centre Cancer Database Canada 24alive3.96
dbDEPC - Database of Differentially Expressed Proteins in Human Cancer China 22unstable2.20
IGDB.NSCLC - Integrated Genomic Database of Non-Small Cell Lung Carcinoma Taiwan 10alive1.65
NCG - Network of Cancer Genes Italy 51alive8.50
SCDE - Stem Cell Discovery Engine United States 23alive3.83
UMD-BRCA1/BRCA2 - Universal mutation database-BRCA1/BRCA2 France 23dead0.00
ADHDgene - Database for Attention Deficit Hyperactivity Disorder China 27alive4.41
ALFRED - The ALlele FREquency Database United States 74unstable1.67
AutismKB China 74unstable8.39
BGMUT - Blood Group Antigen Gene Mutation Database United States 43unstable2.87
DiseaseMeth - Human Disease Methylation Database China 56unstable8.87
DistiLD - Database of Diseases and Traits in Linkage Disequilibrium Denmark 17alive2.83
GWASdb - GWASdb Hong Kong SAR China 82alive13.67
SpliceDisease China 27dead0.00
GeneSigDB - Gene Signature DataBase United States 123unstable9.69
GeneWeaver - GeneWeaver United States 54alive9.00
modMine - A Data Warehouse for the modENCODE Project United Kingdom 50unstable7.67
RecountDB - A Database of Mapped and Count Corrected Transcribed Sequences
Japan 1dead0.00
DAMPD - Dragon Antimicrobial Peptide Database South Africa 39unstable3.90
Germany 273unstable7.10
TDR - Tropical Disease Research Argentina 43unstable6.59
OligoGenome - Stanford Human Oligo Genome Project United States 3unstable0.41
PrimerBank United States 1063unstable63.07
HmtDB - Human Mitochondrial DataBase Italy 99unstable5.64
MitoMiner - A database of the mitochondrial proteome
United Kingdom 97alive10.56
MitoZoa - MitoZoa Italy 66dead0.00
MetaCrop - Metabolic pathways in crop plants Germany 73alive7.23
Phytozome - The Plant Genomics Resource United States 746unstable28.60
PlantNATsDB - Plant Natural Antisense Transcripts Database China 23alive3.68
PLEXdb - Plant Expression Database United States 136alive22.67
GABI-Kat SimpleSearch - GABI-Kat SimpleSearch Germany 206alive13.73 United States 86unstable4.62
LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes United States 27alive4.37
DIGIT - Database of ImmunoGlobulins with Integrated Tools Italy 19alive3.10
DNAtraffic - DNAtraffic Poland 3unstable0.39
Australia 590alive65.56
MethylomeDB - database containing genome-wide brain DNA methylation profiles United States 33unstable1.87
MetaBase - Meta Database
Korea Rep. 21alive3.50
Gene Wiki - Gene Wiki United States 113unstable3.25
GONUTS - Gene Ontology Normal Usage Tracking System United States 13unstable1.13
EcoliWiki - EcoliWiki United States 24unstable3.24
Xanthusbase - Myxococcus xanthus databse United States 16unstable0.45
959 Nematode Genomes United Kingdom 47unstable6.74
WikiPathways - WikiPathways Netherlands 228unstable19.76
SNPedia United States 67unstable9.83
SEQanswers wiki
China 21alive3.40
OrthoDisease - Tracking Disease Gene Orthologs Across 100 Species Sweden 74alive5.29
KGVDB Korea Rep. 4dead0.02
AREsite - AU-rich Elements Site Austria 110alive15.56
GyDB - The Gypsy Database Spain 127alive12.45
ASPicDB - Alternative Splicing Database
Italy 75dead0.00
DBASS - Databases of Aberrant 3'-ss and 5'-ss in Human Disease Genes Italy 19alive2.71
MPromDb - Mammalian Promoter Database United States 79dead0.00
TcoF-DB - Dragon database of transcription co-factors and transcription factor interacting proteins Saudi Arabia 36alive4.94
FlyFactorSurvey - Database of DNA binding specificities for Drosophila transcription factors (TFs) United States 78alive11.14
REDfly - Regulatory Element Database for Drosophila United States 284alive23.43
WebGeSTerDB - Web Genome scanner fot terminators database India 33alive4.62
mESAdb - microRNA sequence and expression database Turkey 18alive2.57
PmiRKB - Plant microRNA Knowledge Base China 19alive2.66
RepTar - A Database of Inverse miRNA Target Predictions Israel 33unstable4.05
RNAMDB - RNA Modification Database United States 1297unstable36.21
tRNADB-CE - The tRNA Gene DataBase Curated manually by experts
Japan 69alive7.59
LocDB - Protein Localization Database for Human and Arabidopsis United States 26unstable2.82
PSORTdb Canada 191unstable12.93
CLIPZ - Cross-linking and Immunoprecipitation
Switzerland 72unstable8.85
PHOSIDA - phosphorylation site database Germany 567unstable48.97
Phospho.ELM - A database of experimentally verified phosphorylation sites in eukaryotic proteins Germany 580unstable7.46
Phospho3D Spain 62alive5.52
PolyQ - Polyglutamine Australia 18unstable2.16
PRIDB - Protein-RNA Interface Database United States 49unstable6.44
IsoBase - IsoRank PPI Network Alignment Based Ortholog Database United States 44alive6.29
RBPDB - The Database of RNA-binding Protein Specificities Canada 133alive19.00
OMPdb - A database of ß-barrel outer membrane proteins from Gram-negative bacteria Greece 28alive3.96
PREX - PeroxiRedoxin classification indEX United States 47alive6.71
RNA helicase database United States 30unstable3.90
ThYme - Thioester-active Enzymes
United States 30alive4.29
TMPad - The TransMembrane Protein Helix-Packing Database
Taiwan 18unstable1.26
VKCDB - voltage-gated potassium channels databse Canada 34alive2.43
GlycomeDB - A Carbohydrate Structure Metadatabase
United States 122alive12.08
SuperSweet - Sweetening Agents Database
Germany 18alive2.57
Belgium 78alive9.56
BSDB - Bio-molecule Stretching Database
Poland 21alive2.97
CDDB - Conformational Dynamics Databank
United States 11unstable0.99
PCDB - A database of protein conformational diversity Argentina 18alive2.55
PCDDB - Protein Circular Dichroism Data Bank United Kingdom 91alive7.58
SAHG - Structure Atlas of Human Genome Japan 8unstable0.63
TOPSAN - The Open Protein Structure Annotation Network
United States 63unstable4.09
AgBase United States 301alive25.08
BTO - BRENDA Tissue Ontology Germany 49alive6.93
IGRhCellID - Integrated Genomic Resources of Human Cell Lines for Identification Taiwan 2alive0.28
SCLD - Stem Cell Lineage Database United States 4unstable0.05
PRO - Protein Ontology United States 163unstable20.72
CAMERA United States 257unstable34.88
ODB - Operon DataBase Japan 79unstable7.99
PhEVER - phylogenetic exploration of virues' evolutionary relationships France 4unstable0.07
Effective - Effective Germany 48alive6.79
Pseudomonas Genome DB Canada 565alive62.78
PSSRdb - Polymorphic Simple Sequence Repeats database India 6unstable0.42
TADB - Toxin-antitoxin Data Base China 94unstable12.35
AmoebaDB - Amoeba Genome Resource United States 35alive4.95
MicrosporidiaDB - Microsporidia Genomics Resource United States 35alive4.95
Full-parasites - Full-parasites Indonesia 13alive1.86
ParameciumDB - Paramecium Database France 128alive11.64
FGDB - Fusarium graminearum Genome Databas Germany 128unstable8.96
CiF - Cyber-infrastructure for Fusarium United States 40unstable5.26
YPA - Yeast Promoter Atlas Taiwan 25unstable2.14
ArachnoServer - ArachnoServer Australia 131dead0.00
HGD - The Hymenoptera Genome Database United States 121alive16.94
KaPPA-View4 - Kazusa Plant Pathway Viewer Japan 36alive5.14
Pathway Commons - Search and visualize public biological pathway information United States 395alive56.43
BISC - BInary SubComplex Database
United Kingdom 3unstable0.13
DIMA - Domain Interaction MAp
Germany 69unstable4.43
DOMINE - Database of Protein Domain Interaction
United States 205unstable13.32
DroID - Drosophila Interactions Database United States 183alive18.12
HitPredict Japan 57alive8.14
KUPS - University of Kansas Proteomics Service United States 21unstable0.39
PCRPi-DB - Presaging Critical Residues in Protein interfaces - DataBase United Kingdom 10alive1.43
ProtCID - Protein Common Interfaces Database United States 44alive6.22
RegPhos - Regulatory Network in Protein Phosphorylation Taiwan 49alive6.86
REPAIRtoire - A Database of DNA Repair Pathways Poland 24alive3.39
SPIKE - Signaling Pathways Integrated Knowledge Engine Israel 38alive5.43
CIPRO - Ciona Intestinalis Protein Database Japan 25alive3.57
cBARBEL - Catfish Genome Database United States 26unstable0.97
BGD - Bovine Genome Database United States 42alive5.14
IKMC - The International Knockout Mouse Consortium United States 62unstable3.01
FANTOM - Functional and taxonomic analysis of metagenomes Japan 144alive8.91
RIKEN Japan 28unstable0.68
TIARA - Total Integrated Archive of Short-Read and Array database Korea Rep. 15alive2.12
DAnCER - Disease Annotated Chromatin Epigenetics Resource Canada 17alive2.38
dbCRID - Chromosomal Rearrangements In Diseases United States 23unstable0.26
dbDNV - DNV Database Taiwan 11unstable1.32
IGDD India 13unstable1.49
VnD - Variations and Drugs Korea Rep. 7dead0.00
CancerResource Germany 59alive8.34
CaSNP China 17unstable1.53
CCDB - Cervical Cancer Gene Database India 42alive6.00
DDPC - Dragon Database of Genes associated with Prostate Cancer South Africa 26unstable3.45
The Autophagy Database Japan 25dead0.00
CADgene - Coronary Artery Disease Gene Database China 42unstable5.52
T1DBase - type 1 diabetes susceptibility Base United Kingdom 178unstable4.93
CPLM - Compendium of Protein Lysine Modifications
China 27unstable0.81
EDULISS - EDinburgh University Ligand Selection System
United Kingdom 17unstable0.68
FragmentStore - FragmentStore
Germany 11alive1.57
HIT - Herbal Ingredients' Targets Database China 60unstable5.31
PROMISCUOUS Germany 109alive15.57
Protegen - Protective Antigens United States 28unstable3.56
MitoGenesisDB - Mitochondrial Spatio-Temporal Expression Database France 3alive0.43
GreenPhylDB - GreenPhylDB France 130unstable2.99
NIASGBdb - NIAS Genebank database Japan 14alive1.98
AGRIS - Arabidopsis Gene Regulatory Information Server United States 701alive46.73
AHD2 - Arabidopsis Hormone Database 2.0 China 60unstable4.00
AtPID - Arabidopsis thaliana Protein Interactome Database China 136unstable12.65
PAIR - Predicted Arabidopsis Interactome Resource China 32unstable1.23
TFGD - Tomato Functional Genomics Database United States 46alive6.51
iRefWeb - Literature curation of protein interactions
Canada 66alive6.47
GATMD - GABA Transporter Mutagenesis Database United States 7dead0.00
Pigment_Cell United States 3unstable0.15
EuroDia - EuroDia MicroArray Database Switzerland 9dead0.00
human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions Germany 14alive1.73
HOMD - The Human Oral Microbiome Database United States 216alive27.00
Shewanella knowledgebase United States 12dead0.00
PROFESS - PROtein Function, Evolution, Structure and Sequence United States 13alive1.63
MRB - Mouse Resource Browser Greece 3alive0.38
PDBWiki Germany 24alive3.00
CGDSNPdb - Center for Genome Dynamics Single Nucleotide Polymorphism Database United States 7dead0.00
BrainTrap - Fly Brain Protein Trap Database United Kingdom 14alive1.72
TRedD - Tandem Repeats Database United States 12unstable0.54
OpenFluDB - A Database for Human and Animal Influenza Virus Switzerland 17alive2.13
GOOD - Gene-Oriented Ortholog Database Taiwan 3unstable0.31
PhosphoGRID Canada 63unstable2.91
United Kingdom 5alive0.62
Varietas - Varietas Finland 8dead0.00
AthaMap - Arabidopsis thaliana Map Germany 275alive19.45
GermOnline - GermOnline France 63unstable4.05
GeneCards - GeneCards Israel 900unstable21.60
HyperCAT Norway 20alive2.45
RAC - Repository of Antibiotic Australia 15dead0.00
hUbiquitome - ubiquitination cascades in humans China 14dead0.00
CPGR - Comprehensive Phytopathogen Genomics Resource United States 10alive1.43
INOH Japan 13dead0.00
SalmonDB - A Database for salmonids species Chile 14alive1.92
CELLPEDIA Japan 10alive1.43
Reactome BioMart - Reactome BioMart United Kingdom 8dead0.00
NetSlim - High-confidence Curated Signaling Maps
United States 18unstable2.29
Canada 49alive6.79
Neisseria Base - A Comparative Genomics Database for Neisseria Meningitidis United States 5dead0.00
ICGC - International Cancer Genome Consortium Data Portal Canada 80dead0.00
SigReannot-mart France 7alive0.99
GETPrime - Gene and Transcript-specific Primer Database Switzerland 28alive3.88
modENCODE - The model organism Encyclopedia of DNA Elements United States 18alive2.57
The strategies WDK United States 9unstable1.14
hERGAPDbase Japan 5unstable0.30
TparvaDB - Theileria parva vaccine development Database Kenya 2dead0.00
Allie - A Search Service for Abbreviation / Long Form
Japan 13alive1.86
LccED - The Laccase Engineering Database
Germany 42dead0.00
FunSecKB - Fungal Secretome KnowledgeBase United States 56unstable7.52
the CEREALAB database - Cereals genotypic phenotypic source Italy 16unstable1.19
LPS-annotate Canada 8dead0.02
QlicRice - QTL and Loci Interaction Channels in Rice India 6unstable0.27
3DSwap - Knowledgebase of proteins involved in 3D domain swapping
India 14alive2.00
ParkDB - Parkinson's disease gene expression database United Kingdom 18dead0.00
Histone Database - Histone Database United States 19unstable0.60
CTD - Comparative Toxicogenomics Database United States 1016alive67.73
eFIP - eFIPonline
United States 13unstable1.93
United States 87unstable5.80
DFVF - Database of Known Fungal Virulence Factors United States 5alive0.82
The Units Ontology
United Kingdom 16dead0.00
CreZOO - CreZOO Greece 4unstable0.28
MuteinDB - The Mutein Database
Austria 4dead0.00
PRINTS - A compendium of protein fingerprints United Kingdom 42unstable6.65
GrameneMart - BioMart data portal for the Gramene project United States 16alive2.67
The gene-specific codon counting database - The gene-specific codon counting database United States 8dead0.00
dbPTB - Database for Preterm Birth United States 16alive2.67
BFGR - Biofuel Feedstock Genomics Resource United States 12alive2.00
YeastMine - YeastMine United States 54alive8.73
United Kingdom 62unstable6.92
TGD Wiki - Tetrahymena genome database Wiki United States 8alive1.33
Aptamer base - Aptamer database
Canada 21unstable1.33
MEDIC - CTD's MEDIC disease vocabulary United States 54alive9.00
United Kingdom 10dead0.00
Dr. PIAS - Druggable Protein-protein Interaction Assessment System Japan 28unstable3.08
RefPrimeCouch - A Reference Gene Primer CouchApp Germany 1unstable0.15
wwpdb - worldwide protein data bank archive
United States 8alive1.58
CoIN - Co-occurrence Interaction Nexus
Taiwan 2dead0.00
HypoxiaDB - Hypoxia regulated proteins database India 3alive0.59
United States 6alive1.20
RAvariome - Rheumatoid Arthritis Genetic Variants Database Japan 4alive0.78
HTS-DB - High-Throughput Screening DataBase United Kingdom 0alive0.00
yApoptosis - yeast apoptosis database Sweden 1alive0.20
United States 50alive9.80
IQdb - IQ genetic database China 8unstable0.46
metabolicMine - metabolicMine United Kingdom 10dead0.00
BGDB - Bivalent Genes Database China 4unstable0.04
BmTEdb - Bombyx mori Transposable Elements Database China 10unstable1.74
lncRNome - long noncoding RNA knowledgebase India 37unstable7.03
ESCAPE - Embryonic Stem Cell Atlas from Pluripotency Evidence United States 23alive4.60
CARLSBAD United States 5alive0.98
The Banana Genome Hub France 19alive3.80
RiceSRTFDB - Rice Stress-Responsive Transcription Factor Database India 9alive1.76
PhenoDigm - PHENOtype comparisons for DIsease and Gene Models United Kingdom 44unstable8.36
PCorral - Protein Corral
United Kingdom 6unstable0.19
PMP - Protein Model Portal Switzerland 43unstable6.79
hLGDB - The Human lysosome Gene Database Italy 6alive1.19
Variome - Variome Japan 4unstable0.41
MalaCards - The Human Disease Database Israel 97unstable9.12
curatedOvarianData United States 30unstable4.32
YY1TargetDB - Yin Yang 1 Target loci Database Hong Kong SAR China 3alive0.60
T-HOD - Text-mined Hypertension, Obesity and Diabetes candidate gene database Taiwan 9unstable1.58
CrossTope - Structural Data Bank for Cross-Reactivity Brazil 8unstable1.04
PPInterFinder - Protein-Protein Interactions Finder India 17unstable0.24
Nencki Genomics Database - Ensembl Funcgen Enhanced With Intersections, User Data and Genome-wide TFBS Motifs. Poland 5alive0.96
BBGRE - Brain & Body Genetic Resource Exchange United Kingdom 2unstable0.02
SUS-BAR - Statistically Validated Annotation of Sus Scrofa Protein Sequences Italy 2unstable0.26
GnpIS - Genetic and Genomic Information System France 9unstable0.45
United Kingdom 11unstable1.89
MisPred - Miss Predict Protein Database Hungary 5unstable0.86
T2D@ZJU - Type 2 Diabetes Database at Zhejiang University China 6unstable0.38
CHD@ZJU - Coronary Heart Disease Research Platform China 7unstable0.56
GoSynthetic - Synthetic Biology Workbench Germany 2alive0.40
eFG - Electronic Resource for Fusarium Graminearum China 1alive0.20
FSRD - Fungal Stress Response Database Hungary 8alive1.58
dbWFA - Database of Wheat Functional Annotation France 2unstable0.10
Eimeria TDB - The Eimeria Transcript DB Brazil 3alive0.60
pseudoMap Taiwan 10alive2.00
PIPEMicroDB - PIgeonPEa Microsatellite DataBase India 5dead0.00
bc-GenExMiner - Breast Cancer Gene-Expression Miner France 13alive2.60
dbPPT - Database of Protein Phosphorylation in Plants China 5alive1.25
EssOilDB - ESSential OIL DataBase India 4unstable0.90
HGV&TB - Database for Human Genes and Genetic Variants associated with Tuberculosis India 0unstable0.00
AIM - Arabidopsis Interactome Modules Database United States 0unstable0.00
CBMAR - Comprehensive Beta-lactamase Molecular Annotation Resource
India 2unstable0.14
AromaDeg - Aromatic Hydrocarbon Degradation Database
Germany 8alive2.00
HProtDB - Halophile Protein Database India 1unstable0.15
piRBase - piRNA database China 6unstable1.41
ChloroSSRdb - Chloroplastic Simple Sequence Repeats Database India 5unstable1.00
VIRmiRNA - Resource for experimental viral miRNA and their targets India 7alive1.75
PolyprOnline France 2unstable0.44
MelGene - Field Synopsis of Genetic Association Studies in Cutaneous Melanoma Greece 4unstable0.80
BactPepDB - Bacteria Peptide Database France 3alive0.74
DEOP - Database on Osmoprotectants and Associated Pathways Saudi Arabia 4unstable0.94
MetaProx - The Database of Metagenomic Proximons Canada 2alive0.50
Sweden 4unstable0.91
CarrotDB China 14unstable2.90
CGHub - Cancer Genomics Hub United States 26unstable1.50
RGED - Renal Gene Expression Database China 1alive0.25
RADB - A Database of Rheumatoid Arthritis Related Polymorphisms China 1alive0.25
GOCat4FT - Gene Ontology Categorizer
Switzerland 2unstable0.41
LiverCancerMarkerRIF Taiwan 2unstable0.43
miRBase Tracker - miRBase Tracker Belgium 14unstable3.26
FusoBase - online Fusobacterium comparative genomic analysis platform Malaysia 0unstable0.00
Mouse IDGenes - Gene interactions in the developing mouse brain Germany 1alive0.25
LeishMicrosatDB - Database of leishmania genomic sequence repeats India 2unstable0.46
RLIMS-P - A Rule-based Literature Mining System for Protein Phosphorylation
United States 8unstable1.64
BioCreAtIvE - Critical Assessment of Information Extraction systems in Biology
United States 2832alive213.49
tmBioC - text-mining BioC
United States 2unstable0.20
APADB Germany 8alive1.98
RTeQTL - Real-Time Online Engine for Expression Quantitative Trait Loci
United States 1unstable0.22
yStreX - Yeast stress expression database Sweden 2alive0.50
IFIM - Integrated Fitness Information for Microbial genes China 4unstable0.75
miRror-Suite - A dual view on sets of microRNAs and their targets Israel 33alive4.04
RegulonDB - Regulon DataBase Mexico 2506alive124.05
PhenotypeAnnotation Spain 4alive0.97
Osteosarcoma Database - An Osteosarcoma-gene Association Database Germany 4alive0.99
PTM-SD - Post Translational Modification Structural Database France 6alive1.50
iSimp - A Sentence Simplification System for Biomedical Text
United States 2unstable0.40
HeteroGenome Russian Federation 2alive0.48
dbCRY - Cryptochrome Database
Korea Rep. 2unstable0.28
TuberQ Argentina 7unstable1.10
FixPred - FixPred
Hungary 1unstable0.22
PhylOPDb - phylogenetic oligonucleotide probe database France 24unstable3.56
tagtog - tagtog United Kingdom 4alive1.00
EpimiR - Database of Curated Mutual Regulation Between epigenetic Modifications and miRNAs China 8unstable1.44
DBatVir - the Database of Bat-Associated Viruses China 5alive1.25
YTRP - Yeast Transcriptional Regulatory Pathway Taiwan 5alive1.23
BambooGDB - Bamboo Genome Database China 12unstable1.62
ALE-HSA21 - AnaLysis of Expression of HSA21 Italy 5alive1.25
TSLP signaling pathway map - Thymic stromal lymphopoietin signaling pathway map United States 10unstable2.25
NONATObase - A Database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean Brazil 3unstable0.68
RegaDB - Rega database South Africa 2unstable0.37
ANIA - ANnotation and Integrated Analysis of the 14-3-3 interactome United Kingdom 6unstable0.34
tbvar - Mycobacterium tuberculosis variome resource India 5unstable1.19
Kin-Driver Argentina 7unstable1.64
iPathDB - INSECT PATHWAY DATABASE China 2unstable0.23
miRIAD - Intragenic MicroRNA Database Germany 4unstable0.48
WholeCellSimDB United States 4unstable0.92
PlantCAZyme - A database for plant carbohydrate-active enzymes United States 3unstable0.69
ChiloDB - Chilo suppressalis Database China 11unstable1.26