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

There are 638 database records in BioDBCore.

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BioDBCore ID Name Domain(s) Covered Organism(s) Covered Condition of Access
biodbcore-000003 ADHDgene: a genetic database for attention deficit hyperactivity disorder
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
biodbcore-000010 BuG@Sbase: a microbial gene expression and comparative genomic database
biodbcore-000011 BYKdb: The Bacterial protein tYrosine Kinase database
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
biodbcore-000024 DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
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
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
biodbcore-000033 ELM: the database of eukaryotic linear motifs. Mission 2012. Free
biodbcore-000035 eQuilibrator - the biochemical thermodynamics calculator
biodbcore-000036 ExoCarta 2012: database of exosomal proteins, RNA and lipids Free
biodbcore-000037 FlyBase 101: The Basics of Navigating FlyBase Free
biodbcore-000038 the Database of the Drosophila RNAi Screening Center: 2012 Update
biodbcore-000004 ALFRED: an allele frequency resource for research and teaching
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
biodbcore-000045 GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
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
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
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
biodbcore-000071 MOPED: Model Organism Protein Expression Database
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
biodbcore-000077 NucleaRDB: information system for nuclear receptors Free
biodbcore-000078 OGEE: an online gene essentiality database Free
biodbcore-000079 Openmods
biodbcore-000081 The Pfam Protein Families Database
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 Mass Spectrometry-based Arabidopsis Metabolomics-database and tools update
biodbcore-000085 PlantNATsDB: a comprehensive database of plant natural antisense transcripts Free
biodbcore-000086 PLEXdb: Gene Expression Resources for Plants and Plant Pathogens
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
biodbcore-000089 PolymiRTS 2.0: Linking polymorphisms in microRNA target sites with human diseases and complex traits
biodbcore-000090 ProGlycProt: an exclusive repository of experimentally characterized prokaryotic glycoproteins
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
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
biodbcore-000097 ModelDB open access
biodbcore-000098 SCRIPDB: A Portal for Easy Access to Syntheses, Chemicals, and Reactions In Patents
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
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
biodbcore-000112 ccPDB
biodbcore-000113 CUBE-DB
biodbcore-000114 Death Domain Database
biodbcore-000115 DiseaseMeth
biodbcore-000116 Gene3D
biodbcore-000117 GOLD, Genomes OnLine Database Free
biodbcore-000119 IGDB.NSCLC: Integrated Genomic Database of Non-Small Cell Lung Cancer
biodbcore-000120 IndelFR
biodbcore-000121 IPAVS Free
biodbcore-000122 MethylomeDB Free
biodbcore-000123 miRNEST
biodbcore-000124 MitoZoa, MITOchondrial genome database of metaZOAns Free
biodbcore-000125 Free
biodbcore-000126 NRG-CING
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
biodbcore-000129 SpliceDisease
biodbcore-000130 TarBase6.0
biodbcore-000131 VIRsiRNAdb
biodbcore-000132 UMD-BRCA1 Free
biodbcore-000133 Gene Wiki
biodbcore-000134 HFV sequence database Free
biodbcore-000135 hiPathDB Free
biodbcore-000136 MetaCyc
biodbcore-000138 PASS2.4
biodbcore-000139 PomBase Free
biodbcore-000140 Predictive Networks (PN) Free
biodbcore-000141 PrimerBank: PCR Primers for Gene Expression Detection and Quantification
biodbcore-000142 Prokaryotic Operon DataBase
biodbcore-000143 ProPortal
biodbcore-000145 SNPedia
biodbcore-000146 SubtiWiki
biodbcore-000147 SuperTarget
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
biodbcore-000153 VFDB, Virulence Factor Database Free
biodbcore-000155 WikiPathways Free
biodbcore-000157 YMDB
biodbcore-000158 WholeCellKB - Whole-Cell Knowledge Base
Open access
biodbcore-000159 RhesusBase: a Knowledgebase for the Monkey Research Community
biodbcore-000160 Human Ageing Genomic Resources
biodbcore-000144 Stem Cell Discovery Engine
biodbcore-000161 PTMcode Free
biodbcore-000162 SecReT4
biodbcore-000163 OrtholugeDB
biodbcore-000165 Dfam
biodbcore-000166 Nordic Control Allele Frequency and Genotype Database
restricted access
biodbcore-000167 Worm Developmental Dynamics Database
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-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 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