Database Commons a catalog of biological databases

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Database name Data type(s) Major organism(s) Location Citation* Status z-index
REBASE - The Restriction Enzyme Database United States 927alive61.80
PhosphoSitePlus United States 653alive108.83
BioModels
United Kingdom 23alive7.67
CeCaFDB - Central Carbon Metabolic Flux Database China 0unstable0.00
Super Natural II
Germany 11alive3.67
PubAngioGen China 0unstable0.00
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana Korea Rep. 0unstable0.00
KEGG - Kyoto Encyclopedia of Genes and Genomes Japan 25114alive1321.79
UniCarbKB - UniCarb KnowledgeBase Australia 85alive11.90
FunCoup - Database of Genome-wide Functional Coupling Networks.
Sweden 73alive11.92
MetaCyc database - A database describing metabolic pathways and enzymes from all domains of life.
United States 199unstable17.91
Reactome - A Curated Pathway Database United States 615unstable103.01
Gramene - A comparative resource for plants United States 79alive19.75
RNApathwaysDB - RNA Pathways Database Poland 5alive0.99
SwissSidechain - A Molecular and Structural Database of Non-natural Sidechains
Switzerland 16unstable2.53
KEGG OC - KEGG Ortholog Cluster Japan 37alive7.40
The Genome Properties database - The Genome Properties database United States 65unstable12.22
EcoCyc - BioCyc Database Collection United States 3517unstable57.55
ECMDB - Escherichia coli Metabolome Database Canada 32alive6.40
WholeCellKB - WholeCellKB United States 16alive3.20
HMDB - The Human Metabolome Database Canada 2615alive235.35
METscout - METscout
Germany 2alive0.40
SUBA - The SUBcellular localisation Database for Arabidopsis Proteins Australia 168alive33.60
BacMap Canada 47alive3.62
UniPathway - UniPathway Switzerland 54unstable6.84
MACiE - Mechanism, Annotation and Classification in Enzymes
United Kingdom 45unstable6.60
hiPathDB - human integrated Pathway DB with facile visualization Korea Rep. 24unstable3.68
IPAVS - Integrated Pathway Resources,Analysis and Visualization System
Korea Rep. 11unstable1.61
ADHDgene - Database for Attention Deficit Hyperactivity Disorder China 27alive4.45
MetaCrop - Metabolic pathways in crop plants Germany 73alive7.23
Plantmetabolomics.org United States 86unstable3.98
DNAtraffic - DNAtraffic Poland 3unstable0.34
WikiPathways - WikiPathways Netherlands 228unstable17.10
PmiRKB - Plant microRNA Knowledge Base China 19alive2.69
Pathway Commons - Search and visualize public biological pathway information United States 395alive56.43
Pigment_Cell United States 3unstable0.13
INOH Japan 13dead0.00
NetSlim - High-confidence Curated Signaling Maps
United States 18unstable2.34
The Banana Genome Hub France 19alive3.80
CHD@ZJU - Coronary Heart Disease Research Platform China 7unstable0.69
DEOP - Database on Osmoprotectants and Associated Pathways Saudi Arabia 4unstable0.93
BambooGDB - Bamboo Genome Database China 12unstable1.41
iPathDB - INSECT PATHWAY DATABASE China 2unstable0.20
BioCyc database United States 1unstable0.24
ConsensusPathDB Germany 368unstable28.21
PathLocdb - Pathway Localization Database China 10unstable0.23
KEGGtranslator - KEGGtranslator Germany 69unstable9.36
PhosphoNetworks United States 11alive2.75
KNApSAcK-3D - KNApSAcK-3D Japan 11alive2.20
SKPDB - ShiKimate Pathway DataBase Brazil 22dead0.00
LipidGO - Lipid-related Gene Ontology Terms
Singapore 1unstable0.20
CathaCyc - Metabolic Pathway Database of Catharanthus roseus Belgium 49unstable8.53
CAP - Citrus sinensis Annotation Project China 8alive1.98
ProFITS - Protein Families Involved in the Transduction of Signalling China 7alive0.84
EXPath - EXPath Taiwan 2alive0.67
PA-GOSUB - Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization Canada 29unstable2.05
Metagrowth - A new resource for the building of metabolic hypotheses in microbiology France 12dead0.00
CYGD - Comprehensive Yeast Genome Database Germany 327unstable21.63
GeneNet - The GeneNet system Russian Federation 68alive5.18
UCSC Proteome Browser - UCSC Proteome Browser United States 51alive3.88
MiST2 - Microbial Signal Transduction Database United States 147unstable11.94
PeroxisomeDB - PEROXISOME database Spain 61alive7.55
NURSA - Nuclear Receptor Signaling Atlas
United States 93alive7.67
BIOZON
United States 53unstable3.80
TrichDB United States 115alive12.52
metaTIGER - A Metabolic Evolution Resource United Kingdom 34alive3.78
PlasmoDB - Plasmodium Genomics Resource United States 413alive44.97
Bionemo - Biodegradation Network Molecular Biology Database
Spain 15alive1.67
PMAP - The Proteolysis MAP United States 31unstable1.89
EcID - Escherichia coli Interaction Database Spain 26alive2.89
KDBI - Kinetic Data of Biomolecular Interactions
Singapore 13alive1.42
PID - Pathway Interaction Database United States 593unstable44.80
APD - Antimicrobial Peptide Database United States 572alive62.92
RAPESEED - The Shanghai RAPESEED Database China 21unstable0.65
TAIR - The Arabidopsis Information Resource United States 768unstable40.70
WormBook - the online review of Caenorhabditis elegans biology United States 51alive4.64
SYSTOMONAS - SYSTOMONAS Germany 43unstable2.93
Sentra - Sentra United States 20dead0.00
ShiBASE China 22alive1.82
Pathguide - the Pathway Resource List United States 310alive25.57
TRANSPATH - a database of mammalian signal transduction and metabolic pathways Germany 849unstable4.02
DRASTIC - Database Resource for the Analysis of Signal Transduction in Cells United Kingdom 17unstable0.33
Phytome United States 38alive3.17
MERAV - Metabolic gEne RApid Visualizer United States 0alive0.00
Aging Chart Russian Federation 0unstable0.00
CRN - Cancer RNA-Seq Nexus Taiwan 0alive0.00
EBI - The European Bioinformatics Institute United Kingdom 610unstable16.52
enviPath - The Environmental Contaminant Biotransformation Pathway Resource Germany 1unstable0.40
WeGET - Weighted Gene Expression Tool and database Netherlands 0unstable0.00
PCOSKB - KnowledgeBase on Polycystic Ovary Syndrome India 1alive0.49
InsectBase China 1unstable0.46
WITHDRAWN - Database of withdrawn and discontinued drugs Germany 1alive0.50
HMA - Human Metabolic Atlas Sweden 3alive0.99
kpath
Spain 0unstable0.00
KIR - Kiwifruit Information Resource China 0unstable0.00
MouseNet - Probabilistic Functional Gene Network for Laboratory Mouse,Mus Musculus Korea Rep. 0unstable0.00
ccmGDB - Cancer Cell Metabolism Gene DataBase United States 2unstable0.16
sRNATarBase - sRNATarBase China 32unstable2.28
Colorectal Cancer Atlas Australia 1alive0.50
SigMol India 1alive0.49
Metabolomics Workbench United States 0alive0.00
SIGNOR - SIGnaling Network Open Resource Italy 2unstable0.75
BiGG Models
United States 1dead0.00
MitoCarta - An Inventory of Mammalian Mitochondrial Genes United States 2unstable0.50
MetaNetX/MNXref  - Reconciliation of Metabolites and Biochemical Reactions to Bring Together Genome-scale Metabolic Networks
Switzerland 0unstable0.00
MTD - mammalian transcriptomic database China 0alive0.00
HRGD - Heterosis Related gene Database China 6unstable0.63
miRPathDB - miRNA Pathway Dictionary Database Germany 1dead0.00
antiSMASH-DB - antibiotics & Secondary Metabolite Analysis SHell database Denmark 2unstable0.76
IMG-ABC - the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters United States 22dead0.00
Plant Reactome United States 2alive2.00
ArthropodaCyc France 1unstable0.25
MODEM - Multi-Omics Data Envelopment and Mining in maize China 0unstable0.00
ToxDB
Germany 1unstable0.38
miRnalyze - Analyzing microRNA-pathway relationships
India 0alive0.00
PathwaysWeb
United States 0alive0.00
ConceptMetab
United States 3unstable1.28
* Citations derived from Google Scholar.
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