Databases

A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them; partly compiled with the support of Oxford University Press (NAR Database Issue and DATABASE Journal) and Re3Data.org.

There are 637 database records in BioDBCore.

Contribute by submitting another BioDBCore Entry
BioDBCore ID Name Domain(s) Covered Organism(s) Covered Condition of Access
biodbcore-000003 ADHDgene: a genetic database for attention deficit hyperactivity disorder
Free
biodbcore-000005 AnimalTFDB: a comprehensive animal transcription factor database Free
biodbcore-000006 AH-DB: collecting apo and holo structure pairs of proteins Free
biodbcore-000008 The BioSample Database (BioSD) at the European Bioinformatics Institute Free
biodbcore-000009 BitterDB: a database of bitter compounds
Free
biodbcore-000010 BuG@Sbase: a microbial gene expression and comparative genomic database
Free
biodbcore-000011 BYKdb: The Bacterial protein tYrosine Kinase database
Free
biodbcore-000012 CADRE: The Central Aspergillus Data REpository 2012 Free
biodbcore-000013 canSAR: An integrated cancer translational research and drug discovery resource Free
biodbcore-000014 CASP-DB: a structural classification of helix-capping motifs Free
biodbcore-000017 ConoServer:updated content, knowledge, and discovery tools in the conopeptide database Free
biodbcore-000018 CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands Free
biodbcore-000019 DAMPD: A manually curated antimicrobial peptide database Free
biodbcore-000020 The DARC site: a Database of Aligned Ribosomal Complexes Free
biodbcore-000021 DOMMINO: A comprehensive database of macromolecular interactions Free
biodbcore-000022 dbDEPC 2.0: updated database of differentially expressed proteins in human cancers Free
biodbcore-000023 DBETH: A Database of Bacterial Exotoxins for Human
Free
biodbcore-000024 DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
Free
biodbcore-000025 Disease Ontology: A backbone for Disease Semantic Integration
biodbcore-000026 DistiLD Database: Diseases and Traits in Linkage Disequilibrium Blocks
biodbcore-000028 DNAtraffic: a new database for systems biology of DNA dynamics during the cell life
Free
biodbcore-000029 doRiNA: a database of RNA interactions in post-transcriptional regulation Free
biodbcore-000030 Dr.VIS: A Database of Human Disease-Related Viral Integration Sites Free
biodbcore-000031 EcoliWiki: A Wiki-based community resource for Escherichia coli
Free
biodbcore-000033 ELM: the database of eukaryotic linear motifs. Mission 2012. Free
biodbcore-000035 eQuilibrator - the biochemical thermodynamics calculator
Free
biodbcore-000036 ExoCarta 2012: database of exosomal proteins, RNA and lipids Free
biodbcore-000037 FlyBase 101: The Basics of Navigating FlyBase Free
biodbcore-000038 FlyRNAi.org: the Database of the Drosophila RNAi Screening Center: 2012 Update
Free
biodbcore-000004 ALFRED: an allele frequency resource for research and teaching
Free
biodbcore-000002 GlycoNAVI
biodbcore-000032 Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups Free
biodbcore-000027 The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments
biodbcore-000007 Aspergillus Genome Database Free
biodbcore-000034 ENCODE Data in the UCSC Genome Browser
biodbcore-000040 FungiDB: an integrated functional genomics database for fungi Free
biodbcore-000041 FunTree: A Resource For Exploring The Functional Evolution Of Structurally Defined Enzyme Superfamilies Free
biodbcore-000042 GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database Free
biodbcore-000043 Gene Expression Atlas update: a value-added database of microarray and sequencing-based functional genomics experiments
Free
biodbcore-000045 GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
Free
biodbcore-000046 HaploReg: a resource for exploring chromatin states, conservation, ENCODE data, and regulatory motif alterations within sets of genetically linked variants. Free
biodbcore-000047 HGPD: Human Gene and Protein Database, 2012 update Free
biodbcore-000048 HIstome - A relational knowledge-base of human histone proteins and histone modifying enzymes Free
biodbcore-000049 HmtDB, a genomic resource for Mitochondrion Based Human Variability studies Free
biodbcore-000050 HotRegion: A database of hot spot clusters Free
biodbcore-000051 ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria Free
biodbcore-000052 IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature Free
biodbcore-000053 IMG/M: the integrated metagenome data management and comparative analysis system Free
biodbcore-000055 InterEvol database : Diving into the structure and evolution of protein complex interfaces Free
biodbcore-000056 LegumeIP: An Integrative Database Platform for Comparative Genomics and Transcriptomics of Model Legumes Free
biodbcore-000057 MACiE: Exploring the diversity of biochemical reactions Free
biodbcore-000058 The MAPPER-2 database: A multi-genome catalog of putative transcription factor binding sites
Free
biodbcore-000059 MetaBase - The wiki-database of biological databases Free
biodbcore-000060 MetaCrop 2.0: managing and exploring information about crop plant metabolism Free
biodbcore-000061 The Mouse Genome Database (MGD): Comprehensive Resource for Genetics and Genomics of the Laboratory Mouse Free
biodbcore-000062 MimoDB 2.0: a mimotope database and beyond Free
biodbcore-000063 MINAS - A Database of Metal Ions in Nucleic AcidS
Free
biodbcore-000064 Minimotif Miner 3.0: database expansion and significantly improved reduction of false positive predictions from consensus sequences
biodbcore-000065 MINT, the molecular interaction database: 2012 update Free
biodbcore-000066 MIPModDB: A Central Resource for the Superfamily of Major Intrinsic Proteins Free
biodbcore-000067 mirEX: a platform for comparative exploration of plant microRNA precursors expression data Free
biodbcore-000069 MitoMiner: A data warehouse for mitochondrial proteomics data
Free
biodbcore-000071 MOPED: Model Organism Protein Expression Database
Free
biodbcore-000074 Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes Free
biodbcore-000076 NONCODE v3.0: Integrative annotation of long noncoding RNAs
Free
biodbcore-000077 NucleaRDB: information system for nuclear receptors Free
biodbcore-000078 OGEE: an online gene essentiality database Free
biodbcore-000079 Openmods
Free
biodbcore-000081 The Pfam Protein Families Database
Free
biodbcore-000080 The DNA Replication Origin Database Free
biodbcore-000070 modMine: flexible access to modENCODE data
biodbcore-000068 MIRIAM Registry collection Free
biodbcore-000075 Newt-omics: A comprehensive repository for omics data from the newt Notophthalmus viridescens
biodbcore-000082 PhenoM: a morphological database of essential genes in Saccharomyces cerevisiae Free
biodbcore-000083 PINA v2.0: Mining Interactome modules Free
biodbcore-000084 Plantmetabolomics.org: Mass Spectrometry-based Arabidopsis Metabolomics-database and tools update
Free
biodbcore-000085 PlantNATsDB: a comprehensive database of plant natural antisense transcripts Free
biodbcore-000086 PLEXdb: Gene Expression Resources for Plants and Plant Pathogens
Free
biodbcore-000087 Pocketome: an encyclopedia of small-molecule binding sites in 4D Free
biodbcore-000088 Polbase: a repository of biochemical, genetic, and structural information about DNA polymerases
Free
biodbcore-000089 PolymiRTS 2.0: Linking polymorphisms in microRNA target sites with human diseases and complex traits
Free
biodbcore-000090 ProGlycProt: an exclusive repository of experimentally characterized prokaryotic glycoproteins
Free
biodbcore-000091 ProRepeat: An Integrated Repository for Studying Amino Acid Tandem Repeats in Proteins Free
biodbcore-000092 ProtChemSI: a network of protein-chemical structural interactions
Free
biodbcore-000094 PSCDB: a database for protein structural change upon ligand binding Free
biodbcore-000095 Rhea: a manually curated resource of biochemical reactions Free
biodbcore-000096 RNA CoSSMos: Characterization of Secondary Structure Motifs - A searchable database of secondary structure motifs in RNA three dimensional structures
Free
biodbcore-000097 ModelDB open access
biodbcore-000098 SCRIPDB: A Portal for Easy Access to Syntheses, Chemicals, and Reactions In Patents
Free
biodbcore-000099 The SEQanswers wiki: A wiki database of tools for high throughput sequencing analysis.
biodbcore-000101 SMART 7: Recent updates to the protein domain annotation resource Free
biodbcore-000102 SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
Free
biodbcore-000103 STAP Refinement of NMR Database: a database of 2,405 refined solution NMR Structures Free
biodbcore-000106 The Human OligoGenome Resource: A Database for Customized Targeted Resequencing Covering the Human Genome Free
biodbcore-000110 AutismKB, an evidence-based knowledgebase of autism genetics
Free
biodbcore-000112 ccPDB
Free
biodbcore-000113 CUBE-DB
free
biodbcore-000114 Death Domain Database
Free
biodbcore-000115 DiseaseMeth
Free
biodbcore-000116 Gene3D
Free
biodbcore-000117 GOLD, Genomes OnLine Database Free
biodbcore-000119 IGDB.NSCLC: Integrated Genomic Database of Non-Small Cell Lung Cancer
Free
biodbcore-000120 IndelFR
Free
biodbcore-000121 IPAVS Free
biodbcore-000122 MethylomeDB Free
biodbcore-000123 miRNEST
Free
biodbcore-000124 MitoZoa, MITOchondrial genome database of metaZOAns Free
biodbcore-000125 Nematode.net Free
biodbcore-000126 NRG-CING
Free
biodbcore-000104 STITCH: Chemical-Protein Interactions Free
biodbcore-000108 zfishbook: connecting you to a world of zebrafish revertible mutants
biodbcore-000109 Group II introns database
biodbcore-000111 BacMap
biodbcore-000127 PoSSuM
Free
biodbcore-000129 SpliceDisease
free
biodbcore-000130 TarBase6.0
Free
biodbcore-000131 VIRsiRNAdb
Free
biodbcore-000132 UMD-BRCA1 Free
biodbcore-000133 Gene Wiki
Free
biodbcore-000134 HFV sequence database Free
biodbcore-000135 hiPathDB Free
biodbcore-000136 MetaCyc
Free
biodbcore-000138 PASS2.4
Free
biodbcore-000139 PomBase Free
biodbcore-000140 Predictive Networks (PN) Free
biodbcore-000141 PrimerBank: PCR Primers for Gene Expression Detection and Quantification
Free
biodbcore-000142 Prokaryotic Operon DataBase
Free
biodbcore-000143 ProPortal
Free
biodbcore-000145 SNPedia
Free
biodbcore-000146 SubtiWiki
Free
biodbcore-000147 SuperTarget
Free
biodbcore-000148 TDR Targets Free
biodbcore-000149 TopFIND Free
biodbcore-000150 TTD, Therapeutic Target Database Free
biodbcore-000151 The UCSC Archaeal Genome Browser Free
biodbcore-000152 VectorBase
Free
biodbcore-000153 VFDB, Virulence Factor Database Free
biodbcore-000155 WikiPathways Free
biodbcore-000157 YMDB
Free
biodbcore-000158 WholeCellKB - Whole-Cell Knowledge Base
Open access
biodbcore-000159 RhesusBase: a Knowledgebase for the Monkey Research Community
Free
biodbcore-000160 Human Ageing Genomic Resources
biodbcore-000144 Stem Cell Discovery Engine
biodbcore-000161 PTMcode Free
biodbcore-000162 SecReT4
Free
biodbcore-000163 OrtholugeDB
biodbcore-000165 Dfam
biodbcore-000166 Nordic Control Allele Frequency and Genotype Database
restricted access
biodbcore-000167 Worm Developmental Dynamics Database
free
biodbcore-000169 Aptamer Base
biodbcore-000170 PlantRNA
biodbcore-000171 IMGT/HLA
Creative Commons Attribution-NoDerivs Licence
biodbcore-000172 Immuno-Polymorphism Database
biodbcore-000137 neXtProt
biodbcore-000164 GenomeRNAi
biodbcore-000174 2P2Idb
open access
biodbcore-000175 MODOMICS
open access
biodbcore-000176 HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO) open access
biodbcore-000177 MetalPDB
open access
biodbcore-000178 PRGdb
biodbcore-000179 HemaExplorer
open access
biodbcore-000413 Greengenes:16S rRNA gene database
biodbcore-000187 Bacterial Carbohydrate Structure Database
biodbcore-000414 Maize Genetics and Genomics Database
biodbcore-000503 PRIAM: PRofils pour l'Identification Automatique du M_tabolisme
biodbcore-000185 wiki-pain
biodbcore-000015 ChEMBL: a large-scale bioactivity database for drug discovery
biodbcore-000180 The Cell: An Image Library-CCDB
open access
biodbcore-000181 mycoCLAP Free
biodbcore-000504 ArachnoServer: Spider toxin database
biodbcore-000505 Japan Collection of Microorganisms
biodbcore-000506 RIKEN Bioresource
biodbcore-000528 SWISS-MODEL repository of 3D protein structure models
biodbcore-000173 CTD: Comparative Toxicogenomics Database Free
biodbcore-000182 antibodyregistry.org
Free
biodbcore-000044 GeneDB Free
biodbcore-000183 Influenza Research Database (IRD) Free
biodbcore-000212 Mammalian Protein Localization Database
biodbcore-000186 Golm Metabolome Database
biodbcore-000154 Virus Pathogen Database and Analysis Resource (ViPR) Free
biodbcore-000073 NAPP: the Nucleic Acid Phylogenetic Profile Database
biodbcore-000184 FlowRepository
biodbcore-000188 CellFinder
biodbcore-000190 Glycosciences.de DB
biodbcore-000189 MonosaccharideDB
biodbcore-000093 ProtoNet 6.0: Organizing 10 million protein sequences into a compact hierarchical family tree
biodbcore-000193 Human Endogenous Retrovirus database
biodbcore-000253 Uniprobe
biodbcore-000192 Encyclopedia of Hepatocellular Carcinome Genes Online II
biodbcore-000196 addgene
biodbcore-000197 RNAJunction: A Database of RNA Junction and Kissing loop Structure
biodbcore-000199 Assembling the Fungal Tree of Life
biodbcore-000198 Nottingham Arabidopsis Stock Centre Seeds Database
biodbcore-000200 AgBase
biodbcore-000202 The Arabidopsis Gene Regulatory Information Server
biodbcore-000203 Animal Genome Size Database
biodbcore-000209 Telomerase database
biodbcore-000205 CAS: A Divison of the American Chemical Society
biodbcore-000206 Evolutionary Annotation Database
biodbcore-000210 American Type Culture Collection database
biodbcore-000211 Arabidopsis thaliana trans-factor and cis-element prediction database
biodbcore-000208 DNASU Plasmid Repository
biodbcore-000194 autoSNPdb
biodbcore-000195 miRNEST
biodbcore-000204 Allergome: a platform for allergen knowledge
biodbcore-000207 AntWeb: Ant of the World
biodbcore-000215 Evolutionary Trace
biodbcore-000216 Drosophila Gene Disruption Database
biodbcore-000217 Non-Redundant B.subtilis database
biodbcore-000218 PHI-base: The Pathogen Host Interactions
biodbcore-000219 UK Stem Cell Bank
biodbcore-000220 cis-Regulatory Element Database
biodbcore-000221 Beijing Genomics Institute Rice Information System
biodbcore-000222 Chicken Variation Database
biodbcore-000223 Influenza Virus Database
biodbcore-000224 Pig Genomic Informatics System
biodbcore-000225 YanHuang - The first Asian Diploid Genome
biodbcore-000226 Berkeley Drosophila Genome Project EST database
biodbcore-000227 EPConDB: A resource of the Beta Cell Biology Consortinum
biodbcore-000228 Bgee DataBase for Gene Expression Evolution
biodbcore-000229 Signal Transduction Classification Database
biodbcore-000232 Non-Ribosomal Peptides Database
biodbcore-000230 BindingDB database of measured binding affinities
biodbcore-000231 The Barcode of Life Data Systems
biodbcore-000213 Functional Coverage of the Proteome
biodbcore-000214 Drosophila polymorphism database
biodbcore-000235 The Database of Viral siRNA / shRNA
biodbcore-000236 Ciona intestinalis Protein Database
biodbcore-000237 PRODORIC
biodbcore-000234 Agile Protein Interaction Data Analyzer
biodbcore-000239 siRecords
biodbcore-000240 Structure, Interfaces and Alignments for Protein-Protein Interactions
biodbcore-000241 Human-Transcriptome Database for Alternative Splicing
biodbcore-000242 Human Gene and Protein Database
biodbcore-000243 Database of MHC Ligands and Peptide Motifs
biodbcore-000244 Cnidarian Evolutionary Genomics Database
biodbcore-000245 StellaBase
biodbcore-000246 Tandem Repeats Database
biodbcore-000248 Comparative Fungal Genomics Platform
biodbcore-000249 The Comprehensive Enzyme Information System
biodbcore-000252 MutDB
biodbcore-000415 The Global Proteome Machine Database
biodbcore-000416 DragonDB
biodbcore-000417 Rat Genome Database
biodbcore-000238 National Microbial Pathogen Data Resource
biodbcore-000250 Open Regulatory Annotation
biodbcore-000251 Magnaporthe grisea Database
biodbcore-000418 SUPERFAMILY database of structural and functional annotation
biodbcore-000419 Melanoma Molecular Map Project
biodbcore-000420 Pathway Commons
biodbcore-000527 PROSITE; a protein domain and family database
biodbcore-000255 Catalog of Fishes genus database
biodbcore-000256 The Cambridge Crystallographic Data Centre
biodbcore-000257 BloodExpress: a Database of Gene Expression in Mouse Haematopoiesis
biodbcore-000258 Erythropoiesis Database
biodbcore-000259 Automatic molecular interaction predictions
biodbcore-000260 Cell Signaling Technology Pathway Database
biodbcore-000261 PhosphoSite Protein
biodbcore-000262 The Autism Chromosome Rearrangement Database
biodbcore-000263 The Chromosome 7 Annotation Project
biodbcore-000264 Database of Arabidopsis Transcription Factors
biodbcore-000265 Database of Rice Transcription Factors
biodbcore-000266 Ontology-based Knowledgebase for Cell Adhesion Molecules
biodbcore-000267 Plant Transcription Factor Database
biodbcore-000268 ROSPath
biodbcore-000269 RNAiDB
biodbcore-000270 RTPrimerDB
biodbcore-000271 SURFACE
biodbcore-000272 Knottin database
biodbcore-000254 CutDB
biodbcore-000421 Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
biodbcore-000422 REFOLD
biodbcore-000276 Candida Genome Database
biodbcore-000277 Receptor Tyrosine Kinase database
biodbcore-000278 The Coli Genetic Stock Center
biodbcore-000279 Human siRNA database
biodbcore-000280 IRESite: The database of experimentally verified IRES structures
biodbcore-000281 Eukaryotic Paralog Group Database
biodbcore-000282 The Database of Human DNA Methylation and Cancer
biodbcore-000283 MiCroKit - An Integrated Database of Midbody, Centrosome, and Kinetochore
biodbcore-000284 Shanghai Rapeseed Database
biodbcore-000285 GenomeTraFaC
biodbcore-000286 PolyDoms: Mapping of Human Coding SNPs onto Protein Domains
biodbcore-000287 GreenPhylDB: A phylogenomic database for plant comparative genomics
biodbcore-000288 OryGenesDB: an interactive tool for rice reverse genetics
biodbcore-000289 Oryza Tag Line: An integrated database for the functional analysis of the rice genome
biodbcore-000290 TropGENE DB
biodbcore-000291 CleanEx
biodbcore-000273 Catalogue of Transmission Genetics in Arabs
biodbcore-000274 Insect Microsatellite Database
biodbcore-000293 fireDB: a database of annotated functionally important residues
biodbcore-000294 The Carbohydrate-Active enZYmes Database
biodbcore-000295 The Diatom EST Database
biodbcore-000296 IS Finder
biodbcore-000297 Gramene; a comparative mapping resource for grains
biodbcore-000299 PDB-REPRDB: Representative Protein Chains from PDB
biodbcore-000300 Plant Genome Network
biodbcore-000301 Sol Genomics Network
biodbcore-000304 DrugBank
biodbcore-000302 Tomato Functional Genomics Database
biodbcore-000303 figshare
biodbcore-000306 A Database of Annotated Published Models
biodbcore-000307 Chemical Component Dictionary
biodbcore-000308 CiteXplore
biodbcore-000309 Catalytic Site Atlas
biodbcore-000310 EMBL nucleotide sequence database
biodbcore-000311 European Nucleotide Archive
biodbcore-000312 European Patent Office - Protein and Nucleic Acid Sequences
biodbcore-000423 Structural Classification Of Proteins
biodbcore-000502 PIRSF; a whole-protein classification database
biodbcore-000314 Integrated relational Enzyme database
biodbcore-000320 Ligand-Gated Ion Channel database
biodbcore-000316 The European Searchable Tumour Line Database
biodbcore-000317 Human Platelet Antigens
biodbcore-000318 Killer-cell Immunoglobulin-like Receptors
biodbcore-000319 Major Histocompatibility Complex Database
biodbcore-000323 PDBsum; at-a-glance overview of macromolecular structures
biodbcore-000321 MACiE
biodbcore-000322 Protein Data Bank Europe
biodbcore-000324 Protein Quaternary Structure database
biodbcore-000326 PROCOGNATE
biodbcore-000328 The European Genome -phenome Archive
biodbcore-000327 Reaction database
biodbcore-000329 Reactome - a curated knowledgebase of biological pathways
biodbcore-000330 Ensembl
biodbcore-000367 Conformation Angles Database
biodbcore-000315 Integrated resource of protein families, domains and functional sites
biodbcore-000368 Transmembrane Helices in Genome Sequences
biodbcore-000333 MycoBrowser leprae
biodbcore-000334 MycoBrowser marinum
biodbcore-000335 MycoBrowser smegmatis
biodbcore-000336 MycoBrowser tuberculosis
biodbcore-000337 4DXpress gene expression in major animals
biodbcore-000325 PRoteomics IDEntifications database
biodbcore-000338 the Eukaryotic Linear Motif
biodbcore-000339 Simple Modular Architecture Research Tool; a protein domain database
biodbcore-000340 STRING: functional protein association networks
biodbcore-000341 Side Effect Resource
biodbcore-000342 STINGreport
biodbcore-000343 Cryptosporidum Genomics Resource
biodbcore-000344 Eukaryotic Pathogen Database Resources
biodbcore-000345 GiardiaDB
biodbcore-000346 MicrosporidiaDB
biodbcore-000347 PlasmoDB
biodbcore-000348 Toxoplasma Genomics Resource
biodbcore-000331 HGNC-Identifier
biodbcore-000332 Escherichia coli strain K12 genome database
biodbcore-000351 Human Oral Microbiome Database
biodbcore-000352 Small Molecule Pathway Database
biodbcore-000358 MatrixDB: Extracellular Matrix interactions database
biodbcore-000353 GlycomeDB Carbohydrate Structure Database
biodbcore-000354 The Gene Index Project
biodbcore-000355 Health Canada Drug Product Database
biodbcore-000356 SABIO-Reaction Kinetic Database
biodbcore-000357 European Hepatitis C Virus database
biodbcore-000359 Protein Classification Benchmark Collection
biodbcore-000360 BAliBASE (version 2.0): A benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations
biodbcore-000361 Interrupted coding sequences
biodbcore-000362 PeroxisomeDB
biodbcore-000363 ImMunoGeneTics Information System
biodbcore-000364 ABS: a database of Annotated regulatory Binding Sites from Orthologous Promoters
biodbcore-000365 ArchDB
biodbcore-000366 KinMutBase: A registry of disease-causing mutations in protein kinase domains
biodbcore-000369 Database of protein disorder
biodbcore-000350 TriTrypDB
biodbcore-000466 Nematode Expression Pattern DataBase
biodbcore-000371 Eukaryotic Genes