Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
IPD - Immuno Polymorphism Database United Kingdom 323unstable16.15
PomBase United Kingdom 131unstable14.63
FlyBase - Database of Drosophila Genes & Genomes United States 3836alive159.83
MGD - Mouse Genome Database United States 2658alive126.57
Xenbase - Xenopus model organism database Canada 214alive21.40
OMIM - Online Mendelian Inheritance in Man United States 3217unstable32.17
GRASP - Genome-Wide Repository of Associations between SNPs and Phenotypes United States 28unstable2.52
MTB - Mouse Tumor Biology System United States 105alive6.18
DAA - Digital Ageing Atlas United Kingdom 9alive3.00
Organ system heterogeneity DB - A Database for the Visualization of Phenotypes at the Organ System Level Germany 0alive0.00
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana Korea Rep. 0unstable0.00
RiceVarMap - Rice Variation Map China 9alive2.97
SNP-Seek database - SNP-Seek Database Philippines 53unstable9.72
SGN - Sol Genomics Network United States 0unstable0.00
Cyclebase - Cell-cycle Database Denmark 105unstable6.72
PolymiRTS - Polymorphism in microRNAs and their TargetSites United States 264alive23.76
DPRP - Database of Phenotype-specific Regulatory Programs Taiwan 0alive0.00
PortEco - potral for E. coli research United States 13alive3.15
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
MPD - Mouse Phenome Database United States 201unstable10.96
AgeFactDB - Ageing Factor Database Germany 8alive2.00
PED - Pancreatic Expression Database United Kingdom 75unstable5.66
CellFinder Germany 5alive1.25
dbGaP - Database of Genotypes and Phenotypes United States 85unstable7.44
DECIPHER - Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. United Kingdom 41unstable1.95
rSNPBase - A Database for Curated Regulatory SNPs China 35alive8.75
SoyKB - Soybean Knowledge Base United States 26alive6.43
NCBI Epigenomics - NCBI Epigenomics United States 51unstable1.46
RNApathwaysDB - RNA Pathways Database Poland 5alive0.99
The Genome Properties database - The Genome Properties database United States 65unstable12.22
SEVA - Standard European Vector Architecture Spain 87alive17.40
NetwoRx - Connecting Drugs to Networks and Phenotypes in Saccharomyces Cerevisiae Canada 6alive1.19
GTR - National Institutes of Health Genetic Testing Registry United States 33unstable2.31
GenomeRNAi - A Database for Cell-based and In Vivo RNAi Phenotypes Germany 45alive8.82
CIL-CCDB - Cell Image Library United States 14alive2.69
PhenoM - Phenomics of yeast Mutants Canada 196unstable22.30
InterEvol
France 15alive2.48
Plantmetabolomics.org United States 86unstable3.98
SNPedia United States 67unstable9.05
IKMC - The International Knockout Mouse Consortium United States 62unstable2.66
MRB - Mouse Resource Browser Greece 3alive0.38
Varietas - Varietas Finland 8dead0.00
the CEREALAB database - Cereals genotypic phenotypic source Italy 16unstable1.03
QlicRice - QTL and Loci Interaction Channels in Rice India 6unstable0.22
RAvariome - Rheumatoid Arthritis Genetic Variants Database Japan 4alive0.78
PhenoDigm - PHENOtype comparisons for DIsease and Gene Models United Kingdom 44unstable7.13
BBGRE - Brain & Body Genetic Resource Exchange United Kingdom 2dead0.02
RADB - A Database of Rheumatoid Arthritis Related Polymorphisms China 1alive0.25
RetinoGenetics China 5unstable1.17
Planform - planarian formalization United States 8alive1.54
RARGE II - Arabidopsis Genome Encyclopedia Japan 7alive1.73
SNPxGE2 United States 4unstable0.43
WheatGenome.info - WheatGenome.information Australia 30alive4.95
TOMATOMA - Tomato Mutants Archive Japan 66alive9.43
UMD-CFTR - UMD-CFTR France 11alive1.35
GEPdb - Genotype-Expression-Phenotype Database Korea Rep. 1alive0.25
SDOP-DB - A comparative standardised-protocol database Japan 3alive0.38
SNP@lincTFBS - SNP in human lincRNA TFBS database China 3alive0.72
TPMD - Taiwan Polymorphic Marker Database Taiwan 6unstable0.30
DED - Diatom EST Database Italy 88unstable1.83
SilkDB China 293unstable7.44
SilkSatDb India 28alive2.15
Polymorphix France 23unstable0.18
EuroPhenome - EuroPhenome United Kingdom 73unstable5.38
MouseBook - An Integrated Portal of Mouse Resources United Kingdom 9unstable0.70
PlantMarkers - A database of predicted molecular markers from plants Finland 62dead0.00
PoMaMo - Potato Maps and More Germany 29dead0.00
The imprinted gene and parent-of-origin effect database New Zealand 551unstable19.01
HGVbaseG2P - The Human Genome Variation database United Kingdom 63unstable5.32
Panzea - Panzea United States 84unstable3.22
OTL - Oryza Tag Line Database France 51alive5.10
TAIR - The Arabidopsis Information Resource United States 768unstable40.70
PharmGKB - The Pharmacogenomics Knowledgebase United States 67unstable1.27
EMPReSS - European Mouse Phenotyping Resource of Standardised Screens United Kingdom 64unstable3.78
PhenomicDB - A multi-species genotype-phenotype database for comparative phenomics Germany 121unstable3.72
PEDE - Pig Expression Data Explorer Japan 52unstable4.11
WormBook - the online review of Caenorhabditis elegans biology United States 51alive4.64
QTL MatchMaker United States 5unstable0.34
OMIA - Online Mendelian Inheritance in Animals Australia 27unstable2.05
CTGA - Catalogue of Transmission Genetics in Arabs United Arab Emirates 42alive3.50
CRN - Cancer RNA-Seq Nexus Taiwan 0alive0.00
UET - Universal Evolutionary Trace United States 1alive0.49
Lynx United States 0alive0.00
IC4R - Information Commons for Rice China 1alive0.50
EBI - The European Bioinformatics Institute United Kingdom 610unstable16.52
hPSCreg - human pluripotent stem cell research community Germany 1alive0.50
GEneSTATION United States 1alive0.48
NCBI - National Center for Biotechnology Information United States 16174unstable305.51
BRAD - Brassica database China 155alive22.14
PhenoMiner - Online database of phenotypes and associated disorders
United Kingdom 0alive0.00
DMDD - Deciphering the Mechanisms of Developmental Disorders United Kingdom 13unstable0.57
ccmGDB - Cancer Cell Metabolism Gene DataBase United States 2unstable0.16
Digital Development - Digital Development United States 0alive0.00
PhytoPath United Kingdom 1alive0.50
BiGG Models
United States 1dead0.00
MethSMRT China 0unstable0.00
POSTAR - POST-trAnscriptional Regulation China 1unstable0.95
SNP2TFBS Switzerland 0unstable0.00
The Monarch Initiative United States 2unstable0.18
mirDNMR China 1unstable0.87
denovo-db United States 0alive0.00
IGSR - The International Genome Sample Resource United Kingdom 1alive1.00
HPO - Human Phenotype Ontology United States 975unstable73.13
GWAS Catalog United Kingdom 3886unstable405.87
AraPheno Germany 0unstable0.00
MODEM - Multi-Omics Data Envelopment and Mining in maize China 0unstable0.00
Fish Karyome India 4alive0.66
PGP - Plant Genomics and Phenomics Research Data Repository Germany 4alive2.00
TMC-SNPdb - Tata Memorial Centre-SNP data base India 1alive0.50
RiceATM Taiwan 0unstable0.00
VertNet United States 1unstable0.47
BISQUE - Biological Sequence Exchange United States 1alive0.50
PhenoScanner United Kingdom 6alive3.00
LD Hub United Kingdom 12alive11.88
* Citations derived from Google Scholar.
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