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BioDBCore

A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them; compiled in collaboration with NAR Database.

There are 183 database records in BioDBCore.

Contribute by submitting another BioDBCore Entry
BioDBCore ID Name Description Domain(s) Covered Organism(s) Covered Condition of Access
biodbcore-000002 GlycoNAVI- chemical abbreviation database In scientific studies, many are using abbreviations. However, it is difficult to understand all the abbreviations. Thus, in this database is being developed as a system that can easily find the chemical structure of abbreviations.
  • chemistry Domain
  • organic chemisty Domain
  • protective group Domain
 other condition of use
biodbcore-000003 ADHDgene: a genetic database for attention deficit hyperactivity disorder Genetics of Attention Deficit Hyperactivity Disorder
  • literature citations about genetic ... Domain
  • published genes, SNPs, CNVs, chromo ... Domain
  • ADHD-related genes, SNPs, and pathw ... Domain
 Homo sapiens Free
biodbcore-000005 AnimalTFDB: a comprehensive animal transcription factor database Animal Transcription Factor Database
  • transcription factor(TF), transcrip ... Domain
  • gene basic information (via NCBI an ... Domain
  • gene structure Domain
  • functional domains(via Pfam) Domain
  • 3D structure hits (via PDB) Domain
  • Gene Ontology annotations Domain
  • protein-protein interaction (via Bi ... Domain
  • pathway information (via Biocarta a ... Domain
  • targets and TF binding sites (via T ... Domain
  • orthologs Domain
  • paralogs Domain
  • other cross references Domain
 Ailuropoda melanoleuca Anolis carolinensis Free
biodbcore-000006 AH-DB: collecting apo and holo structure pairs of proteins Apo- and Holo- structure pairs of proteins
  • structure pair Domain
 All Free
biodbcore-000007 The Aspergillus Genome Database (AspGD): Recent Developments in Comprehensive Multispecies Curation, Comparative Genomics, and Community Resources Aspergillus genome database
  • gene, protein and sequence informat ... Domain
  • current and historical archived ver ... Domain
 Emericella nidulans Aspergillus clavatus Aspergillus flavus Aspergillus fumigatus Aspergillus niger Aspergillus oryzae Aspergillus terreus Neosartorya fischeri Free
biodbcore-000008 The BioSample Database (BioSD) at the European Bioinformatics Institute Biological samples used as sources of sequence, structure or expression data
  • biological sample descriptors Domain
 All Free
biodbcore-000009 BitterDB: a database of bitter compounds Bitter taste: molecules and receptors
  • bitter compounds,their association ... Domain
 Free
biodbcore-000010 BuG@Sbase: a microbial gene expression and comparative genomic database Microarray datasets for microbial gene expression
  • microarray data Domain
  • comparative genomics Domain
  • gene expression Domain
 Free
biodbcore-000011 BYKdb: The Bacterial protein tYrosine Kinase database Bacterial protein tYrosine Kinase database
  • protein sequence of bacterial tyros ... Domain
 Bacteria Free
biodbcore-000012 CADRE: The Central Aspergillus Data REpository 2012 Central Aspergillus Data Repository
  • genome sequence Domain
  • karyotype Domain
  • gene models including CDS, predicte ... Domain
  • Gene Ontology annotations Domain
  • gene product names Domain
  • strains Domain
  • protein families and domains Domain
  • external database cross-references Domain
  • orthologues, paralogues and gene tr ... Domain
  • genome alignments Domain
  • functional genomics (mapping of RNA ... Domain
 Aspergillus Free
biodbcore-000013 canSAR: An integrated cancer translational research and drug discovery resource Integrated cancer research and drug discovery resource
  • canSAR is an integrative resource t ... Domain
  • Chemical and pharmacological data i ... Domain
  • 3D structural data including 3D coo ... Domain
  • drug and clinical candidate annotat ... Domain
 Homo sapiens Mus musculus Rattus norvegicus Free
biodbcore-000014 CASP-DB: a structural classification of helix-capping motifs Classification of helix cappings in protein structures
  • structure data Domain
  • atomic coordinates Domain
  • sequence information Domain
 All Free
biodbcore-000016 Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration Crystal structures of small molecules
  • crystal structure data Domain
  • atomic coordinates and structure fa ... Domain
 All Free
biodbcore-000017 ConoServer:updated content, knowledge, and discovery tools in the conopeptide database Sequence and structures of peptides expressed by marine cone snails
  • nucleic acid sequence Domain
  • protein sequence Domain
  • three-dimensional structures of con ... Domain
  • conotoxins Domain
  • protein precursor organization Domain
  • synthetic variants Domain
  • patents Domain
  • gene superfamily classification Domain
  • cysteine framework classification Domain
  • pharmacological family classificati ... Domain
  • statistics on classification scheme ... Domain
  • conopeptide activity Domain
  • cone snail information Domain
  • conopeptide masses Domain
  • statistics Domain
 Conus Free
biodbcore-000018 CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands Corynebacterial Regulation Network
  • genome sequence Domain
  • genes Domain
  • Gene Ontology annotations Domain
 aurimucosum ATCC 700975 diphtheriae NCTC 13129 314 glutamicum ATCC 13032 Corynebacterium glutamicum R Corynebacterium jeikeium K411 kroppenstedtii DSM 44385 Corynebacterium pseudotuberculosis 1002 Corynebacterium pseudotuberculosis C231 Corynebacterium pseudotuberculosis FRC41 urealyticum DSM 7109 Escherichia coli K12 Free
biodbcore-000019 DAMPD: A manually curated antimicrobial peptide database Dragon Antimicrobial Peptide Database
  • UniProtKB peptide data Domain
  • links to other data sources Domain
  • FASTA formated sequences Domain
  • Antimicrobial (KW-0929) Domain
  • AND (existence: evidence at protein ... Domain
 All Free
biodbcore-000020 The DARC site: a Database of Aligned Ribosomal Complexes Database for Aligned Ribosomal Complexes
  • PDB and brix files Domain
 All Free
biodbcore-000021 DOMMINO: A comprehensive database of macromolecular interactions Database of MacroMolecular INteractions
  • interaction network Domain
  • 3D structure Domain
 All Free
biodbcore-000022 dbDEPC 2.0: updated database of differentially expressed proteins in human cancers Differentially Expressed Proteins in Human Cancer
  • differentially expressed proteins ( ... Domain
  • low-throughput assays validation da ... Domain
  • cancer proteomics experiments Domain
  • differential expression profiles of ... Domain
  • DEPs association networks Domain
  • genetic variations on protein seque ... Domain
  • functional annotations (Gene Ontolo ... Domain
 Homo sapiens Mus musculus Rattus norvegicus Free
biodbcore-000023 DBETH: A Database of Bacterial Exotoxins for Human Database for Bacterial ExoToxins for Humans
  • human pathogenic bacterial exotoxin Domain
  • protein sequences Domain
  • 3D structures Domain
  • exotoxin Domains Domain
 Free
biodbcore-000024 DBTSS: DataBase of Transcriptional Start Sites progress report in 2012 Transcriptional start sites and adjacent promoters
  • transcriptional start sites based o ... Domain
 Homo sapiens Mus musculus Plasmodium falciparum Cyanidioschyzon merolae Rattus norvegicus Pan troglodytes Macaca fascicularis Free
biodbcore-000025 Disease Ontology: A backbone for Disease Semantic Integration Ontology for a variety of human diseases
  • disease ontology Domain
  • human diseases Domain
  • metadata related to diseases Domain
 Homo sapiens
biodbcore-000026 DistiLD Database: Diseases and Traits in Linkage Disequilibrium Blocks Diseases and Traits In Linkage Disequilibrium blocks
  • genome-wide association studies Domain
  • linkage disequilibirium data Domain
  • single nucleotide polymorphisms Domain
  • genes Domain
  • diseases Domain
 Homo sapiens
biodbcore-000027 The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments Annotated collection of all publicly available nucleotide and protein sequences
  • annotated collection of all publicl ... Domain
 All Free
biodbcore-000028 DNAtraffic: a new database for systems biology of DNA dynamics during the cell life DNA dynamics during the cell cycle
  • Pathway Name, Pathway Description, ... Domain
 Homo sapiens Mus musculus Caenorhabditis elegans Drosophila melanogaster Saccharomyces cerevisiae Schizosaccharomyces pombe Escherichia coli Arabidopsis thaliana Free
biodbcore-000029 doRiNA: a database of RNA interactions in post-transcriptional regulation Database of RNA interactions in post-transcriptional regulation
  • miRNA target site prediction Domain
  • RNA-binding protein target sites Domain
 Homo sapiens Mus musculus Caenorhabditis elegans Free
biodbcore-000030 Dr.VIS: A Database of Human Disease-Related Viral Integration Sites Human Disease-Related Viral Integration Sites
  • genome sequence Domain
  • genomic position Domain
  • gene Domain
  • chromosome region Domain
  • phenotype Domain
  • disease Domain
  • virus. Domain
 Homo sapiens Human papillomavirus Barr virus virus type 1 merkel cell polyomavirus hepatitis b virus related virus Free
biodbcore-000031 EcoliWiki: A Wiki-based community resource for Escherichia coli Community-based pages about non-pathogenic E. coli
  • genomic sequence Domain
  • gene models Domain
  • strains Domain
  • strain genealogy Domain
  • expression & cloning plasmids Domain
  • conjugative plasmids Domain
  • biological databases Domain
  • bioinformatics tools & formats Domain
  • methods Domain
  • education & teaching tools Domain
  • phenotypes Domain
  • phantom genes Domain
  • genes not-mapped-to-a-sequence Domain
  • homologs & orthologs Domain
  • generic information about Escherich ... Domain
  • cryptic prophage Domain
  • prophage Domain
  • phage Domain
  • nomenclature Domain
  • location Domain
  • sequence features Domain
  • alleles Domain
  • genetic interactions Domain
  • accessions Domain
  • genetic resources Domain
  • molecules per cell Domain
  • transcription units Domain
  • operons Domain
  • expression studies Domain
  • E. coli genome-sequencing projects ... Domain
  • literature specific to E. coli Domain
  • transposons Domain
  • insertion-sequences Domain
  • phage taxonomy Domain
  • cis-elements Domain
  • product function Domain
  • Gene Ontology annotations Domain
  • physical interactions Domain
  • localization Domain
  • physical properties Domain
  • domains Domain
  • motifs Domain
  • modification sites Domain
  • structures Domain
  • models Domain
  • families Domain
  • community updates & news Domain
  • user pages Domain
  • Monthly submission of Gene Assocati ... Domain
 Free
biodbcore-000032 eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges Evolutionary genealogy of genes: Non-supervised Orthologous Groups
  • orthologs Domain
  • multiple sequence alignments Domain
  • functional annotation Domain
  • Newick trees Domain
 All Free
biodbcore-000033 ELM: the database of eukaryotic linear motifs. Mission 2012. Eukaryotic linear motif: functional sites in eukaryotic proteins
  • short linear motif classes Domain
  • short linear motif instances Domain
  • interaction domains Domain
  • GO terms Domain
  • PSI-MI methods Domain
 All Free
biodbcore-000034 ENCODE Whole-Genome Data in the UCSC Genome Browser: Update 2012 Encyclopedia of DNA Elements, all functional elements in the human genome
  • Whole genome annotations from ENCOD ... Domain
  • Open chromatin (DNaseI hypersensiti ... Domain
 All Free
biodbcore-000035 eQuilibrator - the biochemical thermodynamics calculator Thermodynamics calculator for biochemical reactions
  • Compound formation energies and rea ... Domain
 All Free
biodbcore-000036 ExoCarta 2012: database of exosomal proteins, RNA and lipids Database on exosomes, membrane vesicles of endocytic origin released by diverse cell types
  • exosomal proteins Domain
  • exosomal mRNA Domain
  • exosomal miRNA Domain
  • exosomal lipids Domain
  • meta-annotations of exosome studies Domain
 All Free
biodbcore-000037 FlyBase 101: The Basics of Navigating FlyBase Drosophila sequences and genomic information
  • aberrations Domain
  • alleles Domain
  • balancers Domain
  • cell lines Domain
  • clones Domain
  • genes Domain
  • gene models Domain
  • genomes Domain
  • images Domain
  • insertions Domain
  • interactions Domain
  • library collections Domain
  • transposons Domain
  • recombinant constructs Domain
  • references Domain
  • sequence features Domain
  • stocks Domain
  • Gene Ontology annotations Domain
  • Gene nomenclature Domain
  • Drosophila anatomy annotations Domain
  • Drosophila phenotypic class annotat ... Domain
  • literature citations Domain
  • database of Drosophila researchers Domain
  • genomes for a number of other inver ... Domain
 Drosophila Free
biodbcore-000038 FlyRNAi.org: the Database of the Drosophila RNAi Screening Center: 2012 Update Genome-wide RNAi analysis data in Drosophila
  • information about Drosophila RNAi s ... Domain
  • experimental data from screens with ... Domain
  • hit lists and information about hit ... Domain
 Drosophila melanogaster Free
biodbcore-000004 ALFRED: an allele frequency resource for research and teaching Allele frequencies and DNA polymorphisms
  • gene frequency data on human popula ... Domain
 Homo sapiens Free
biodbcore-000039 Comparative interactomics with Funcoup 2.0 Networks of Functional Coupling of proteins
  • functional coupling interactions be ... Domain
 Arabidopsis thaliana Homo sapiens Mus musculus Drosophila melanogaster Caenorhabditis elegans Saccharomyces cerevisiae Rattus norvegicus Canis familiaris Gallus gallus Ciona instestinalis Free
biodbcore-000040 FungiDB: an integrated functional genomics database for fungi Functional genomics of fungi
  • genome sequence Domain
  • gene models including CDS and predi ... Domain
  • phenotypes Domain
  • Gene Ontology annotations Domain
  • functional annotation (gene product ... Domain
  • gene nomenclature Domain
  • free text descriptions Domain
  • domains (via InterPro) Domain
  • orthologs (via OrthoMCL) Domain
  • protein subcellular location (via S ... Domain
  • protein existence (via Swiss-Prot) Domain
  • citations Domain
  • community annotation Domain
  • high throughput genomics (RNA-Seq, ... Domain
  • polymorphisms (SNPs and Indels) Domain
 Fungi Oomycetes Free
biodbcore-000041 FunTree: A Resource For Exploring The Functional Evolution Of Structurally Defined Enzyme Superfamilies Evolution of novel enzyme functions in enzyme superfamilies
  • evolution of enzyme function Domain
 All Free
biodbcore-000042 GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database T-DNA insertions in Arabidopsis, their flanking sequence tags
  • T-DNA insertion mutants Domain
  • flanking sequence tags (FST) Domain
  • Arabidopsis thaliana genome annotat ... Domain
  • genetic and molecular data on inser ... Domain
  • primer and insertion allele sequenc ... Domain
  • classification of insertions Domain
 Arabidopsis thaliana Free
biodbcore-000043 Gene Expression Atlas update: a value-added database of microarray and sequencing-based functional genomics experiments Gene Expression Atlas
  • meta-analysis based summary statist ... Domain
  • servicing queries for condition-spe ... Domain
 All Free
biodbcore-000045 GeneSigDB: a manually curated database and resource for analysis of gene expression signatures Gene Signature DataBase
  • GeneSigDB is a database of gene sig ... Domain
 All Currently only Human mouse rat Free
biodbcore-000046 HaploReg: a resource for exploring chromatin states, conservation, ENCODE data, and regulatory motif alterations within sets of genetically linked variants. SNP-centric access to chromatin state information
  • chromatin states (inferred from his ... Domain
  • conserved elements (from mammalian ... Domain
  • bound proteins (from ChIP-Seq) Domain
  • DNAse hypersensitivity Domain
  • allele frequencies and linkage dise ... Domain
  • regulatory motif alterations Domain
  • distance to genes (from GENCODE and ... Domain
  • functional annotation (from dbSNP) Domain
 Homo sapiens Free
biodbcore-000047 HGPD: Human Gene and Protein Database, 2012 update Human Gene and Protein Database: experimental results of human proteomics
  • genome sequence,gene models includi ... Domain
  • phenotypes,protein analysis data Domain
  • images of SDS-PAGE Domain
  • subcellular localization for FLJ cD ... Domain
 Homo sapiens Free
biodbcore-000048 HIstome - A relational knowledge-base of human histone proteins and histone modifying enzymes Human histone database
  • histone and histone variants Domain
  • protein sequences Domain
  • promoter sequences Domain
  • alternates gene symbols and aliases Domain
  • histone post translational modifica ... Domain
  • histone modifying enzymes (writers ... Domain
  • free text descriptions Domain
  • literature citations Domain
  • links to other tools and other data ... Domain
 Homo sapiens Free
biodbcore-000049 HmtDB, a genomic resource for Mitochondrion Based Human Variability studies Human mitochondrial genome variability
  • the data captured consist of partia ... Domain
  • human mitochondrial genomes Domain
 Homo sapiens Free
biodbcore-000050 HotRegion: A database of hot spot clusters Database of interaction Hotspots
  • protein-protein interactions Domain
  • interfaces Domain
  • hot spots and hot regions Domain
 All Free
biodbcore-000051 ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria Integrative and Conjugative Elements in Bacteria
  • integrative and conjugative element ... Domain
  • conjugative transposons Domain
  • genomic islands Domain
 Bacteria Free
biodbcore-000052 IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature Intrinsically Disordered proteins with Extensive Annotations and Literature
  • intrinsically disordered regions in ... Domain
  • ordered regions in proteins Domain
  • supporting evidences for both order ... Domain
  • protean segments in intrinsically d ... Domain
  • domain assignments (SCOP and Pfam) Domain
  • post-translational modification sit ... Domain
  • interaction sites Domain
 All Free
biodbcore-000053 IMG/M: the integrated metagenome data management and comparative analysis system Data management and analysis system for metagenomes
  • Archaea Domain
  • Bateria Domain
  • Eukaryota Domain
  • Microbiome Domain
  • Plasmids Domain
  • Viruses Domain
  • Genome sequence Domain
  • gene models including CDS and predi ... Domain
  • Genome, metagenome/sample meta data ... Domain
 Archaea Bacteria Free
biodbcore-000054 The IntAct molecular interaction database in 2012 Protein-protein interaction data
  • molecular interactions Domain
  • protein-protein Interaction Domain
  • protein-small molecule interaction Domain
  • protein-DNA interaction Domain
  • protein-RNA interaction Domain
  • Gene Ontology annotations Domain
  • dtrains Domain
  • domain (via InterPro) Domain
  • litterature citations Domain
  • binding domain position Domain
  • experimental tags Domain
  • Gene nomenclature Domain
  • Gene product names Domain
  • controlled vocabularies Domain
  • free text description Domain
 All Free
biodbcore-000055 InterEvol database : Diving into the structure and evolution of protein complex interfaces Evolution of protein-protein Interfaces
  • structures Domain
  • multiple sequence alignments Domain
 All Free
biodbcore-000056 LegumeIP: An Integrative Database Platform for Comparative Genomics and Transcriptomics of Model Legumes Model Legumes Integrative database Platform
  • genome sequence Domain
  • gene models including CDS and predi ... Domain
  • microarray-based and RNA-seq-based ... Domain
  • Gene Ontology / Uniprot / KEGG -bas ... Domain
 Medicago truncatula Lotus japonicus Free
biodbcore-000057 MACiE: Exploring the diversity of biochemical reactions Mechanism, annotation and classification in enzymes: enzyme reaction mechanisms
  • enzyme mechanism Domain
  • overall reaction Domain
  • CATH domains Domain
  • EC numbers Domain
  • bond changes Domain
  • reaction steps Domain
 All Free
biodbcore-000058 The MAPPER-2 database: A multi-genome catalog of putative transcription factor binding sites Putative transcription factor binding sites in various genomes
  • locations of predicted transcriptio ... Domain
 Homo sapiens Mus musculus Drosophila melanogaster Free
biodbcore-000059 MetaBase - The wiki-database of biological databases Wiki database of biological databases
  • information about biological databa ... Domain
 All Free
biodbcore-000060 MetaCrop 2.0: managing and exploring information about crop plant metabolism Biochemical pathways and enzymes in crop plants
  • biological processes Domain
  • kinetic information Domain
  • stoichiometry Domain
  • cellular components Domain
  • bibliography information Domain
 Hordeum vulgare Triticum aestivum Oryza sativa Zea mays Solanum tuberosum Brassica napus Beta vulgaris Arabidopsis thaliana Medicago truncatula Free
biodbcore-000061 The Mouse Genome Database (MGD): Comprehensive Resource for Genetics and Genomics of the Laboratory Mouse Mouse Genome Database
  • genes, pseudogenes, gene models inc ... Domain
  • cytogenetic markers Domain
  • genomic and genetic maps Domain
  • nucleotide and protein sequence ass ... Domain
  • spontaneous, induced, and genetical ... Domain
  • transgenes Domain
  • QTL Domain
  • mutant and conditional phenotypes Domain
  • mouse models of human disease annot ... Domain
  • Gene Ontology annotations Domain
  • mouse anatomy, mouse phenotype onto ... Domain
  • Gene nomenclature Domain
  • Strains Domain
  • SNPs Domain
  • protein domains (from InterPro) Domain
  • Mammalian orthologs Domain
  • literature citations Domain
  • experimental molecular reagents Domain
  • functional genomics (gene expressio ... Domain
  • biochemical pathways Domain
  • Images of phenotypic mutants and ge ... Domain
  • links to other tools and other data ... Domain
 Mus musculus Free
biodbcore-000062 MimoDB 2.0: a mimotope database and beyond Mimotope database, active site-mimicking peptides selected from phage-display libraries
  • peptide sequence, including mimotop ... Domain
  • combinatorial peptide library Domain
  • target Domain
  • template Domain
  • structure of target-template comple ... Domain
 All Free
biodbcore-000063 MINAS - A Database of Metal Ions in Nucleic AcidS Metal Ions in Nucleic AcidS
  • coordinates of metal ions bound dir ... Domain
 All Free
biodbcore-000064 Minimotif Miner 3.0: database expansion and significantly improved reduction of false positive predictions from consensus sequences Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules
  • residue sequences Domain
  • protein interactions Domain
  • modified residues Domain
  • protein activity Domain
  • modification sites Domain
 Homo sapiens
biodbcore-000065 MINT, the molecular interaction database: 2012 update Molecular INTeraction database
  • molecular interaction Domain
 All Free
biodbcore-000066 MIPModDB: A Central Resource for the Superfamily of Major Intrinsic Proteins Major Intrinsic Protein superfamily Models
  • genes of major intrinsic proteins Domain
  • gene structure Domain
  • homology models Domain
  • selectivity filter residues Domain
  • NPA substitution Domain
  • structure-based sequence alignment Domain
  • phylogenetic tree Domain
  • channel radius profile Domain
  • molecular plot Domain
 All Free
biodbcore-000067 mirEX: a platform for comparative exploration of plant microRNA precursors expression data Plant microRNA Expression data
  • pri-miRNA sequences Domain
  • primer sequences Domain
  • microRNA sequences Domain
  • real-time PCR-based pri-miRNA gene ... Domain
 Arabidopsis thaliana Free
biodbcore-000068 Identifiers.org and MIRIAM Registry: community resources to provide persistent identification Minimal Information Required In the Annotation of Models
  • data collections and resources (com ... Domain
 All Free
biodbcore-000069 MitoMiner: A data warehouse for mitochondrial proteomics data Mitochondrial proteomics data
  • mitochondrial proteomics data from ... Domain
 Eukaryotes Free
biodbcore-000070 modMine: flexible access to modENCODE data Mining of modENCODE data
  • genome sequence Domain
  • gene models, ChIP-seq, ChIP-Chip, p ... Domain
  • Gene Ontology annotations Domain
  • protein domains (via InterPro) Domain
  • orthologs (via inParanoid, TreeFam) Domain
  • proteins (via UniProt) Domain
  • citations Domain
  • phenotypes Domain
 Drosophila melanogaster Caenorhabditis elegans Drosophila ananassae Drosophila mojavensis Drosophila pseudoobscura Drosophila simulans Drosophila virilis Drosophila yakuba Free
biodbcore-000071 MOPED: Model Organism Protein Expression Database Model Organism Protein Expression Database
  • mass spectrometry based proteomics ... Domain
 Homo sapiens Mus musculus Saccharomyces cerveisiae Caenorhabditis elegans Free
biodbcore-000072 Mouse Phenome Database (MPD) Phenotypic and genotypic data from inbred strains of mice
  • phenotype strain survey data Domain
  • genotype data (SNPs, indels, struct ... Domain
  • gene expression strain survey data. Domain
 Mus musculus Free
biodbcore-000074 Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes Network properties of cancer genes
  • cancer genes identified from the Ca ... Domain
  • high-throughput mutational screenin ... Domain
  • whole genome sequencing of cancer t ... Domain
  • duplicability information, based th ... Domain
  • evolutionary origin Domain
  • orthology relationships Domain
  • protein-protein interactions Domain
  • miRNA-gene interactions Domain
  • protein function Domain
 Homo sapiens Free
biodbcore-000075 Newt-omics: A comprehensive repository for omics data from the newt Notophthalmus viridescens Data on red spotted newt Notophthalmus viridescens
  • transcripts Domain
  • peptides Domain
  • cDNA sequencing Domain
  • Gene Ontology annotations Domain
  • functional annotation Domain
  • protein and gene identification Domain
 Notophthalmus viridescens Free
biodbcore-000076 NONCODE v3.0: Integrative annotation of long noncoding RNAs A database of noncoding RNAs
  • non-coding RNAs (except tRNAs and r ... Domain
  • non-coding RNA annotation including ... Domain
 All Free
biodbcore-000077 NucleaRDB: information system for nuclear receptors Families of nuclear hormone receptors
  • nuclear receptor families Domain
  • protein seqeunces Domain
  • mutations Domain
  • ligand binding data Domain
  • structures Domain
  • structure models Domain
  • multiple sequence alignments Domain
  • sequence annotations Domain
 All Free
biodbcore-000078 OGEE: an online gene essentiality database Online GEne Essentiality database
  • published data / unpublished data r ... Domain
  • genome-wide as well as small scale ... Domain
  • text-mining data with manually cura ... Domain
 All Free
biodbcore-000079 Openmods Openmods
  • genome sequence Domain
 Free
biodbcore-000080 OriDB, the DNA Replication Origin Database updated and extended DNA Replication Origin Database
  • published genome-wide replication o ... Domain
 Saccharomyces cerevisiae Schizosaccharomyces pombe Free
biodbcore-000081 The Pfam Protein Families Database Protein families: Multiple sequence alignments and profile hidden Markov models of protein domains
  • evolutionary relationship between p ... Domain
 All Free
biodbcore-000082 PhenoM: a morphological database of essential genes in Saccharomyces cerevisiae Morphological database of essential yeast genes
  • essential genes Domain
  • mutant phenotypes Domain
  • Images of Phenotypic Mutants Domain
  • links to other tools and databases Domain
 Saccharomyces cerevisiae Free
biodbcore-000083 PINA v2.0: Mining Interactome modules Protein Interaction Network Analysis
  • protein-protein interactions Domain
  • interactome modules Domain
  • module annotations including Gene O ... Domain
 Homo sapiens Saccharomyces cerevisiae Caenorhabditis elegans Drosophila melanogaster Mus musculus Rattus norvegicus Free
biodbcore-000084 Plantmetabolomics.org: Mass Spectrometry-based Arabidopsis Metabolomics-database and tools update Arabidopsis metabolomics database
  • mass spectrometry based concentrati ... Domain
  • morphological images using digital ... Domain
  • web generated plot images in jpg an ... Domain
  • data quality plots between the repl ... Domain
  • annotation of metabolites in HTML a ... Domain
 Arabidopsis thaliana Free
biodbcore-000085 PlantNATsDB: a comprehensive database of plant natural antisense transcripts Plant natural antisense transcripts
  • genome sequence Domain
  • gene models Domain
  • Gene Ontology (Biological Process, ... Domain
  • functional non-coding RNAs Domain
 Viridiplantae Free
biodbcore-000086 PLEXdb: Gene Expression Resources for Plants and Plant Pathogens Gene Expression Resources for Plants and Plant Pathogens
  • gene expression data for Affymetrix ... Domain
 Viridiplantae Fungi Oomycetes Nematoda Sinorhizobium meliloti Free
biodbcore-000087 Pocketome: an encyclopedia of small-molecule binding sites in 4D Small-molecule and/or peptide binding pockets in the structural proteome
  • Protein sequences Domain
  • 3D protein structures Domain
  • 3D structural ensembles Domain
  • protein-ligand interactions Domain
  • protein-ligand compatibility Domain
 All Free
biodbcore-000088 Polbase: a repository of biochemical, genetic, and structural information about DNA polymerases Biochemical, genetic, and structural information about DNA polymerases
  • genetics, biochemistry and structur ... Domain
 All Free
biodbcore-000089 PolymiRTS 2.0: Linking polymorphisms in microRNA target sites with human diseases and complex traits Polymorphism in microRNA Target Site
  • The database contains naturally occ ... Domain
 Homo sapiens Mus musculus Free
biodbcore-000090 ProGlycProt: an exclusive repository of experimentally characterized prokaryotic glycoproteins Experimentally characterized Prokaryotic GlycoProteins
  • Organism (bacteria/ archaea) name, ... Domain
  • Organism/Gene/ Protein/ OST Protein ... Domain
 Bacteria Archaea Free
biodbcore-000091 ProRepeat: An Integrated Repository for Studying Amino Acid Tandem Repeats in Proteins Amino acid tandem Repeats in Proteins
  • amino-acid repeats in proteins Domain
 All Free
biodbcore-000092 ProtChemSI: a network of protein-chemical structural interactions Protein-Chemical Structural Interactions
  • protein, small molecules, 3D models ... Domain
 All Free
biodbcore-000093 ProtoNet 6.0: Organizing 10 million protein sequences into a compact hierarchical family tree Hierarchical clustering of UniProt proteins
  • UniProtKB proteins Domain
  • UniRef Domain
  • annotations: Gene Ontology, UniPro ... Domain
  • SCOP Domain
  • CATH Domain
  • Gene3D Domain
  • Pfam Domain
  • SUPERFAMILY Domain
  • ENZYME Domain
  • SMART Domain
  • PRINTS Domain
  • PROSITE Domain
  • PRODOM Domain
  • TIGRFAMs Domain
  • PIRSF Domain
  • SSF Domain
  • PDB Domain
  • PANTHER Domain
  • NCBI Taxonomy Domain
  • links to other tools and other data ... Domain
 All Free
biodbcore-000094 PSCDB: a database for protein structural change upon ligand binding Protein Structural Change upon ligand binding
  • protein structural changes classifi ... Domain
  • ligand-free and ligand-bound struct ... Domain
  • ligand molecules Domain
  • enzyme commission number and cataly ... Domain
  • regions corresponding to DynDom dom ... Domain
  • RMSD of the motion Domain
  • residues exhibiting order/disorder ... Domain
  • results of analysis using the linea ... Domain
  • influence of crystal environments Domain
 All Free
biodbcore-000095 Rhea: a manually curated resource of biochemical reactions EBI's biochemical reaction database
  • biochemical reactions, manually cur ... Domain
 All Free
biodbcore-000096 RNA CoSSMos: Characterization of Secondary Structure Motifs - A searchable database of secondary structure motifs in RNA three dimensional structures RNA Characterization of Secondary Structure Motifs
  • three-dimensional structural parame ... Domain
 All Free
biodbcore-000097 ModelDB ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. ModelDB is tightly coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downl ...
  • neuron Domain
  • ion channel receptor Domain
  • simulation Domain
  • computational biology Domain
  • software Domain
  • neuroscience Domain
  • network Domain
  • behavior Domain
  • multi-scale model Domain
 All open access
biodbcore-000098 SCRIPDB: A Portal for Easy Access to Syntheses, Chemicals, and Reactions In Patents Search for Chemicals and Reactions In Patents
  • full patent text Domain
  • chemical structure files Domain
  • original and computed chemical stru ... Domain
 Free
biodbcore-000099 The SEQanswers wiki: A wiki database of tools for high throughput sequencing analysis. Wiki on all aspects of next-generation genomics
  • free text descriptions and literatu ... Domain
  • software annotations Domain
  • citations Domain
 All
biodbcore-000100 Saccharomyces Genome Database: The genomics resource of budding yeast. Saccharomyces Genome Database
  • reference genome sequence Domain
  • gene models including CDS and predi ... Domain
  • chromosomal features including telo ... Domain
  • mutant phenotypes described using t ... Domain
  • Gene Ontology annotations Domain
  • systematic gene product names Domain
  • gene and chromosomal element nomenc ... Domain
  • strains Domain
  • strain genome sequences Domain
  • plasmids Domain
  • free text description for each locu ... Domain
  • literature annotations defined by e ... Domain
  • protein domains (from InterPro) Domain
  • orthologs Domain
  • literature citations Domain
  • database of yeast researchers Domain
  • functional genomics (gene expressio ... Domain
  • biochemical pathways Domain
  • genetic and physical interactions ( ... Domain
  • images of protein subcellular locat ... Domain
  • portal to other tools and databases ... Domain
 Saccharomyces cerevisiae Free
biodbcore-000101 SMART 7: Recent updates to the protein domain annotation resource Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains
  • protein domain profiles Domain
  • multiple-sequence alignments Domain
  • Hidden Markov Models Domain
 All Free
biodbcore-000102 SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants Phenotypic effects of human coding SNPs
  • protein aggregation Domain
  • chaperone binding Domain
  • free energy predictions Domain
  • mutation analysis Domain
  • GO terms Domain
  • protein sequences Domain
  • structural models Domain
 Free
biodbcore-000103 STAP Refinement of NMR Database: a database of 2,405 refined solution NMR Structures Refined solution NMR structures
  • protein structure files (CHARMM PDB ... Domain
  • Ramachandran KiNG Domain
  • various quality scores Domain
 All Free
biodbcore-000104 STITCH 3: zooming in on protein-chemical interactions Search Tool for Interactions of Chemicals
  • molecular interactions between chem ... Domain
 All Free
biodbcore-000105 The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools The Arabidopsis information resource
  • TAIR contains genetic and genomic d ... Domain
 Free
biodbcore-000106 The Human OligoGenome Resource: A Database for Customized Targeted Resequencing Covering the Human Genome Oligonucleotides for targeted resequencing of the human genome
  • N/A Domain
 Homo sapiens Free
biodbcore-000107 The UCSC Genome Browser database: Extensions and updates 2011 Genome assemblies and annotation
  • genome sequence Domain
  • uniqueness mapping Domain
  • repeats Domain
  • phenotype and disease associations Domain
  • gene and gene predictions Domain
  • mRNA and EST Domain
  • expression Domain
  • regulation Domain
  • comparative genomics Domain
  • variations Domain
 Homo sapiens Takifugu rubripes Free
biodbcore-000108 zfishbook: connecting you to a world of zebrafish revertible mutants Transposon-labeled mutants in zebrafish
  • Spatio-temporal expression of mRFP- ... Domain
  • Zebrafish Anatomical (ZFA) Ontology ... Domain
  • Sequence data for transposon integr ... Domain
  • Loss of function assessment using m ... Domain
 Danio rerio Free
biodbcore-000109 Group II introns database Group II introns database
  • group II introns in eubacteria, arc ... Domain
  • ORF-less introns in eubacteria and ... Domain
  • truncated introns in bacteria and a ... Domain
  • GenBank accession numbers and coord ... Domain
  • species Domain
  • host genes Domain
  • intron DNA sequences Domain
  • exon DNA sequences Domain
  • intron-encoded protein sequences Domain
  • intron-encoded protein phylogenetic ... Domain
  • intron-encoded protein domains Domain
  • intron-encoded protein sizes Domain
  • intron RNA secondary structures Domain
  • secondary structure classes Domain
  • sequences from Bacteria (2) Domain
  • Archaea (2157) Domain
  • a few mitochondrial and chloroplast ... Domain
 Bacteria Archaea Free
biodbcore-000110 AutismKB, an evidence-based knowledgebase of autism genetics Autism genetics KnowledgeBase
  • autism spectrum disorder(ASD) relat ... Domain
 Homo Sapiens Free
biodbcore-000111 BacMap Picture atlas of annotated bacterial genomes
  • genome maps, prophage maps, RNA map ... Domain
 Bacteria Archaea Free
biodbcore-000112 ccPDB Compilation and Creation of datasets from Protein Data Bank
  • ccPDB is a database of datasets ... Domain
  • i) compilation of datasets, ii) cre ... Domain
 Free
biodbcore-000113 CUBE-DB Functional divergence in human protein families
  • Alignment of sequences of multi-mem ... Domain
  • pre-evaluated conservation and spec ... Domain
  • color-coded visualization of the pr ... Domain
  • structure mapping for the pre-evalu ... Domain
 Vertebrata free
biodbcore-000114 Death Domain Database Protein interaction data for Death Domain superfamily
  • Molecular Interactions, 3D structur ... Domain
 Homo Sapiens Mus musculus Rattus norvegicus Canis lups familiaris Danio rerio Free
biodbcore-000115 DiseaseMeth Human disease methylation database
  • Methylation datasets, literature ab ... Domain
 Homo sapiens Free
biodbcore-000116 Gene3D Precalculated structural assignments for whole genomes
  • Protein domains, Protein interactio ... Domain
 All Free
biodbcore-000117 GOLD, Genomes OnLine Database Genomes online database: a listing of completed and ongoing genome projects
  • Metadata for genomic and metagenomi ... Domain
  • google maps Domain
  • trees Domain
 All Free
biodbcore-000118 GWASdb Human genetic variants identified by genome wide association studies
  • Genomic Variants (from GWAS studies ... Domain
 Homo sapiens Free
biodbcore-000119 IGDB.NSCLC: Integrated Genomic Database of Non-Small Cell Lung Cancer Integrated Genomic Database of Non-Small Cell Lung Cancer
  • altered Gene expression, copy numbe ... Domain
 Homo sapiens Free
biodbcore-000120 IndelFR Indel Flanking Region Database
  • Indels and their flanking regions i ... Domain
 All Free
biodbcore-000121 IPAVS Integrated Pathway Analysis and Visualization System
  • Biological pathways Domain
 Homo sapiens Free
biodbcore-000122 MethylomeDB DNA methylation profiles in human and mouse brain
  • DNA methylation Domain
 Homo sapiens Mus musculus Free
biodbcore-000123 miRNEST microRNAs in animal and plant EST sequences
  • miRNA sequences Domain
  • miRNA targets Domain
  • deep sequencing reads aligned to mi ... Domain
  • pre-miRNA secondary structures Domain
  • miRNA regulation, promoters, genomi ... Domain
 Free
biodbcore-000124 MitoZoa, MITOchondrial genome database of metaZOAns Mitochondrial genomes in Metazoa
  • Mitochondrial (mt) genome sequences Domain
  • mitochondrial tRNA, tRNA and CDS se ... Domain
  • mt pseudogenes Domain
  • mt introns Domain
  • mt gene order Domain
  • mt non-coding region (NCR) sequence ... Domain
  • mt gene nomenclature Domain
  • correction of erroneous mt gene ann ... Domain
  • literature citations Domain
 Metazoa excluding Placozoa Free
biodbcore-000125 Nematode.net Parasitic nematode sequencing project
  • Transcript assemblies Domain
  • Genomic assemblies Domain
  • Predicted proteins Domain
  • Functional annotations (KEGG KO Ass ... Domain
  • Gene annotation relevant to drug di ... Domain
  • Gene Orthologies (via OrthoMCL) Domain
  • Nematode gene family domain structu ... Domain
  • Codon usage bias tables Domain
  • Microarray data Domain
  • Nematode species general informatio ... Domain
  • Literature citations Domain
  • links to species-specific external ... Domain
  • Collaborator and Grant listing Domain
 Ancylostoma caninum Ancylostoma ceylanicum Ancylostoma duodenale Ascaris suum Brugia malayi Caenorhabditis elegans Caenorhabditis brenneri Caenorhabditis briggsae Caenorhabditis japonica Caenorhabditis remanei Cooperia oncophora Dictyocaulus viviparus Dirofilaria immitis Ditylenchus africanus Globodera pallida Globodera rostochiensis Haemonchus contortus Heterodera schachtii Heterorhabditis bacteriophora Meloidogyne chitwoodi Meloidogyne hapla Meloidogyne incognita Meloidogyne javanica Meloidogyne paranaensis Necator americanus Oesophagostomum dentatum Onchocerca flexuosa Ostertagia ostertagi Parastrongyloides trichosuri Pristionchus pacificus Radopholus similus Steinernema carpocapsae Strongyloides ratti Strongyloides stercoralis Teladorsagia circumcincta Toxocara canis Trichinella spiralis Trichostrongylus colubriformis Trichuris muris Trichuris vulpis Xiphinema index Zeldia punctata Free
biodbcore-000126 NRG-CING Validated NMR structures of proteins and nucleic acid
  • NMR validation data Domain
 Free
biodbcore-000127 PoSSuM Ligand-binding POcket Similarity Search Using Multiple-Sketches
  • Enumerating similar pairs of known ... Domain
 Free
biodbcore-000128 SitEx Projections of protein functional Sites on Exons
  • cds sequence, protein sequence and ... Domain
  • internal exon and functional identi ... Domain
  • discontinuity coefficient Domain
 Eukaryotes Free
biodbcore-000129 SpliceDisease Links between RNA splicing and disease
  • Gene mutation that cause abnormal R ... Domain
 All free
biodbcore-000130 TarBase6.0 Identification and ranking of targets against neglected tropical diseases
  • miRNAs, genes, miRNA-gene interacti ... Domain
 Homo sapiens Caenorhabditis elegans Rattus norvegicus Mus musculus Medicago truncatula Arabidopsis thaliana Danio rerio KSHV Physcomitrella patens Oryza sativa Glycine max Vitis vinifera Ovis aries Human cytomegalovirus Xenopus laevis Gallus gallus Bos taurus Bombyx mori Drosophila melanogaster Xenopus tropicalis Free
biodbcore-000131 VIRsiRNAdb Experimentally validated Viral siRNA/shRNA
  • siRNA/shRNA sequences, siRNA effica ... Domain
 Free
biodbcore-000132 UMD-BRCA1 BRCA1 and BRCA2 mutations detected in France
  • Mutations/variants of the French po ... Domain
  • bibliography Domain
  • co-occurrence Domain
 Homo Sapiens Free
biodbcore-000133 Gene Wiki An informal collection of pages on human genes
Homo sapiens Free
biodbcore-000134 HFV sequence database Curation is limited and mainly automated. It includes checks for sequence orientation, closest reference sequence, gene and CDS locations, quality of the nucleotide sequence, and NCBI origin database - e.g. patent sequences are automatedally excluded ...
  • viral sequences Domain
 Nairovirus Free
biodbcore-000135 hiPathDB Human Integrated Pathway Database
  • Pathway information Domain
 Homo Sapiens Free
biodbcore-000136 MetaCyc MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...
  • MetaCyc is the largest curated coll ... Domain
 All Free
biodbcore-000137 neXtProt A knowledge for human proteins
  • human protein annotations Domain
  • HTP data with manual filtering Domain
 Homo Sapiens Free
biodbcore-000138 PASS2.4 Structural motifs of protein superfamilies
  • superfamily details,Alignments, Str ... Domain
 All Free
biodbcore-000139 PomBase Genome database on S. pombe
  • Genome sequence Domain
  • experimentally verified and predict ... Domain
  • chromosomal features including telo ... Domain
  • mutant phenotypes Domain
  • Gene Ontology annotations Domain
  • gene product names Domain
  • Gene nomenclature Domain
  • protein domains (from InterPro) Domain
  • protein modifications Domain
  • Orthologs Domain
  • literature citations Domain
  • gene expression Domain
  • genetic and physical interactions ( ... Domain
  • links to other tools and databases ... Domain
 Schizosaccharomyces pombe Free
biodbcore-000140 Predictive Networks (PN) Integration, navigation, visualization, and analysis of gene interaction networks
  • gene lists Domain
  • genomic data or gene-gene interacti ... Domain
  • All data Domain
  • except users private data Domain
  • are available for download as flat ... Domain
  • RDF files) Domain
  • spreadsheets for list of triples (c ... Domain
  • CSV Domain
  • or tab-delimited text files) and im ... Domain
  • PNG Domain
  • and portable document format Domain
  • PDF). Domain
 All Free
biodbcore-000141 PrimerBank: PCR Primers for Gene Expression Detection and Quantification PCR primers for most known human and mouse genes
Mus musculus Homo sapiens Free
biodbcore-000142 Prokaryotic Operon DataBase Prokaryotic Operon DataBase
  • Genome sequences, Cluster of orthol ... Domain
 Bacteria Archaea Free
biodbcore-000143 ProPortal Prochlorococcus marinus and its phages
  • Genome sequences with associated me ... Domain
  • genomic maps Domain
  • gene models including DNA and predi ... Domain
  • functional annotation Domain
  • orthologous gene clusters Domain
  • Affymetrix microarray data on stres ... Domain
  • global ocean metagenomic data with ... Domain
  • wild population frequencies and dyn ... Domain
  • citations. Domain
 Free
biodbcore-000144 Stem Cell Discovery Engine Comparison system for cancer stem cell analysis
  • Experimental descriptions, model or ... Domain
 Mus musculus Homo sapiens Rattus norvegicus Free
biodbcore-000145 SNPedia SNPedia is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). Curati ...
Homo sapiens Free
biodbcore-000146 SubtiWiki Collaborative resource for the Bacillus community
  • Genes, proteins and RNAs of Bacillu ... Domain
 Bacillus subtilis Free
biodbcore-000147 SuperTarget Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins
  • Drug-target interaction data includ ... Domain
 All Free
biodbcore-000148 TDR Targets Identification and ranking of targets against neglected tropical diseases
  • Complete genome sequence Domain
  • basic genome annotation data: gene ... Domain
  • functional annotation data: protein ... Domain
  • structure data (crystal structures ... Domain
  • Expression data Domain
  • Antigenicity data (prediction of pu ... Domain
  • Drug-like compounds structured data ... Domain
  • Compound names and synonyms Domain
  • Identifiers Domain
  • Chemical properties such as structu ... Domain
  • Bioactivity data Domain
  • Associated target organisms or targ ... Domain
  • Compound information source Domain
 Leishmania major Toxoplasma gondii Schistosoma mansoni Brugia malayi Free
biodbcore-000149 TopFIND Protein N- and C-termini and protease processing
  • Protein sequence (via UniProt) Domain
  • protein N termini Domain
  • protein C termini Domain
  • terminal amino acid modifications Domain
  • proteolytic processing Domain
  • protease cleavage site patterns Domain
  • protease substrates Domain
  • Molecular interactions (protease - ... Domain
 Homo Sapiens Mus musculus Arabidopsis thaliana Saccharomyces cerevisiae Eschericha coli Free
biodbcore-000150 TTD, Therapeutic Target Database Therapeutic target database
  • The known efficacy targets and the ... Domain
  • The targeted disease Domain
  • Target-based Quantitative Structure ... Domain
  • Target Validation Information Domain
  • Multi Target Agents Data Domain
  • Drug Combination Information Domain
  • Nature-derived Drugs Domain
  • Information of pathway which drug t ... Domain
  • Target therapeutic class, clinical ... Domain
  • Ligand binding properties Domain
  • Enzyme nomenclature Domain
  • Citations Domain
 All Free
biodbcore-000151 The UCSC Archaeal Genome Browser Archaeal genome assemblies and annotation
  • Genome sequence Domain
  • GC percent graph showing the G+C co ... Domain
  • CRISPR predictions Domain
  • protein-coding gene annotations fro ... Domain
  • protein-coding gene predictions usi ... Domain
  • operon predictions from MicrobesOnl ... Domain
  • independent gene entries at GenBank Domain
  • genomic mappings of Pfam database e ... Domain
  • NCBI conserved domain database sear ... Domain
  • non-coding RNA gene annotations fro ... Domain
  • tRNA gene predictions by tRNAscan-S ... Domain
  • insertion sequence elements annotat ... Domain
  • palindromic transcription factor bi ... Domain
  • promoter and ribosomal binding site ... Domain
  • poly-T motifs as possible transcrip ... Domain
  • RNA sequencing and microarray expre ... Domain
  • high similarity nucleotide alignmen ... Domain
  • paralogs within genome identified b ... Domain
  • multiple sequence alignment similar ... Domain
  • orthologous gene annotations in clo ... Domain
  • phylogenetic breakdown of BLASTP pr ... Domain
 Archaea Plasmodium falciparum Free
biodbcore-000152 VectorBase Invertebrate Vectors of Human Pathogens
  • Annotations, including genes (codin ... Domain
  • Transcriptomic alignments (EST, RNA ... Domain
  • Comparative genomics data Domain
  • Variations Domain
  • Expression data Domain
  • Population genetics Domain
  • Ontologies and Controlled Vocabular ... Domain
 Free
biodbcore-000153 VFDB, Virulence Factor Database Virulence Factors Database
  • Medical important bacterial pathoge ... Domain
  • virulence associated genes, pseudog ... Domain
  • genome sequence Domain
  • literature citations Domain
 Bacteria Free
biodbcore-000155 WikiPathways Wiki for curation of biological pathways
  • Biological pathways Domain
 Anopheles gambiae Arabidopsis thaliana Bos taurus Bacillus subtilis Caenorhabditis elegans Canis familiaris Danio rerio Drosophila melanogaster Equus caballus Gallus gallus Homo sapiens Mus musculus Mycobacterium tuberculosis Oryza sativa Pan troglodytes Rattus norvegicus Saccharomyces cerevisiae Sus scrofa Zea mays Free
biodbcore-000156 WormBase Data repository for C. elegans and C. briggsae: curated genome annotation, genetic and physical maps, pathways
  • Genes, pseudogenes, and gene models ... Domain
  • Sequence Features inc. Operons, Pol ... Domain
  • cytogenetic markers Domain
  • genomic and genetic maps for multip ... Domain
  • nucleotide and protein sequence ass ... Domain
  • spontaneous, induced, and genetical ... Domain
  • reagents: transgenes, antibodies, c ... Domain
  • mutant, conditional, and natural v ... Domain
  • human disease connections, Gene Ont ... Domain
  • nematode anatomy, nematode phenotyp ... Domain
  • gene product names Domain
  • Gene nomenclature Domain
  • strains (also via the Caenorhabditi ... Domain
  • SNPs Domain
  • protein domains (from InterPro) Domain
  • orthologs Domain
  • literature citations Domain
  • experimental molecular reagents Domain
  • gene expression Domain
  • biochemical pathways Domain
  • Images of gene expression Domain
  • links to other tools and other data ... Domain
  • free text concise gene descriptions ... Domain
  • mass spec, protein-protein interact ... Domain
 Trichinella spiralis Caenorhabditis japonica Strongyloides ratti Heterorhabditis bacteriophora Steinernema carpocapsae Meloidogyne hapla Meloidogyne incognita Free
biodbcore-000157 YMDB Yeast Metabolome Database
  • Metabolite information, metabolite ... Domain
 Saccharomyces cerevisiae Free
biodbcore-000158 WholeCellKB - Whole-Cell Knowledge Base WholeCellKB is a collection of open-access model organism databases specifically designed to enable whole-cell models. Currently, WholeCellKB contains a database of Mycoplasma genitalium, a Gram-positive bacterium and common human pathogen. The M. ge ...
  • Prokaryotic genome databases Domain
  • Genomics Databases (non-vertebrate) Domain
 Open access
biodbcore-000159 RhesusBase: a Knowledgebase for the Monkey Research Community A comprehensive online knowledgebase for the monkey research community.
  • Genes, pseudogenes, and gene models ... Domain
 Rhesus macaques Free
biodbcore-000160 Human Ageing Genomic Resources The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools for the biology and genetics of ageing. HAGR features several databases with high-quality, manually-curated data: 1) GenAge, a database of genes associated with ageing i ...
Homo sapiens
biodbcore-000161 PTMcode PTMcode is a web resource for exploration of known and predicted functional associations between post-translational modifications (PTMs) within proteins. In its first release it contains 13 different PTM types (phosphorylation, N-linked glycosylation ...
  • post-translational modification (PT ... Domain
  • functional assosciations between PT ... Domain
 Homo sapiens Mus musculus Rattus norvegicus Bos taurus Gallus gallus Drosophila melanogaster Caenorhabditis elegans Saccharomyces cerevisiae Free
biodbcore-000162 SecReT4 type IV secretion systems (T4SSs) and cognate effectors in bacteria
  • Genome sequence; gene models includ ... Domain
 Bacteria Free
biodbcore-000163 OrtholugeDB OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ort ...
  • orthologues, paralogues and gene tr ... Domain
 Bacteria Archaea
biodbcore-000164 GenomeRNAi The GenomeRNAi database collects RNAi phenotypes recorded in the literature for Homo sapiens and Drosophila melanogaster, as well as details on RNAi reagents. The data is well integrated with information from other resources, allowing comparison with ...
  • RNAi phenotypes and reagents Domain
 Homo sapiens Drosophila melanogaster open access
biodbcore-000165 Dfam We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enabl ...
Homo sapiens
biodbcore-000166 Nordic Control Allele Frequency and Genotype Database Database of SNP genotype control data
Homo sapiens restricted access
biodbcore-000167 Worm Developmental Dynamics Database Quantitative information about cell division dynamics in RNAi-treated C. elegans embryos
  • quantitative information about cell ... Domain
 Caenorhabditis elegans free
biodbcore-000168 MetaboLights MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentratio ...
  • metabolite Domain
  • metabolomics Domain
  • lipidomics Domain
  • mass spectrometry Domain
  • nuclear magnetic resonance spectros ... Domain
 All Free
biodbcore-000169 Aptamer Base Aptamer Base, a database that provides detailed, structured information about the experimental conditions under which aptamers were selected and their binding affinity quantified. The open collaborative nature of the Aptamer Base provides the communi ...
biodbcore-000170 PlantRNA The PlantRNA database compiles 4375 tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. For each tRNA gene, the linear secondary structure is given as well as biological information. This includes 5 ...
biodbcore-000171 IMGT/HLA The IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System.
Creative Commons Attribution-NoDerivs Licence
biodbcore-000172 Immuno-Polymorphism Database The Immuno Polymorphism Database (IPD), was developed in 2003 to provide a centralised system for the study of polymorphism in genes of the immune system
biodbcore-000174 2P2Idb 2P2Idb is a hand-curated structural database dedicated to the modulation of protein-protein interactions (PPIs). It includes all interactions for which both the protein-protein and protein-modulator complexes have been structurally characterized by ...
  • 3D structural data including 3D coo ... Domain
  • protein-protein interaction modulat ... Domain
 open access
biodbcore-000175 MODOMICS MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that ...
  • RNA sequences Domain
  • RNA modifications Domain
  • enzymes acting on RNA Domain
 open access
biodbcore-000176 HOmo sapiens transcription factor COmprehensive MOdel COllection (HOCOMOCO) We present the Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models obtained by careful integration of data from different sources. HOCOMOCO contains 426 non-redundant curated binding models for 401 human ...
  • Other Molecular Biology Databases Domain
 Homo sapiens open access
biodbcore-000177 MetalPDB MetalPDB is a resource aimed at conveying the information available on the three-dimensional structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representat ...
All open access
biodbcore-000178 PRGdb PRGdb is an open and daily update space about plant resistance gene, in which all information about this family is stored, curated and discussed. The purpose of our work is creating a worldwide community working on plant resistance genes with a const ...
Viridiplantae
biodbcore-000179 HemaExplorer The HemaExplorer is a curated database of processed mRNA Gene expression profiles (GEPs) that provides an easy display of gene expression in haematopoietic cells. The HemaExplorer contains GEPs derived from mouse/human haematopoietic stem and pro ...
  • Normalized and batch corrected micr ... Domain
  • Normal hematopoetic cell gene expre ... Domain
  • leukemic bulk bonemarrow gene expre ... Domain
 open access
biodbcore-000015 ChEMBL: a large-scale bioactivity database for drug discovery EMBL's database of bioactive drug-like small molecules
  • small molecules Domain
  • peptides Domain
  • approved drugs Domain
 Free
biodbcore-000180 The Cell: An Image Library-CCDB This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular ...
  • images Domain
  • videos Domain
  • animations Domain
 open access
biodbcore-000001 Genbank GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration , which comprises the DNA DataBank of Japan (DDBJ), the ...
  • nucleic acid sequence Domain
  • Gene Domain
  • Genome Domain
  • nucleic acid Domain
  • DNA sequence Domain
  • DNA sequencing Domain
 All free
biodbcore-000181 mycoCLAP mycoCLAP is a searchable resource for the knowledge and annotation of Characterized Lignocellulose-Active Proteins of fungal origin. Fungi Free
biodbcore-000173 CTD: Comparative Toxicogenomics Database The Comparative Toxicogenomics Database (CTD) advances understanding of the effects of environmental chemicals on human health. Biocurators manually curate chemical-gene, chemical-disease, and gene-disease relationships from the scientific literatur ...
  • Chemical-gene interactions Domain
  • Chemical-disease relationships Domain
  • Gene-disease relationships Domain
 Vertebrata Free
biodbcore-000044 GeneDB: an annotation database for pathogens. Curated database for various Sanger-sequenced genomes
  • pathogen genomes Domain
 Bacteria Free
biodbcore-000182 antibodyregistry.org The Antibody Registry exists to give researchers a way to universally identify antibodies used in publications. The registry lists many commercial antibodies from about 200 vendors, which have been assigned a unique identifier. If the antibody that y ...
Free
biodbcore-000183 Influenza Research Database (IRD) The Influenza Research Database (IRD, http:// www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a co ...
  • Genomics Databases (non-vertebrate) Domain
  • proteomics Domain
  • gene expression Domain
  • 3D protein structures Domain
  • sequence features Domain
 influenza virus Free
biodbcore-000154 Virus Pathogen Database and Analysis Resource (ViPR) The Virus Pathogen Database and Analysis Resource (ViPR, www.ViPRbrc.org) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatic ...
  • Genomics Databases (non-vertebrate) Domain
  • proteomics Domain
  • gene expression Domain
  • 3D protein structures Domain
  • sequence features Domain
 Paramyxoviridae Hepeviridae Poxviridae Coronaviridae caliciviridae flaviviridae picornaviridae togaviridae arenaviridae bunyaviridae filoviridae rhabdoviridae reoviridae herpesviridae Free
biodbcore-000073 NAPP: the Nucleic Acid Phylogenetic Profile Database Nucleic Acid Phylogenetic Profile database
Bacteria Archaea