// Validation / correction to perform: // ID is a lower-case word (no spaces) // EDAM is a valid term from EDAM # dbxref.dat # Information on biological databases # Created: June 2009 (Jon Ison) # Updated: July 2009 (Jon Ison) # # Databases might be cross-referenced from an EMBL entry (db_xref field in feature table) or SwissProt entry (DR line) # # Database identifiers are same as those given on db_xref field / DR line. # Database identifiers and names are taken (where available) from: # http://www.expasy.ch/sprot/userman.html#DR_line (DR line) # http://www.insdc.org/page.php?page=db_xref (db_xref field) # SwissProt identifiers are also given in dbxref.txt (http://www.expasy.org/cgi-bin/lists?dbxref.txt) # # URLs, contact names and email addresses taken from correspondence with database providers. # # Comment lines begin with '#' and can appear anywhere. # # Lines are as follows: # ID Recommended / official unique identifier (from DR line / dbxref.txt, or db_xref field of feature table) # IDOther Other (alternative) identifiers # Name Name / short description (from dbxref.txt) # Desc Description of database (from home page) # Server URL of database server # Cat Database category (from dbxref.txt) # EDAM Database category (from EDAM ontology); any number may be given (Type1;Type2;TypeN) # Link "SP_implicit" (inferable from SP), "SP_explicit" (SP DR line), "db_xref" (from db_xref feature table qualifier) or "None" (more than one token may be given, separated by '|') # LinkNB Notes about link (particularly implicit links) # Query Data type|Data format|Query term|URL (for data retrieval). "Data type" is the type of data retrieved, e.g. "Protein entry". "Data format" is the format, e.g. "Text", "HTML" or "XML". "Query term" is the type of code e.g. "Sequence accession", "EC number" etc. that's used in a database cross-reference from SwissProt / EMBL. "ULR" is used for data retrieval - "%s" in the URL should be replaced by an instance of the query term, e.g. a particular accession number. Where query term has two parts, these are separated by a '|' - in such cases, the URL should have two instances of '%s'. # Contact Name of contact person (or "helpdesk") # Email Email address of contact person or helpdesk # Note Miscellaneous notes # Status "Supported", "Referenced", "Unavailable" # # Please keep entries in alphabetical order ! # ID 2dpage IDOther None Name 2D-PAGE proteome database system for microbial research Desc Two-dimensional gel electrophoresis (2-DE) and mass spectrometry data of diverse microorganisms and other organisms. Server http://www.mpiib-berlin.mpg.de/2D-PAGE Cat None EDAM Two-dimensional gel electrophoresis database; Mass spectrometry database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email jungblut@mpiib-berlin.mpg.de Note None Status None ID 3Dgenomics IDOther None Name 3D-Genomics database of structural annotations for proteomes Desc Structural annotations for the proteomes of just under 100 organisms. Using data derived from public databases of translated genomic sequences, representatives from the major branches of Life are included: Prokaryota, Eukaryota and Archaea. Server http://www.sbg.bio.ic.ac.uk/3dgenomics Cat None EDAM Proteome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email s.ali@imperial.ac.uk Note None Status None ID 3did IDOther None Name 3DID database of 3D interacting domains Desc A collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. Server http://gatealoy.pcb.ub.es/3did/ Cat None EDAM Protein-protein interaction database; Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Amelie Stein Email astein@irbbarcelona.org Note None Status None ID 4dxpress IDOther None Name 4DXpress cross species gene expression pattern database Desc A platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Server http://4dx.embl.de/4DXpress Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Thorsten Henrich Email henrich@embl.de Note None Status None ID 5srrna IDOther None Name 5S rRNA database Desc Information on nucleotide sequences of 5S rRNAs and their genes. Server http://biobases.ibch.poznan.pl/5SData/ Cat None EDAM rRNA database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Maciej Szymanski Email jbarcisz@ibch.poznan.pl Note None Status None ID a1atvar IDOther None Name A1ATVar A1-antitrypsin database Desc Database of human SERPINA1 gene variants leading to alpha1-antitrypsin deficiency Server http://www.goldenhelix.org/a1atvar/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact George Patrinos Email g.patrinos@erasmusmc.nl Note None Status None ID abcdb IDOther None Name Archaeal and bacterial ABC transporter database (ABCdb) Desc Archaeal and bacterial ABC transporter database. Server http://www-abcdb.biotoul.fr Cat None EDAM Membrane protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Yves Quentin Email Yves.Quentin@ibcg.biotoul.fr Note None Status None ID abs IDOther None Name ABS database of binding sites from orthologous promoters Desc Annotated regulatory binding sites from orthologous promoters. Server http://genome.imim.es/datasets/abs2005/ Cat None EDAM Transcription regulatory sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Enrique Blanco Garcia Email eblanco@imim.es Note None Status None ID aceview IDOther None Name AceView genes database Desc A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). Server http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ Cat Not available EDAM mRNA, EST or cDNA database; Genes database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="AceView/WormGenes:vha-6" Status Referenced ID ACLAME IDOther None Name ACLAME classification of mobile genetic elements Desc Collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. Server http://aclame.ulb.ac.be Cat None EDAM Mobile genetic elements database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Raphael Leplae Email raphael@bigre.ulb.ac.be Note None Status None ID ADDA IDOther None Name ADDA protein domain families Desc Domain decomposition and clustering of protein into domain families using automatic domain decomposition algorithm (ADDA). Server http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andreas Heger Email andreas.heger@helsinki.fi Note None Status None ID AffinDB IDOther None Name Affinity database (AffinDB) for protein–ligand complexes Desc Affinity database for protein–ligand complexes Server http://www.agklebe.de/affinity Cat None EDAM Protein-ligand interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Peter Block Email peter.block@staff.uni-marburg.de Note None Status None ID AFTOL IDOther None Name Assembling the Fungal Tree of Life (AFTOL) database Desc Fungal structural and biochemical database. Server http://www.aftol.org/index.php Cat Not available EDAM General fungal database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="AFTOL:959" Status Referenced ID AGD IDOther None Name Ashbya genome database (AGD) Desc A genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from Ashbya gossypii and the model organism Saccharomyces cerevisiae. It also provides access to comparative genomics data from those two fungi as well as Schizosaccharomyces pombe and Neurospora crassa. Server http://agd.vital-it.ch/ Cat Organism-specific databases EDAM Fungal genome database; Comparative genomics database; Gene expression and microarray database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| agd.vital-it.ch/Ashbya_gossypii/geneview?gene=%s Contact Unknown Email Unknown Note None Status Referenced ID AMYPdb IDOther None Name Amyloid precursor proteins database (AMYPdb) Desc Amyloid precursor families and their amino acid sequence signatures. Server http://amypdb.univ-rennes1.fr/ Cat None EDAM Disease-associated protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sandrine Pawlick Email sandrine.pawlicki@laposte.net Note None Status None ID ANPR IDOther None Name Arabidopsis nucleolar protein database (ANPR) Desc Comparative analysis of human and Arabidopsis nucleolar proteomes Server http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/proteome_comparison Cat None EDAM Proteome database; Arabidopsis database; Comparative genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID Antibodypedia IDOther None Name Antibodypedia database of antibodies to human proteins Desc Application-specific validation of publicly available antibodies to human protein targets. Server http://www.antibodypedia.org Cat None EDAM Immunological genes or proteins database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Erik Björling Email erik@biotech.kth.se Note None Status None ID AntiJen IDOther None Name AntiJen database for peptides binding to immunity related proteins Desc Quantitative binding data for peptides binding to MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological protein-protein interactions. AntiJen includes Peptide Library, Copy Numbers and Diffusion Coefficient data. Server http://www.jenner.ac.uk/AntiJen Cat None EDAM Immunological database; Protein-protein interaction database; General peptides database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Darren Flower Email darren.flower@jenner.ac.uk Note None Status None ID ANU-2DPAGE IDOther None Name Australian National University 2-DE database (ANU-2DPAGE) Desc 2-DE PAGE database. Server http://semele.anu.edu.au Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query ANU-2DPAGE entry| HTML| Sequence accession number| http://semele.anu.edu.au/cgi-bin/get-2d-entry?%s Contact Unknown Email Unknown Note Server unavailable - obsolete ? Status Referenced ID AphidBase IDOther None Name Aphid genome database (AphidBase) Desc Aphid genome database Server http://www.aphidbase.com/aphidbase/ Cat None EDAM Invertebrate genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Denis Tagu Email denis.tagu@rennes.inra.fr Note None Status None ID APID IDOther None Name Agile protein interaction data analyzer (APID) Desc Integrated database of protein-protein interactions providing access to all known experimentally validated protein-protein interactions (BIND, BioGRID, DIP, HPRD, IntAct and MINT). Server http://bioinfow.dep.usal.es/apid/index.htm Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dr. Javier DE LAS RIVAS, Carlos PRIETO Email jrivas@usal.es, cprietos@usal.es Note None Status None ID ApiDB IDOther EuPathDB Name Apicomplexan database resources (ApiDB) Desc A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Cryptosporidium, Giardia, Leishmania, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma). Server http://eupathdb.org/eupathdb/ Cat Not available EDAM Unicellular eukaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ApiDB:cgd1_1090" Status Referenced ID ApiDB_CryptoDB IDOther None Name Cryptosporidium genome resources (CryptoDB) Desc Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium. Server http://cryptodb.org/cryptodb/ Cat Not available EDAM Unicellular eukaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ApiDB_CryptoDB:cgd7_20" Status Referenced ID ApiDB_PlasmoDB IDOther None Name Plasmodium genome resources (PlasmoDB) Desc Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium. Server http://plasmodb.org/plasmo/ Cat Not available EDAM Unicellular eukaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ApiDB_PlasmoDB: PF11_0344" Status Referenced ID ApiDB_ToxoDB IDOther None Name Toxoplasma genome resources (ToxoDB) Desc Genomic-scale datasets associated with the eukaryotic pathogens Toxoplasma. Server http://toxodb.org/toxo/ Cat Not available EDAM Unicellular eukaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ApiDB_ToxoDB:49.m00014" Status Referenced ID ApiDB_TrichDB IDOther None Name Trichomonas genome resources (TrichDB) Desc Genomic-scale datasets associated with the eukaryotic Trichomonas. Server http://trichdb.org/trichdb/ Cat Not available EDAM Unicellular eukaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status Referenced ID ApiDB_TriTrypDB IDOther None Name Kinetoplastid genome resources (TriTrypDB) Desc Kinetoplastid genome resources. Server http://tritrypdb.org/tritrypdb/ Cat Not available EDAM Unicellular eukaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status Referenced ID ApiDB_GiardiaDB IDOther None Name Giardia genome resources (GiardiaDB) Desc Genomic-scale datasets for the eukaryotic pathogen Giardia. Server http://giardiadb.org/giardiadb/ Cat Not available EDAM Unicellular eukaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status Referenced ID AppaDB IDOther None Name Pristionchus.org P. pacificus database (AppaDB) Desc Genomic data of P.pacificus, including the physical map, genetic linkage map, EST and BAC end sequence and hybridization data. Server http://www.pristionchus.org Cat None EDAM Vertebrate genome database; Genetic mapping database; mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christoph Dieterich Email christoph.dieterich@tuebingen.mpg.de Note None Status None ID AraC-XylS IDOther None Name AraC-XylS database of a family of Helix-Turn-Helix transcription factors from bacteria Desc A database on a family of Helix-Turn-Helix transcription factors from bacteria. Server http://www.eez.csic.es/arac-xyls/ Cat Protein family/group databases EDAM Specific protein database; Transcription factor and binding site database Link SP_implicit LinkNB All bacterial Swiss-Prot entries with a cross-reference to PROSITE PS01124 Query Unknown| HTML| ???| www.eez.csic.es/arac-xyls/wfichas/%s.HTM Contact Unknown Email Unknown Note None Status Referenced ID AtReactome IDOther None Name Arabidopsis reactome database (AtReactome) Desc A curated knowledgebase of plant biological pathways Server http://www.arabidopsisreactome.org/ Cat None EDAM Biological pathways database; Arabidopsis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Janet Higgins Email janet.higgins@bbsrc.ac.uk Note None Status None ID ARAMEMNON IDOther None Name ARAMEMNON database of plant membrane proteins Desc Plant membrane proteins. Server http://aramemnon.botanik.uni-koeln.de/ Cat None EDAM Membrane protein database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Rainer Schwacke Email rainer.schwacke@uni-koeln.de Note None Status None ID ArchDB IDOther None Name ArchDB database of loop strucutres Desc ArchDB database of loop strucutres. Server http://sbi.imim.es/ Cat None EDAM Protein structural motif database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Baldo Oliva Email boliva@imim.es Note No URL for database server. Status None ID Argonaute IDOther None Name Argonaute database of mammalian microRNAs regulatory function Desc A database on mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their coexpression and proteins known to be involved in miRNA processing. Server http://argonaute.uni-hd.de Cat None EDAM miRNA database; Transcription regulatory sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Benedikt Brors Email b.brors@dkfz.de Note None Status None ID ArrayExpress IDOther None Name ArrayExpress repository for microarray data Desc A public archive for functional genomics data compliant with MIAME- and MINSEQE requirements in accordance with compliant data in accordance with MGED recommendations. Includes gene-indexed expression profiles. Server http://www.ebi.ac.uk/arrayexpress/ Cat Gene expression databases EDAM Gene expression and microarray database Link SP_explicit LinkNB None Query ArrayExpress entry| HTML| ArrayExpress experiment ID| http://www.ebi.ac.uk/arrayexpress/genes/uniprot/%s Contact Alvis Brazma Email brazma@ebi.ac.uk Note None Status Referenced ID ASAP IDOther None Name Systematic annotation package for community analysis of genomes (ASAP) Desc Genome sequences, associated annotations and functional characterization data for E. coli K-12. Server http://www.genome.wisc.edu/tools/asap.htm Cat Not available EDAM Prokaryote genome database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ASAP:ABE-0000006" Status Referenced ID ASC IDOther None Name Active sequence collection (ASC) Desc A collection of active protein sequences, or protein fragments or subsequences, collected in the form of function-oriented databases. The sequences have known biological activity. Server http://bioinformatica.isa.cnr.it/ASC/ Cat None EDAM Protein sequence database; General peptides database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email angelo.facchiano@isa.av.cnr.it Note None Status None ID ASPICdb IDOther None Name Alternative splicing prediction database (ASPICdb) Desc A database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano' et al. 2006), and to the functional annotation of predicted isoforms. Server http://t.caspur.it/ASPicDB/ Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Graziano Pesole Email graziano.pesole@biologia.uniba.it Note None Status None ID ASTD IDOther None Name Alternative splicing and transcript diversity (ASTD) database Desc Alternative splicing and transcript diversity. Server http://www.ebi.ac.uk/astd/ Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Daniel Gautheret Email asd-ebi@ebi.ac.uk Note None Status None ID ATCC IDOther None Name American type culture collection database (ATCC) Desc ATCC cultures and bioproducts. Server http://www.lgcstandards-atcc.org/ Cat Not available EDAM Cell culture database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ATCC:123456". No URL for database server. Status Referenced ID ATCC(in host) IDOther None Name American type culture collection database (ATCC) Desc ATCC cultures and bioproducts Server http://www.lgcstandards-atcc.org/ Cat Not available EDAM Cell culture database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ATCC(in host):123456". No URL for database server. Status Referenced ID ATCC(dna) IDOther None Name American type culture collection database (ATCC) Desc ATCC cultures and bioproducts. Server http://www.lgcstandards-atcc.org/ Cat Not available EDAM Cell culture database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ATCC(dna):123456". No URL for database server. Status Referenced ID ATSD IDOther None Name Aminoacyl-tRNA synthetases database (ATSD) Desc Aminoacyl-tRNA synthetases database. Server http://rose.man.poznan.pl/aars/index.html Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email jbarcisz@ibch.poznan.pl Note None Status None ID AthaMap IDOther None Name AthaMap database of Arabidopsis TFBS predictions Desc Genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana. Server http://www.athamap.de/ Cat None EDAM Transcription regulatory sites database; Transcription factor and binding site database; Arabidopsis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Reinhard Hehl Email r.hehl@tu-braunschweig.de Note None Status None ID AutoPSI IDOther None Name AutoPSI database of predicted SCOP classifications Desc Predicted SCOP classifications. Server http://services.bio.ifi.lmu.de:1046/AutoPSIDB/ Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Fabian Birzele Email birzele@bio.ifi.lmu.de Note None Status None ID Axeldb IDOther None Name Axeldb database of gene expression in Xenopus laevis Desc Gene expression in Xenopus laevis. Server http://www.dkfz.de/en/mol_embryology/axeldb.html Cat None EDAM Gene expression and microarray database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email pollet@infobiogen.fr Note Example cross-reference: /db_xref="Axeldb:32B3.1" Status None ID BAliBASE IDOther None Name BAliBASE benchmark alignment database Desc A benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations. Server http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html Cat None EDAM Sequence alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email poch@igbmc.u-strasbg.fr Note None Status None ID BCSDB IDOther None Name BCSDB database of bacterial carbohydrate structures Desc Bacterial carbohydrate structures. Server http://www.glyco.ac.ru/bcsdb/start.shtml Cat None EDAM Carbohydrate structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Willi von der Lieth Email w.vonderlieth@dkfz-heidelberg.de Note None Status None ID BDGP_EST IDOther None Name Berkeley Drosophila genome project EST database (BDGP_EST) Desc Berkeley Drosophila genome project EST database. Server http://www.fruitfly.org/ Cat Not available EDAM mRNA, EST or cDNA database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="BDGP_EST:123456" Status Referenced ID BDGP_INS IDOther None Name Berkeley Drosophila genome project database: insertion (BDGP_INS) Desc Berkeley Drosophila genome project database: insertion Server http://www.fruitfly.org/ Cat Not available EDAM Invertebrate genome database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="BDGP_INS:123456". Status Referenced ID Bgee IDOther None Name Bgee database for gene expression evolution Desc Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed. Server http://bgee.unil.ch Cat Gene expression databases EDAM Gene expression and microarray database Link SP_explicit LinkNB None Query Bgee gene entry| HTML| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s Query Bgee expression pattern| HTML| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s Query Bgee all expression data| HTML| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=expression&action=data&gene_id=%s Query Bgee ID file| Text| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv Query Bgee ID file with expression data| Text| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv&gene_information=2 Query Bgee ID file with expression data count| Text| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv&gene_information=1 Query Bgee ID file| HTML| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s Query Bgee ID file with expression data| HTML| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=2 Query Bgee ID file with expression data count| HTML| Ensembl gene ID| http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=1 Contact Marc Robinson-Rechavi Email BGee@isb-sib.ch Note None Status Referenced ID BindingDB IDOther None Name BindingDB database of measured binding affinities Desc Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. Server http://www.bindingdb.org/ Cat Other EDAM Protein-ligand interaction database; Drug and drug design database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.bindingdb.org/uniprot/%s Contact Unknown Email Unknown Note None Status Referenced ID BioCyc IDOther None Name BioCyc collection of Pathway/Genome Databases Desc BioCyc collection of Pathway/Genome Databases. Each BioCyc database describes the genome and metabolic pathways of a single organism. This includes Escherichia coli K-12 MG1655 model-organism database (EcoCyc) and Multiorganism metabolic pathway and enzyme database (MetaCyc) Server http://www.biocyc.org/ Cat Enzyme and pathway databases; Metabolic pathways database EDAM Genome database; Enzyme database; Metabolic pathways database Link SP_explicit LinkNB None BioCyc pathway HTML| Pathway ID| http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=5s| BioCyc compound| HTML| Compound ID| http://biocyc.org/ECOLI/NEW-IMAGE?type=COMPOUND&object=%s| BioCyc reaction| HTML| Reaction ID| http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=%s| BioCyc enzyme| HTML| Enzyme ID| http://biocyc.org/ECOLI/new-image?type=ENZYME&object=%s| BioCyc chromosome map| HTML| Chromosome id| http://biocyc.org/ECOLI/substring-search?type=%s BioCyc genome map| HTML| EcoGene Accession Number| http://biocyc.org/ECOLI/new-image?type=LOCUS-POSITION&object=%s| BioCyc genome map| HTML| Map position| http://biocyc.org/ECOLI/substring-search?type=MAPTICK&object=%s Contact Unknown Email Unknown Note None Status Referenced ID biomodels IDOther None Name BioModels database of annotated published models Desc A data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. Server http://www.ebi.ac.uk/biomodels-main/ Cat None EDAM Biological models database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Nicolas Le Novere Email lenov@ebi.ac.uk Note None Status None ID BIPA IDOther None Name BIPA database for interaction between protein and nucleic acid Desc Protein-nucleic acid interactions, with various features of protein-nuleic acid interfaces. Server http://www-cryst.bioc.cam.ac.uk/bipa Cat None EDAM Protein-nucleic acid interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Semin Lee Email semin@cryst.bioc.cam.ac.uk Note None Status None ID BloodExpress IDOther None Name BloodExpress database of gene expression in mouse heamatopoesis Desc BloodExpress integrates 271 individual microarray experiments derived from 15 distinct studies done on most characterised mouse blood cell types. Gene expression information has been discretised to absent/present/unknown calls. Server http://hscl.cimr.cam.ac.uk/bloodexpress/ Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email bg200@cam.ac.uk Note None Status None ID BlotBase IDOther None Name BlotBase Northern blots database Desc Northern blots database. Server http://www.medicalgenomics.org/Databases/BlotBase Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email teufel@uni-mainz.de Note None Status None ID BNDB IDOther None Name Biochemical network database (BNDB) Desc Biochemical network database for analyzing and visualizing complex biochemical networks and processes. Server http://www.bndb.org/index.php?idx=main Cat None EDAM Biological pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jan Küntzer Email kuentzer@bioinf.uni-sb.de Note None Status None ID BOLD IDOther None Name Barcode of Life database (BOLD) Desc An online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community. Server http://www.barcodinglife.org/views/login.php Cat Not available EDAM Genotype / phenotype database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref=Bold:EPAF263 Status Referenced ID BRENDA IDOther None Name BRENDA comprehensive enzyme information system Desc Comprehensive enzyme information. Server http://www.brenda-enzymes.org Cat Enzyme and pathway databases EDAM Enzyme database Link SP_explicit LinkNB None Query BRENDA entry| HTML| EC number| http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s Contact Dietmar Schomburg Email D.Schomburg@tu-bs.de Note None Status Referenced ID BriX IDOther None Name BriX classification of protein fragments Desc BriX is a structural classification of protein fragments. The library comprises fragments ranging from 4 to 14 amino acids that are clustered against 6 different distance thresholds. Server http://brix.vub.ac.be/ Cat None EDAM Protein structure classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Lies Baeten Email lbaeten@vub.ac.be Note None Status None ID BTKbase IDOther None Name BTKbase database of X-linked agammaglobulinemia (XLA) mutations Desc Database of defects in the Bruton tyrosine kinase (BTK) gene causing agammaglobulinemia. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement. Server http://bioinf.uta.fi/BTKbase/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jouni Väliaho Email Jouni.Valiaho@uta.fi Note None Status None ID BuchneraBase IDOther None Name BuchneraBase database of Buchnera species Desc A database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera species. Server http://www.buchnera.org/ Cat None EDAM Prokaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gavin Thomas Email ght2@york.ac.uk Note None Status None ID BuruList IDOther None Name BuruList Mycobacterium ulcerans genome database Desc Mycobacterium ulcerans genome database. Server http://genolist.pasteur.fr/BuruList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/BuruList/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID ButterflyBase IDOther None Name ButterflyBase database of comparative Genomics of Lepidoptera Desc Gene database for butterflies and moths. Server http://www.butterflybase.org Cat None EDAM Invertebrate genome database; Comparative genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Alexie Papanicolaou Email apapanicolaou@ice.mpg.de Note None Status None ID CelegansProject IDOther None Name C. elegans genome project database Desc C. elegans genome project database Server http://www.sanger.ac.uk/Projects/C_elegans Cat None EDAM Invertebrate genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID CADRE IDOther None Name Central aspergillus data repository (CADRE) Desc Central aspergillus data repository (CADRE). Server http://www.cadre-genomes.org.uk/Aspergillus_fumigatus/ Cat None EDAM Organism-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID CandidaDB IDOther None Name CandidaDB database of Candida albicans genome Desc An integrated environment for the analysis of the Candida albicans genome and other genomes from related species belonging to the CTG clade of Saccharomycotina. Server http://genodb.pasteur.fr/cgi-bin/WebObjects/CandidaDB Cat None EDAM Yeast genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christophe d'Enfert Email denfert@pasteur.fr Note None Status None ID CanGEM IDOther None Name CanGEM database of clinical tumor samples and microarray data Desc A public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes. Server http://www.cangem.org/ Cat None EDAM Gene expression and microarray database; Cancer genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ilari Scheinin Email ilari.scheinin@helsinki.fi Note None Status None ID CATdb IDOther None Name Complete Arabidopsis transcriptome database (CATdb) Desc CATdb contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples). The data are released one year after their production. Server http://urgv.evry.inra.fr/CATdb Cat None EDAM Gene expression and microarray database; Arabidopsis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Brunaud Véronique Email brunaud@evry.inra.fr Note None Status None ID CATH IDOther None Name CATH protein structure classification database Desc CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis. Server http://www.cathdb.info/ Cat None EDAM Protein domain classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ian Sillitoe Email sillitoe@biochem.ucl.ac.uk Note None Status None ID CATMA IDOther None Name Arabidopsis transcriptome microarray database (CATMA) Desc The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments. Server http://www.catma.org/ Cat None EDAM Gene expression and microarray database; Arabidopsis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Alain Lecharny Email alain.lecharny@u-psud.fr Note None Status None ID CAZy IDOther None Name Carbohydrate-active enzymes database (CAZy) Desc The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. Server http://www.cazy.org/ Cat Protein family/group databases EDAM Enzyme database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.cazy.org/fam/%s.html Contact Bernard Henrissat Email Bernard.Henrissat@afmb.univ-mrs.fr Note None Status Referenced ID CBS IDOther None Name Genome atlas database (CBS) Desc Summary of genomic information currently available for various organisms. Server http://www.cbs.dtu.dk/services/GenomeAtlas/ Cat None EDAM General genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Kristoffer Rapacki Email rapacki@cbs.dtu.dk Note None Status None ID CC+ IDOther None Name CC+ database of coiled-coil structures Desc A relational database of coiled-coil structures. Server http://coiledcoils.chm.bris.ac.uk/ccplus Cat None EDAM Protein structural motif database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email d.n.woolfson@bristol.ac.uk Note None Status None ID CCSD IDOther None Name Complex carbohydrate structure database (CCSD) Desc Complex carbohydrate structure database. Server http://www.boc.chem.uu.nl/sugabase/carbbank.html Cat None EDAM Carbohydrate structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Alternative ID: CarbBank Status None ID CellCycleDB IDOther None Name Cell cycle database (CellCycleDB) Desc A collection of genes and proteins involved in human and yeast cell cycle. Server http://www.itb.cnr.it/cellcycle/index.html Cat None EDAM Specific protein database; Cell cycle database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Roberta Alfieri Email roberta.alfieri@itb.cnr.it Note None Status None ID CellLineDB IDOther None Name Cell line database (CellLineDB) Desc Information on 4.850 human and animal cell lines that are available in many Italian laboratories and in some of the most important European cell banks and cell culture collections. Server http://bioinformatics.istge.it/interlab/cldb.html Cat None EDAM Cell culture database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Paolo Romano Email paolo.romano@istge.it Note None Status None ID CellMINT IDOther None Name CellMINT database of protein localization and interactions Desc A database tool to integrate protein localization and interaction information Server http://mint.bio.uniroma2.it/CellMINT/welcome.do Cat None EDAM Protein-protein interaction database; Protein localization database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Luana Licata Email luana.licata@gmail.com Note None Status None ID Centrosome:db IDOther None Name Centrosomal proteins database (Centrosome:db) Desc Centrosome:db contains a set of human genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors. Server http://centrosome.dacya.ucm.es/ Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Alberto Pascual-Montano Email pascual@cnb.csic.es Note None Status None ID CEPHdb IDOther None Name CEPH genotype database Desc A database of genotypes for genetic markers that have been typed on the CEPH reference family resource for linkage mapping. Server http://www.cephb.fr/fr/cephdb/ Cat None EDAM Genetic map or linkage database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Emmanuel Tubacher Email webmaster@cephb.fr Note None Status None ID CG IDOther None Name Comparative genometrics (CG) database Desc Devoted to the characterization of complete chromosome sequences by standardized genometric methods, the Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarly focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles. Server http://www2.unil.ch/comparativegenometrics/ Cat None EDAM Comparative genomics database; Chromosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Lionel Guy Email lionel.guy@unil.ch Note None Status None ID CDD IDOther None Name Conserved domain database (CDD) Desc A collection of multiple sequence alignments for ancient domains and full-length proteins. Server http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml Cat Not available EDAM Sequence alignment database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="CDD:02194 Status Referenced ID CGD IDOther None Name Candida genome database (CGD) Desc A resource for genomic sequence data and gene and protein information for Candida albicans. Server http://www.candidagenome.org/ Cat Organism-specific databases EDAM Yeast genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.candidagenome.org/cgi-bin/locus.pl?dbid=%s Contact Unknown Email Unknown Note None Status Referenced ID ChEBI IDOther None Name Database of chemical entities of biological interest (ChEBI) Desc Dictionary of molecular entities focused on small chemical compounds. "Molecular entity" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. Server http://www.ebi.ac.uk/chebi/ Cat None EDAM Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Paula de Matos Email pmatos@ebi.ac.uk Note None Status None ID CiteXplore IDOther None Name CiteXplore literature database Desc CiteXplore combines literature search with text mining tools for biology. Server http://www.ebi.ac.uk/citexplore Cat None EDAM Literature database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Peter Stoehr Email stoehr@ebi.ac.uk Note None Status None ID CleanEx IDOther None Name CleanEx database of gene expression profiles Desc Public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons. Server http://www.cleanex.isb-sib.ch/ Cat Gene expression databases EDAM Gene expression and microarray database Link SP_explicit LinkNB None Query CleanEx entry| HTML| CleanEx entry name| http://www.cleanex.isb-sib.ch/cgi-bin/get_doc?db=cleanex&format=nice&entry=%s Query CleanEx dataset| HTML| CleanEx Dataset code| http://www.cleanex.isb-sib.ch/cgi-bin/get_doc?db=cleanex_ref&format=nice&entry=%s_DOC Contact Philipp Bucher Email Philipp.Bucher@isrec.unil.ch Note None Status Referenced ID CLIMA IDOther None Name Database for cell line integrated molecular authentication (CLIMA) Desc Cell line integrated molecular authentication. Server http://bioinformatics.istge.it/clima/ Cat None EDAM Cell culture database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email paolo.romano@istge.it Note None Status None ID CluSTr IDOther None Name CluSTr protein classification database Desc Automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Server http://www.ebi.ac.uk/clustr/ Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Robert Petryszak Email rpetry@ebi.ac.uk Note None Status None ID CMR IDOther None Name Comprehensive microbial genome resource (CMR) Desc Information on all of the publicly available, complete prokaryotic genomes. Common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. Server http://cmr.tigr.org/ Cat Genome annotation databases EDAM Prokaryote genome database; General genomics database; Link SP_implicit LinkNB All entries from completely sequenced microbial genomes which don't have an explicit link to TIGR CMR gene page| HTML| JCVI identifier| http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=%s CMR gene page| HTML| Genbank ID| http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=SP&acc=%s CMR gene page| HTML| Uniprot Accession http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=protein_id&acc=%s CMR genome page| HTML| Taxonomy ID| http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?taxon_id=%s CMR genome page| HTML| NCBI's Genome Project ID http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?ncbi_project_id=%s Contact Unknown Email Unknown Note None Status Referenced ID COGEME IDOther None Name Phytopathogenic fungi and oomycete EST database (COGEME) Desc Phytopathogenic fungi and oomycete EST database. Server http://cogeme.ex.ac.uk/ Cat None EDAM mRNA, EST or cDNA database; Pathogen database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Darren Soanes Email d.m.soanes@exeter.ac.uk Note None Status None ID ColiBase IDOther None Name ColiBase Enterobactericaiae genome database Desc A database for comparative genome analysis of Enterobactericaiae, e.g. Escherichia, Shigella etc.. Server http://colibase.bham.ac.uk/ Cat None EDAM Comparative genomics database; Prokaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID Colibri IDOther None Name Colibri database Desc A database dedicated to the analysis of the genome of Escherichia coli: Colibri. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Server http://genolist.pasteur.fr/Colibri/ Cat None EDAM Prokaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID CMD IDOther None Name Collagen Mutation Database (CMD) Desc Database of osteogenesis imperfecta and type III collagen variants. Server http://www.le.ac.uk/genetics/collagen/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email ray@le.ac.uk Note None Status None ID Columba IDOther None Name Columba protein structure annotation database Desc Annotations for protein structures from the Protein Data Bank (PDB) from several protein structure related sources, including KEGG and ENZYME. The calculated secondary structure from DSSP is included as well as the protein-fold classification databases SCOP and CATH. Further functional and taxonomic annotation is available from Swiss-Prot, the Gene Ontology (GO) and the NCBI Taxonomy. Server http://www.columba-db.de Cat None EDAM Protein structure annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Kristian Rother Email kristian.rother@charite.de Note None Status None ID COMPLUYEAST-2DPAGE IDOther None Name COMPLUYEAST-2DPAGE database Desc A two-dimensional polyacrilamide gel electrophoresis federated database. Server http://compluyeast2dpage.dacya.ucm.es/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query COMPLUYEAST-2DPAGE entry| HTML| UniProt accession| http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s Query COMPLUYEAST-2DPAGE entry| HTML| Entry name| http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s Contact Unknown Email Unknown Note None Status Referenced ID ConsensusPathDB IDOther None Name ConsensusPathDB database of human functional interaction networks Desc Information on physical molecular interactions, biochemical pathways, and gene regulatory networks in human. Server http://cpdb.molgen.mpg.de/ Cat None EDAM Protein-protein interaction database; Biological pathways database; Gene regulation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Atanas Kamburov Email kamburov@molgen.mpg.de Note None Status None ID CORG IDOther None Name Comparative regulatory genomics database(CORG) Desc Conserved non-coding blocks from a collection of vertebrate species. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements. Server http://corg.molgen.mpg.de Cat None EDAM Transcription regulatory sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christoph Dieterich Email christoph.dieterich@molgen.mpg.de Note None Status None ID CORUM IDOther None Name CORUM comprehensive resource of mammalian protein complexes Desc The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. Server http://mips.gsf.de/genre/proj/corum Cat None EDAM Protein-protein interaction database; Protein localization database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andreas Ruepp Email andreas.ruepp@helmholtz-muenchen.de Note None Status None ID CoryneRegNet4 IDOther None Name CoryneRegNet 4.0 cornyebacterial gene regulation database Desc Reference database for cornyebacterial transcription factors and gene regulatory networks. Server http://www.coryneregnet.de/ Cat None EDAM Gene regulation database; Transcription factor and binding site database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jan Baumbach Email Jan.Baumbach@CeBiTec.Uni-Bielefeld.DE Note None Status None ID COSMIC IDOther None Name Catalogue of somatic mutations in cancer (COSMIC) Desc Somatic mutation information and related details and information relating to human cancers. Server http://www.sanger.ac.uk/genetics/CGP/cosmic/ Cat None EDAM Cancer genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andy Futreal Email paf@sanger.ac.uk Note None Status None ID Cornea-2DPAGE IDOther None Name Human cornea 2-DE database (Cornea-2DPAGE) Desc Two-dimensional polyacrylamide gel electrophoresis federated database. Server http://www.cornea-proteomics.com/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query Cornea-2DPAGE entry| HTML| Sequence accession number| http://www.daimi.au.dk/cgi-jje/2d/2d.cgi#%s Query Cornea-2DPAGE entry| Text| Sequence accession number| http://www.daimi.au.dk/cgi-jje/2d/2d.cgi?ac=%s&format=text&database=cornea Contact Unknown Email Unknown Note None Status Referenced ID CREST IDOther None Name Crop ESTs database (CREST) Desc Sequence, classification, clustering, and annotation data of crop EST projects. Server http://pgrc.ipk-gatersleben.de/cr-est/ Cat None EDAM mRNA, EST or cDNA database; Nucleic acid sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Uwe Scholz Email scholz@ipk-gatersleben.de Note None Status None ID CRISPRdb IDOther None Name Database of clustered regularly interspaced short palindromic repeats (CRISPRdb) Desc Clustered regularly interspaced short palindromic repeats. Server http://crispr.u-psud.fr/ Cat None EDAM Repeat sequence database; Nucleic acid sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christine Pourcel Email christine.pourcel@igmors.u-psud.fr Note None Status None ID CSA IDOther None Name Catalytic site atlas (CSA) Desc Catalytic sites in proteins. Server http://www.ebi.ac.uk/thornton-srv/databases/CSA/ Cat None EDAM Protein functional sites database; Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Nicholas Furnham Email nickf@ebi.ac.uk Note None Status None ID CSD IDOther None Name Cambridge structural database (CSD) Desc Repository of small molecule crystal structures. Server http://www.ccdc.cam.ac.uk/prods/csd/csd.html Cat None EDAM Chemical and small molecule database; Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email support@ccdc.cam.ac.uk Note None Status None ID CSDBase IDOther None Name Database of cold shock domain (CSD)-containing proteins (CSDBase) Desc An interactive database for cold shock domain (CSD) containing proteins and the bacterial cold shock response. Server http://www.chemie.uni-marburg.de/~csdbase/ Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael H.W. Weber Email weberm@staff.uni-marburg.de Note None Status None ID CSS IDOther None Name Carbohydrate structure suite (CSS) Desc Carbohydrate structure suite. Server http://www.glycosciences.de/sweetdb/index.php Cat None EDAM Carbohydrate structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID CuticleDB IDOther None Name Structural proteins of the arthropod cuticle (CuticleDB) Desc A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif responsible for chitin binding in Arthropod cuticle. Server http://biophysics.biol.uoa.gr/cuticleDB/ Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stavros Hamodrakas Email shamodr@biol.uoa.gr Note None Status None ID CycleBase IDOther None Name CycleBase cell cycle database Desc A standardized resource for researchers to inspect and download cell-cycle datasets. Server http://cyclebase.org/ Cat None EDAM Cell cycle database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Soren Brunak Email brunak@cbs.dtu.dk Note Alternative contact : Thomas S. Jensen (skot@cbs.dtu.dk) Status None ID CYGD IDOther None Name Comprehensive yeast genome database (CYGD) Desc Information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. Server http://mips.gsf.de/genre/proj/yeast Cat Organism-specific databases EDAM Biological pathways database; Fungi-specific database; Comparative genomics database Link SP_explicit LinkNB None Query Unknown| HTML| ???| mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=%s Contact Ulrich Gueldener Email u.gueldener@helmholtz-muenchen.de Note None Status Referenced ID CyMoBase IDOther None Name Database for cytoskeletal and motor proteins (CyMoBase) Desc Structure, function and phylogeny of cytoskeletal and motor proteins. Server http://www.cymobase.org Cat None EDAM Specific protein database; Phylogenetic database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dr. Martin Kollmar Email mako@nmr.mpibpc.mpg.de Note None Status None ID Cytokine IDOther None Name Cytokine gene polymorphism database Desc Cytokine gene polymorphism in human disease. Server http://www.nanea.dk/cytokinesnps/ Cat None EDAM Polymorphism database; Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jeffrey Bidwell Email jeff.bidwell@bris.ac.uk Note None Status None ID Dali IDOther None Name Dali database of 3D structure alignments Desc The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighbourhoods and alignments are automatically maintained and regularly updated using the Dali search engine. Server http://ekhidna.biocenter.helsinki.fi/dali/start Cat None EDAM Structure alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Liisa Holm Email holm@ebi.ac.uk Note None Status None ID DBAli IDOther None Name DBAli structure alignment database Desc Database of protein structure alignments. Server http://salilab.org/DBAli/ Cat None EDAM Structure alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Marc A. Marti-Renom Email mmarti@cipf.es Note None Status None ID DBD IDOther None Name Transcription factor prediction database Desc Predicted transcription factors in completely sequenced genomes. Server http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Home Cat None EDAM Transcription factor and binding site database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Derek Wilson Email dbd@mrc-lmb.cam.ac.uk Note None Status None ID dbEST IDOther None Name dbEST database of EST sequences Desc dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Server http://www.ncbi.nlm.nih.gov/dbEST/ Cat Not available EDAM mRNA, EST or cDNA database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="dbEST:BP535535" Status Referenced ID dbProbe IDOther Probe Name NCBI Probe database of nucleic acid reagents (dbProbe) Desc Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. Server http://www.ncbi.nlm.nih.gov/probe Cat Not available EDAM Molecular probes or primers database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="dbProbe:38" Status Referenced ID dbSNP IDOther None Name Database of single nucleotide polymorphism (dbSNP) Desc Single nucleotide polymorphisms. Server http://www.ncbi.nlm.nih.gov/SNP/ Cat Polymorphism databases EDAM Polymorphism database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="dbSNP:4647", /db_xref="dbSNP:rs133073" Status Referenced ID dbSTS IDOther None Name STS database maintained at the NCBI (dbSTS) Desc An NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. All STS sequences are incorporated into the STS Division of GenBank. Server http://www.ncbi.nlm.nih.gov/dbSTS/ Cat Not available EDAM Genetic map or linkage database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="dbSTS:456789", /db_xref="dbSTS:BV210161" Status Referenced ID DDBJ IDOther None Name DNA databank of Japan (DDBJ) Desc A nucleotide sequence database. Server http://www.ddbj.nig.ac.jp/ Cat Sequence databases EDAM Nucleotide sequence database Link SP_implicit LinkNB All Swiss-Prot entries with >=1 EMBL Xref. Query Unknown| HTML| ???| ??? Contact Unknown Email Unknown Note None Status Referenced ID Degradome IDOther None Name Degradome database of mammalian proteases and diseases Desc Mammalian proteases and diseases. Server http://degradome.uniovi.es/ Cat None EDAM Disease-associated protein database; Disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Carlos López-Otín Email clo@uniovi.es Note None Status None ID Diamond IDOther None Name Blackfan Anemia mutation database (Diamond) Desc Blackfan Anemia mutation database. Server http://www.dbagenes.unito.it Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email irma.dianzani@med.unipmn.it Note None Status None ID diArk IDOther None Name diArk eukaryotic genome research database Desc Database for eukaryotic sequencing projects. Server http://www.diark.org/diark/ Cat None EDAM Eukaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Martin Kollmar Email mako@nmr.mpibpc.mpg.de Note None Status None ID Diatom IDOther None Name Diatom EST database Desc A searchable databases of diatom ESTs (expressed sequence tags) that can be used to explore diatom biology. Diatoms are photosynthetic unicellular eukaryotes that play an essential role in marine ecosystems. On a global scale, they generate around one fifth of the oxygen we breathe. Server http://avesthagen.sznbowler.com/ Cat None EDAM mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Chris Bowler Email cbowler@biologie.ens.fr Note None Status None ID dictyBase IDOther None Name Dictyostelium discoideum online informatics resource (dictyBase) Desc Database for the biology and genomics of the social amoeba Dictyostelium discoideum. Server http://dictybase.org/ Cat Organism-specific databases EDAM Organism-specific database; Unicellular eukaryote genome database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| dictybase.org/db/cgi-bin/gene_page.pl?primary_id=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="dictyBase:DDB0191090" Status Referenced ID DIMA IDOther None Name DIMA domain interaction map Desc Resource for functional and physical interactions among conserved protein-domains, including experimental data and computational predictions. Server http://mips.gsf.de/genre/proj/dtest/index.html Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Philipp Pagel Email p.pagel@gsf.de Note None Status None ID DIP IDOther None Name Database of interacting proteins (DIP) Desc The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Server http://dip.doe-mbi.ucla.edu/ Cat Protein-protein interaction databases EDAM Protein-protein interaction database Link SP_explicit LinkNB None Query Unknown| HTML| ???| dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s Contact Unknown Email Unknown Note None Status Referenced ID DiProDB IDOther None Name Dinucleotide property database (DiProDB) Desc The Dinucleotide Property Database is designed to collect and analyse thermodynamic, structural and other dinucleotide properties. The table presenting all the dinucleotide properties can be pruned and rearranged by different criteria. The database contains different export and analysis functions. Server http://diprodb.fli-leibniz.de/ Cat None EDAM Nucleic acid physicochemical properties database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Maik Friedel Email maikfr@fli-leibniz.de Note None Status None ID DisProt IDOther None Name Database of protein disorder (DisProt) Desc A curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Server http://www.disprot.org/ Cat 3D structure databases EDAM Protein structure database Link SP_explicit LinkNB None Query DisProt entry| HTML| DisProt ID| www.disprot.org/protein.php?id=%s Contact Unknown Email Unknown Note None Status Referenced ID DNAReplication IDOther None Name DNA replication database Desc A Resource for eukaryotic DNA replication. Server http://www.dnareplication.net/ Cat None EDAM DNA replication database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email s.cotterill@sgul.ac.uk Note None Status None ID Dockground IDOther None Name Dockground database for molecular modelling of protein interactions Desc Benchmarks, decoys, templates and other knowledge resources for docking. Server http://dockground.bioinformatics.ku.edu/ Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dominique Douguet Email douguet@cbs.cnrs.fr Note None Status None ID DOMINO IDOther None Name DOMINO domain peptide interactions database Desc Database of annotated experiments describing interactions mediated by protein-interaction domains. Server http://mint.bio.uniroma2.it/domino/search/searchWelcome.do Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gianni Cesareni Email cesareni@uniroma2.it Note None Status None ID DoOP IDOther None Name Database of orthologous promoters (DoOP) Desc A database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. Server http://doop.abc.hu/ Cat None EDAM Transcription regulatory sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Endre Barta Email barta@abc.hu Note None Status None ID DOSAC-COBS-2DPAGE IDOther None Name DOSAC-COBS 2D-PAGE database Desc Two-dimensional polyacrylamide gel electrophoresis federated database. Server http://www.dosac.unipa.it/2d/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query DOSAC-COBS-2DPAGE entry| HTML| Sequence accession number| http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=O43818 Contact Unknown Email Unknown Note None Status Referenced ID DPDB IDOther None Name DPDB Drosophila polymorphism database Desc A collection of all the existing polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity. Server http://bioinf3.uab.cat/dpdb/dpdb.asp Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sonia Casillas Email sonia.casillas@uab.cat Note None Status None ID DPVweb IDOther None Name DPVweb database of plant viruses Desc Information about viruses, viroids and satellites of plants, fungi and protozoa, with some additional data on related animal viruses. Server http://www.dpvweb.net/ Cat None EDAM General virus database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Adams Email mike.adams@bbsrc.ac.uk Note None Status None ID DRC IDOther None Name Database of ribosomal crosslinks (DRC) Desc Biochemical data about structure of the ribosome from ribosomal cross-linking. Server http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/ Cat None EDAM Ribosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Pavel V. Baranov Email baranov@howard.genetics.utah.edu Note None Status None ID DrugBank IDOther None Name DrugBank drug and drug target database Desc Detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. Server http://www.drugbank.ca/ Cat Other EDAM Drug and drug design database; Chemical and small molecule database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.drugbank.ca/drugs/%s Contact Unknown Email Unknown Note None Status Referenced ID DSD IDOther None Name DSD database of dehydrogenase stereospecificities Desc Database on dehydrogenases, a class of enzymes that catalyze reversible oxidation-reduction reactions and are largely dependent on nicotinamide adenine dinucleotide coenzymes: NAD(H) or NADP(H). Server http://www.jenner.ac.uk/DSD/ Cat None EDAM Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Darren R. Flower Email Darren.Flower@jenner.ac.uk Note None Status None ID DSMM IDOther None Name Database of simulated molecular motions (DSMM) Desc Movies showing biomolecular motions that have been generated by computer simulation. Molecules simulated include proteins, DNA, RNA, sugars and lipids. Simulation techniques include Molecular Dynamics, Brownian Dynamics and automated docking procedures. Server http://atlas.villa-bosch.de/dbase/dsmm/ Cat None EDAM Molecular motions database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email rebecca.wade@eml.villa-bosch.de Note None Status None ID DSSP IDOther None Name DSSP secondary structure database Desc Secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). Server http://swift.cmbi.ru.nl/gv/dssp/ Cat None EDAM Protein structure annotation database; Protein secondary structure and alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gert Vriend Email Vriend@cmbi.ru.nl Note None Status None ID DynaProt IDOther None Name DynaProt 2D proteome database of Lactococcus lactis Desc 2D reference maps and summarized protein information for Lactococcus lactis. Server http://www.wzw.tum.de/proteomik/lactis/ Cat None EDAM Two-dimensional gel electrophoresis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Oliver Drews Email oliver.drews@wzw.tum.de Note None Status None ID EASED IDOther None Name EASED database Desc Extended Alternatively Spliced EST Database Server http://eased.bioinf.mdc-berlin.de/ Cat None EDAM mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Heike Pospisil Email pospisil@zbh.uni-hamburg.de Note None Status None ID EBI Genomes IDOther None Name EBI genomes database Desc Whole genomes from the EBI. Server http://www.ebi.ac.uk/genomes Cat None EDAM Genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID EcID IDOther None Name E Coli predicted protein interactions database (EcID) Desc Results of running an "in silico 2 hybrid system" for all the possible pairs among E. coli proteins. Server http://www.pdg.cnb.uam.es/i2h/info.html Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Eduardo Andres Leon Email eandres@cnio.es Note None Status None ID ECO2DBASE IDOther 2DBase-Ecoli| EC-2D-GEL Name 2D-PAGE database of Escherichia coli Desc This Database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on varios functional categories enabling quick and subsequent analysis. Server http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query ECO2DBASE entry| HTML| Sequence accession number| http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?%s Contact Unknown Email Unknown Note None Status Referenced ID EcoGene IDOther None Name EcoGene database of Escherichia coli sequence and function Desc Information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. Server http://ecogene.org/ Cat Organism-specific databases EDAM Prokaryote proteome database; Prokaryote genome database; Organism-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.ecogene.org/geneInfo.php?eg_id=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="EcoGene:EG11277" Status Referenced ID EchoBASE IDOther None Name EchoBASE: an integrated post-genomic database for E. coli Desc A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. Server http://www.york.ac.uk/res/thomas/ Cat Organism-specific databases EDAM Organism-specific database; Prokaryote genome database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.york.ac.uk/res/thomas/Gene.cfm?recordID=%s Contact Unknown Email Unknown Note None Status Referenced ID emap IDOther None Name Edinburgh Mouse Atlas project database (emap) Desc The emap Atlas is a digital Atlas of mouse embryonic development. It is based on the definitive books of mouse embryonic development by Theiler (1989) and Kaufman (1992) yet extends these studies by creating a series of interactive three-dimensional computer models of mouse embryos at successive stages of development with defined anatomical domains linked to a stage-by-stage ontology of anatomical names. Server http://genex.hgu.mrc.ac.uk/ Cat None EDAM Embryology and development database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Duncan Davidson Email Duncan.Davidson@hgu.mrc.ac.uk IDOther None Name Electron Density Server PDB electron density map Note None Status None ID EDS IDOther None Name Electron density server at Uppsala university (EDS) Desc A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are provided for assessing the goodness-of-fit between the deposited models (structures) and the experimental data represented by the electron density calculated using the models and their associated structure factor amplitudes. Server http://eds.bmc.uu.se/eds/ Cat None EDAM Tertiary structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gerard Kleywegt Email gerard@xray.bmc.uu.se Note Alternative server: http://eds.bmc.uu.se/ Status None ID EGA IDOther None Name European genome-phenome Archive (EGA) Desc A repository for all types of genotype experiments, including case control, population, and family studies, including SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods. Server http://www.ebi.ac.uk/ega/ Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ilkka Lappalainen Email ilkka@ebi.ac.uk Note None Status None ID eggNOG IDOther None Name Database of evolutionary genealogy of genes: non-supervised Orthologous Groups (eggNOG) Desc Orthologous groups of genes. The orthologous groups are annotated with functional descriptions, which are derived by identifying a common denominator for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. Server http://eggnog.embl.de/ Cat None EDAM Nucleic acid sequence classification database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Lars Juhl Jensen Email Lars.Jensen@embl-heidelberg.de Note None Status None ID ELM IDOther None Name Eukaryotic linear motif resource (ELM) Desc A resource for predicting functional sites in eukaryotic proteins. Putative functional sites are identified by patterns (regular expressions). To improve the predictive power, context-based rules and logical filters are applied to reduce the amount of false positives. Server http://elm.eu.org/ Cat None EDAM Protein functional sites database; Protein sequence motif or profile database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Toby Gibson Email toby.gibson@embl.de Note None Status None ID EMBL IDOther EMBL-Bank Name The EMBL Nucleotide Sequence Database (EMBL) Desc Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. Server http://www.ebi.ac.uk/embl/ Cat Sequence databases EDAM Nucleotide sequence database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.ebi.ac.uk/htbin/expasyfetch?%s Contact Rolf Apweiler Email kulikova@ebi.ac.uk Note None Status Referenced ID EMDB IDOther None Name Electron microscopy databank (EMDB) Desc Deposition and retrieval network for cryoEM map, model and associated metadata, as well as a portal for software tools for standardized map format conversion, map, segmentation and model assessment, visualization, and data integration. Server http://www.emdatabank.org Cat None EDAM Electron microscopy database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christoph Best Email best@ebi.ac.uk Note None Status None ID EMGlib IDOther None Name Enhanced microbial genomes library (EMGlib) Desc A database devoted to the completely sequenced bacterial genomes and the yeast genome. Starting from the sequences available in the "genome" division of GenBank, EMGlib improves and corrects the annotations. Server http://pbil.univ-lyon1.fr/emglib/emglib.html Cat None EDAM Yeast genome database; Prokaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Perrière Bessières Email perriere@biomserv.univ-lyon1.fr Note None Status None ID ENA IDOther None Name European nucleotide short read and trace archive (ENA) Desc European nucleotide short read and trace archive (ENA). Server http://www.ebi.ac.uk/embl Cat None EDAM Nucleotide sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Guy Cochrane Email cochrane@ebi.ac.uk Note None Status None ID EndoNet IDOther None Name Endocrine networks database (EndoNet) Desc Information about endocrine networks. Using information about hormones' donor and acceptor cells a network is built that represents hormonal signaling pathways as a bipartite graph comprising hormones and tissues as node classes. The involved components, the intercellular information flow and the inhibition or activation effects are displayed Server http://endonet.bioinf.med.uni-goettingen.de/index.jsp Cat None EDAM Signalling pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Edgar Wingender Email apo@bioinf.med.uni-goettingen.de Note None Status None ID Ensembl IDOther None Name Ensembl eukaryotic genome annotation project Desc Genome databases for vertebrates and other eukaryotic species. Server http://www.ensembl.org/ Cat Genome annotation databases EDAM Genome annotation database; Eukaryote genome database Link SP_explicit| db_xref LinkNB None Query Ensembl gene| HTML| Ensembl ID| http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s Contact Xose Fernandez Email xose@ebi.ac.uk Note Example cross-reference: /db_xref="ENSEMBL:HUMAN-Clone-AC005612", /db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102" Status Referenced ID ENZYME IDOther None Name Enzyme nomenclature database (ENZYME) Desc A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. Server http://www.expasy.org/enzyme/ Cat Enzyme and pathway databases EDAM Enzyme database Link SP_implicit LinkNB All Swiss-Prot entries that contain >=1 EC numbers in their description lines Query ENZYME entry| Text| EC number| http://www.expasy.ch/enzyme/1.5.99.11.txt Query ENZYME entry| HTML| EC number| http://www.expasy.ch/enzyme/1.5.99.11 Contact G P Moss Email g.p.moss@qmul.ac.uk Note None Status Referenced ID EPD IDOther None Name Eukaryotic promoter database (EPD) Desc An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Server http://www.epd.isb-sib.ch/ Cat None EDAM Transcription regulatory sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Philipp Bucher Email epd@mail.isrec.isb-sib.ch Note None Status None ID ERIC IDOther None Name Enteropathogen resource integration center (ERIC) Desc Annotated enterobacterial genome and associated information. Server http://www.ericbrc.org/portal/eric/ Cat Not available EDAM Prokaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note db_xref="ERIC:ABY-0246137" Status Referenced ID eSLDB IDOther None Name Eukaryotic subcellular localization database (eSLDB) Desc A database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions. Server http://gpcr.biocomp.unibo.it/esldb/ Cat None EDAM Membrane protein database; Protein localization database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andrea Pierleoni Email piero@biocomp.unibo.it Note None Status None ID ESP-SOLDB IDOther None Name Genomic generic database applied to tomato fruit quality (ESP-SOLDB) Desc Genomic generic database applied to tomato fruit quality (ESP-SOLDB). Server http://www.bitlab-es.com/espsol Cat None EDAM Plant-specific database; Genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Oswaldo Trelles Email ots@ac.uma.es Note None Status None ID ESTHER IDOther None Name ESTHER database on alpha/beta hydrolases Desc Database for the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases. Server http://bioweb.ensam.inra.fr/ESTHER/general?what=index Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Arnaud Chatonnet Email chatonne@ensam.inra.fr Note None Status None ID euHCVdb IDOther None Name European Hepatitis C virus database Desc European Hepatitis C virus database. Server http://euhcvdb.ibcp.fr/euHCVdb/ Cat Organism-specific databases EDAM General virus database Link SP_explicit LinkNB None Query Unknown| HTML| ???| http://euhcvdb.ibcp.fr/euHCVdb/jsp/HCVResultTextForm.jsp?AC=%S Contact Christophe Combet Email c.combet@ibcp.fr Note None Status Referenced ID EuroPhenome IDOther None Name EuroPhenome mouse phenotype resource Desc Software system for capturing, storing and analysing raw phenotyping data from SOPs contained in EMPReSS. Server http://www.europhenome.org Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ann-Marie Mallon Email a.mallon@har.mrc.ac.uk Note None Status None ID EVEREST IDOther None Name Evolutionary ensembles of recurrent segments Desc An automatic identification and classification of protein domains. Server http://www.everest.cs.huji.ac.il Cat None EDAM Protein domain classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Elon Portugaly Email elonp@cs.huji.ac.il Note None Status None ID ExplorEnz IDOther None Name The ExplorEnz enzyme database Desc The Enzyme Database with data from the IUBMB Enzyme Nomenclature List. Formatting of chemical names according to IUPAC standards is preserved. Server http://www.enzyme-database.org/ Cat None EDAM Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email amcdonld@tcd.ie Note None Status None ID EXProt IDOther None Name Database for proteins with an experimentally verified function (EXProt) Desc A non-redundant database of protein sequences for which the function has been experimentally verified, from Pseudomonas Community Annotation Project, from E. coli genome and proteome database and from division Prokaryotes of the EMBL Nucleotide Sequence Database. Server http://www.cmbi.kun.nl/EXProt/ Cat None EDAM Prokaryote proteome database; Protein sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email ursing@cmbi.kun.nl Note None Status None ID ExTopoDB IDOther None Name Experimentally derived topological models of transmembrane proteins (ExTopoDB) Desc Experimentally derived topological models of transmembrane proteins. Server http://bioinformatics.biol.uoa.gr/ExTopoDB Cat None EDAM Membrane protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Georgios Tsaousis Email gtsaousis@biol.uoa.gr Note None Status None ID EyeSite IDOther None Name EyeSite eye protein database Desc An information and modelling resource for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity. Server http://eyesite.cryst.bbk.ac.uk/ Cat None EDAM Specific protein database; Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID FaCD IDOther None Name Familial cancer database (FaCD) Desc Database to assist clinicians and genetic counselors in making a genetic differential diagnosis in cancer patients, as well as in becoming aware of the tumor spectrum associated with hereditary disorders that have already been diagnosed in their patients. Server http://www.facd.info Cat None EDAM Cancer genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Rolf Sijmons Email r.h.sijmons@medgen.umcg.nl Note None Status None ID FANTOM_DB IDOther None Name Database of functional annotation of mammalian Genome (FANTOM_DB) Desc Functional annotation of mammalian genome. Server http://fantom.gsc.riken.jp/4/ Cat Not available EDAM Genome annotation database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="FANTOM_DB:0610005A07" Status Referenced ID FASTDB IDOther None Name Friendly alternative splicing and transcripts database (FASTDB) Desc Alternative splicing and transcripts database. Server http://www.fast-db.com Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact DE LA GRANGE Email pierre.delagrange@genosplice.com Note None Status None ID FCP IDOther None Name Functional coverage of the proteome (FCP) Desc Functional coverage of the proteome. Server http://cgl.imim.es/fcp/ Cat None EDAM Proteome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jordi Mestres Email jmestres@imim.es Note None Status None ID FGDB IDOther None Name Fusarium graminearum genome database (FGDB) Desc Information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Fusarium graminearum (Anamorph of Gibberella zeae). Server http://mips.gsf.de/genre/proj/FGDB/ Cat None EDAM Biological pathways database; Fungal genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ulrich Gueldener Email u.gueldener@helmholtz-muenchen.de Note None Status None ID FINDBase IDOther None Name FINDBase Desc Information about the frequency of different mutations leading to inherited disorders in various populations around the globe. Server http://www.findbase.org/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact George Patrinos Email g.patrinos@erasmusmc.nl Note None Status None ID FireDB IDOther None Name Database of functionally important residues from protein structures (FireDB) Desc A database of Protein Data Bank structures, ligands and annotated functional site residues. Server http://firedb.bioinfo.cnio.es/index.php Cat None EDAM Protein functional sites database; Protein-ligand interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gonzalo López Email glopez@cnio.es Note None Status None ID FLAGdb++ IDOther None Name FLAGdb++ a database for the functional analysis of the Arabidopsis genome Desc Integrative database around plant genomes. Server http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/index.shtml Cat None EDAM Genome annotation database; Arabidopsis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sébastien Aubourg Email aubourg@evry.inra.fr Note None Status None ID FLIGHT IDOther None Name FLIGHT database integrating genomic and high-throughput data Desc Database for the integration of data from high-throughput experiments carried out in Drosophila cell culture. It includes phenotypic information from published cell-based RNAi screens, gene expression data from Drosophila cell lines, protein interaction data, together with novel tools to cross-correlate these diverse datasets, such as the phenotype clustering tool Shuffle. Server http://flight.licr.org/ Cat None EDAM Protein-protein interaction database; Gene expression and microarray database; Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Buzz Baum Email buzz@ludwig.ucl.ac.uk Note None Status None ID FlyBase IDOther None Name Database of genetic and molecular data of Drosophila Desc A Database of Drosophila genes and genomes. Server http://flybase.bio.indiana.edu/ Cat Organism-specific databases EDAM Invertebrate genome database; Organism-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| flybase.bio.indiana.edu/.bin/fbidq.html?%s Contact Rachel Drysdale Email gelbart@morgan.harvard.edu Obsolete abbreviation: DMAP Note http://flybase.org/ (alternative URL). Example cross-reference: /db_xref="FLYBASE:FBgn0000024" Status Referenced ID FlyMine IDOther None Name FlyMine Drosophila genome database Desc An integrated database for Drosophila and Anopheles genomics. Server http://www.flymine.org Cat None EDAM Invertebrate genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gos Micklem Email g.micklem@gen.cam.ac.uk Note None Status None ID FLYSNP IDOther None Name SNPs database for Drosophila (FLYSNP) Desc Database of a high-density genome-wide map of single nucleotide polymorphisms (SNPs) and high-throughput assays for SNP genotyping. Server http://flysnp.imp.ac.at/ Cat None EDAM Polymorphism database; Genome map database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Doris Chen Email doris.chen@univie.ac.at Note None Status None ID FlyTF IDOther None Name FlyTF Drosophila Site-Specific Transcription Factor Database Desc Information on the manual curation of FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database Server http://www.flytf.org Cat None EDAM Transcription factor and binding site database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Boris Adryan Email ba255@cam.ac.uk Note None Status None ID FlyView IDOther None Name FlyView database Desc An image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database. Server http://flyview.uni-muenster.de/ Cat None EDAM Organism-specific database; Embryology and development database; Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christian Klimbt Email flyview@nwz.uni-muenster.de Note None Status None ID FPSPD IDOther None Name Functional protein sequence pattern database (FPSPD) Desc Accumulates functional protein sequence patterns derived from the structurally-aligned homologous families in the HOMSTRAD database. Server http://torsa.bioc.cam.ac.uk/~fpspd/home_d.html Cat None EDAM Protein functional sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ricardo Núñez Miguel Email ricardo@cryst.bioc.cam.ac.uk Note None Status None ID FunCoup IDOther None Name FunCoup database Desc FunCoup is a statistical framework of data integration for finding functional coupling (FC) between proteins. It transfers information from model organisms (M. musculus, D. melanogaster, C. elegans, S. cerevisiae etc.) via orthologs found by InParanoid program. Data of different sources and various natures, such as contacts of whole proteins and individual domains, mRNA and protein expression, localization in tissues and cellular compartments, miRNA and TF targeting, similar phylogenetic profiles etc. are collected and evaluated. Server http://funcoup.sbc.su.se/ Cat None EDAM Biological pathways database; Gene expression and microarray database; Protein localization database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Erik Sonnhammer Email Erik.Sonnhammer@sbc.su.se Note None Status None ID FungalGenomeSize IDOther None Name Fungal genome size database Desc Fungal genome size database Server http://www.zbi.ee/fungal-genomesize/ Cat None EDAM General genomics database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Bellis Kullman Email fungal-genomesize@zbi.ee Note None Status None ID FUNPEP IDOther None Name FUNPEP information system for "low complexity sequence regions" Desc Information system for "low complexity sequence regions". Server http://swift.cmbi.kun.nl/swift/FUNPEP/info/ Cat None EDAM Low complexity sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email weare@lionbioscience.com Note None Status None ID FunShift IDOther None Name FunShift database Desc A compilation of function shift analysis performed between subfamilies in protein families. Server http://FunShift.cgb.ki.se Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID FunSimMat IDOther None Name FunSimMat database of semantic and functional similarity Desc A resource of semantic and functional similarity values. It allows searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB. Server http://funsimmat.bioinf.mpi-inf.mpg.de/ Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Mario Albrecht Email mario.albrecht@mpi-inf.mpg.de Note None Status None ID FUNYBASE IDOther None Name FUNYBASE fungal phylogenomic database Desc Database dedicated to the analysis of fungal proteins extracted from complete public fungal genomes, and their classification in clusters of orthologs. Server http://genome.jouy.inra.fr/funybase/funybase_start.cgi Cat None EDAM Proteome database; Protein sequence classification database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email sylvain.marthey@jouy.inra.fr Note None Status None ID FusionDB IDOther None Name FusionDB database of bacterial and archaeal gene fusion events Desc A database of bacterial and archaeal gene fusion events. Server http://www.igs.cnrs-mrs.fr/FusionDB/ Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Karsten Suhre Email Karsten.Suhre@igs.cnrs-mrs.fr Note None Status None ID G2Cdb IDOther None Name Genes to cognition database (G2Cdb) Desc Genes to Cognition (G2C) is a neuroscience research programme that studies genes, the brain and behaviour in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Server http://www.genes2cognition.org Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email sg3@sanger.ac.uk Note None Status None ID GabiPD IDOther None Name GabiPD: primary database of plant integrative biology Desc Primary database of plant integrative biology. Server http://www.gabipd.org/ Cat None EDAM General plant database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Diego Mauricio Riaño-Pachón Email riano@mpimp-golm.mpg.de Note Example cross-reference: /db_xref="GABI:HA05J18" Status None ID GABI-Kat IDOther None Name GABI-Kat tags mutagenised A. thaliana Desc Generation of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants. Server http://www.gabi-kat.de/ Cat None EDAM Genetic map or linkage database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Bernd Weisshaar Email bernd.weisshaar@uni-bielefeld.de Note None Status None ID GBIFFI IDOther None Name Global biodiversity information facility, Finland (GBIFFI) Desc Global biodiversity data. Server http://www.gbif.fi Cat None EDAM Ecological database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Hannu Saarenmaa Email hannu.saarenmaa@helsinki.fi Note None Status None ID GenAtlas IDOther None Name GenAtlas human gene database Desc Information on gene mapping and genetic diseases. Server http://www.dsi.univ-paris5.fr/genatlas/ Cat Organism-specific databases EDAM Human genes, mutation and disease database; Genome map database; Organism-specific database; Disease database Link SP_implicit LinkNB Human sequence entries with >=1 gene name and >=1 HGNC X-ref. Query Unknown| HTML| ???| www.dsi.univ-paris5.fr/genatlas/fiche.php?symbol=%s Contact Unknown Email Unknown Note None Status Referenced ID GenBank IDOther None Name GenBank nucleotide sequence database Desc Nucleotide sequence database. Server http://www.ncbi.nlm.nih.gov/ Cat Sequence databases EDAM Nucleotide sequence database Link SP_implicit LinkNB All Swiss-Prot entries with >=1 EMBL Xref. Query Unknown| HTML| ???| http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=%s EDAM Nucleotide sequence database DOI 10.1093/nar/gkl1031| Contact Unknown Email Unknown Note Server URL is to NCBI homepage. Status Referenced ID Gene3D IDOther None Name Gene3D structural and functional annotation of protein families Desc Gene3D structural and functional annotation of protein families incorporates several different sources including CATH, DRUGBANK, PFAM etc. Server http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ Cat Family and domain databases EDAM Protein sequence classification database Link SP_explicit LinkNB None Query Gene3D entry| HTML| CATH Family| http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?family=%s Query Gene3D entry| HTML| CATH Domain id| http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?domain_id=%s Contact Corin Yeats Email yeats@biochemistry.ucl.ac.uk Note None Status Referenced ID GeneAnnot IDOther None Name Affymetrix probe-sets database (GeneAnnot) Desc GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Server http://bioinfo2.weizmann.ac.il/geneannot/ Cat None EDAM Molecular probes or primers database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Marilyn Safran Email marilyn.safran@weizmann.ac.il Note None Status None ID GeneCards IDOther None Name GeneCards database of human genes, protein and diseases Desc GeneCards is a searchable, integrated database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs & compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents. Server http://www.genecards.org/ Cat Human genes and diseases database; Disease database EDAM Protein-protein interaction database; Biological pathways database; Polymorphism database; Human genes, mutation and disease database; Genome annotation database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.genecards.org/cgi-bin/carddisp.pl?gc_id=%s Contact Marilyn Safran Email marilyn.safran@weizmann.ac.il Note None Status Referenced ID GeneDB IDOther None Name GeneDB database from Sanger Institute Pathogen Sequencing Units Desc Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units). Server http://www.genedb.org/ Cat None EDAM Genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Robin Houston Email rh11@sanger.ac.uk Note Example cross-reference: /db_xref="GeneDB:SPCC285.16c" Status None ID GeneDB_Spombe IDOther None Name S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs. Desc Sequence data and annotation/curation for Schizosaccharomyces pombe Server http://www.genedb.org/genedb/pombe/ Cat Organism-specific databases EDAM Genome annotation database; Yeast genome database; Functional RNA database; Organism-specific database; Mobile genetic elements database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.genedb.org/genedb/Search?submit=Search+for&name=%s&organism=pombe&desc=yes Contact Unknown Email Unknown Note None Status Referenced ID GeneExpressionTooth IDOther None Name Gene expression in tooth database Desc Gene expression in tooth database Server http://bite-it.helsinki.fi/ Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Pekka Nieminen Email pekka.nieminen@helsinki.fi Note None Status None ID GeneFarm IDOther None Name GeneFarm annotation of Arabidopsis thaliana gene and protein families Desc Structural and functionnal annotation of plant gene and protein families by a network of experts. Server http://urgi.versailles.inra.fr/Genefarm/index.htpl Cat Organism-specific databases EDAM Protein sequence classification database; Arabidopsis database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s Contact Sebastien Aubourg Email Unknown Note None Status Referenced ID GeneID IDOther None Name GeneID database of genes from NCBI RefSeq genomes Desc Database of genes from NCBI RefSeq genomes Server http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Cat Genome annotation databases EDAM Genes database; Genome annotation database Link SP_explicit| db_xref LinkNB None Query GeneID gene list| HTML| Keyword| http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=%s Query GeneID gene list| HTML| Sequence accession number| http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[accn] Query GeneID gene list| HTML| Gene name (symbol)| http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[sym] Query GeneID gene list| HTML| PubMed ID| http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[PMID] Query GeneID gene list| HTML| GO terms or identifiers| http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="cell+adhesion"[GO] Query GeneID gene list| HTML| Chromosome name;Species name| http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[CHR]+AND+%s[ORGN] Query GeneID gene list| HTML| EC number| http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[EC] Contact Unknown Email Unknown Note Example cross-reference: /db_xref="GeneID:3054987" Status Referenced ID GeneLoc IDOther None Name GeneLoc map for human chromosomes Desc An integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources. Server http://genecards.weizmann.ac.il/geneloc/index.shtml Cat None EDAM Genome map database; Chromosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email marilyn.safran@weizmann.ac.il Note None Status None ID GeneNest IDOther None Name GeneNest transcript clusters Desc GeneNest is a comprehensive visualization of gene indices of various organisms. Each gene is represented by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artefacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms. Server http://genenest.molgen.mpg.de/ Cat None EDAM Gene structure database; Nucleic acid sequence classification database; mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email T.Beissbarth@dkfz-heidelberg.de Note None Status None ID GeneNote IDOther None Name GeneNote human genes and their expression profiles Desc A database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. Server http://genecards.weizmann.ac.il/genenote/ Cat None EDAM Gene expression and microarray database; Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email orit.shmueli@weizmann.ac.il Note None Status None ID GeneSapiens IDOther None Name GeneSapiens human transcriptome database Desc Human transcriptome database. Server http://www.genesapiens.org/ Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email sami.k.kilpinen@helsinki.fi Note None Status None ID GeneSNPs IDOther None Name SNPs Program at the University of Washington Desc Gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS (National Institute of Evironmental Health Sciences). This database provides a graphical view of all available SNP data including allele frequencies and genotypes in select populations. This information is key in selecting the polymorphic sites needed to examine disease risk in human population studies. Server http://egp.gs.washington.edu/ Cat Polymorphism databases EDAM Polymorphism database; Genome map database; Human genes, mutation and disease database Link SP_implicit LinkNB All entries with >= HGNC X-ref and an RT line starting with "NIEHS-SNPs" Query Unknown| HTML| ???| egp.gs.washington.edu/data/%s/ Contact Unknown Email Unknown Note None Status Referenced ID GeneTide IDOther None Name GeneTide database Desc An automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes. Server http://genecards.weizmann.ac.il/genetide/ Cat None EDAM mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID Génolevures IDOther None Name Génolevures 18 yeast genomes Desc Annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes. Server http://www.genolevures.org/ Cat None EDAM Yeast genome database; Sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email david.sherman@labri.fr Note None Status None ID GenoList IDOther None Name GenoList comparative analysis of microbial genomes Desc An integrated environment for the analysis of microbial genomes. Server http://genolist.pasteur.fr/GenoList Cat None EDAM Prokaryote genome database; ; Comparative genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ivan Moszer Email moszer@pasteur.fr Note None Status None ID GenomeReviews IDOther None Name GenomeReviews database of completely sequenced genomes Desc Annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Server http://www.ebi.ac.uk/GenomeReviews/ Cat Genome annotation databases EDAM Genome annotation database Link SP_explicit LinkNB None Query Unknown| HTML| ???| ??? Contact Unknown Email lmorris@ebi.ac.uk Note None Status Referenced ID GenomicThreadingDatabase IDOther None Name Genomic threading database Desc Structural annotations of proteomes, translated from the genomes of key organisms. Server http://bioinf.cs.ucl.ac.uk/GTD/ Cat None EDAM Proteome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email l.mcguffin@cs.ucl.ac.uk Note None Status None ID GenomeRNAi IDOther None Name GenomeRNAi database Desc Phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. Server http://www.dkfz.de/signaling2/rnai/ernai.html Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Boutros Email m.boutros@dkfz.de Note None Status None ID Germlinep53Mutations IDOther None Name Germline p53 Mutations database Desc Germline p53 mutations Server http://www.lf2.cuni.cz/projects/germline_mut_p53.htm Cat None EDAM Cancer genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Petra Goetz Email Petr.goetz@lfmotol.cuni.cz Note None Status None ID GermOnline IDOther None Name Gametogenesis and reproducutive tissue expression Desc High-throughput expression data relevant for germline development and fertility across species. Server http://www.germonline.org/ Cat Gene expression databases EDAM Gene expression and microarray database Link SP_explicit LinkNB None Query GermOnline entry| HTML| Species name; Gene name| http://www.germonline.org/%s/geneview?gene=%s Query GermOnline entry| HTML| Species name; SGD gene identifier| http://www.germonline.org/%s/geneview?db=core|gene=%s Contact Mike Primig Email michael.primig@unibas.ch Note Species name in URL is full name with spaces replaced with underscores. Gene name is any identifier for the gene. Status Referenced ID GlycateBase IDOther None Name GlycateBase glycation prediction Desc Glycation of amino groups of lysines in mammalian proteins. Server http://www.cbs.dtu.dk/databases/GlycateBase-1.0/ Cat None EDAM Protein functional sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Morten Bo Johansen Email mbj@cbs.dtu.dk Note None Status None ID GlycomeDB IDOther None Name Glycome database Desc Integrated database of carbohydrate structure and annotations, incorporating data from all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank). Server http://www.glycome-db.org/About.action Cat None EDAM Carbohydrate structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email r.ranzinger@dkfz.de Note None Status None ID GlycoSuiteDB IDOther None Name GlycoSuiteDB glycan database Desc An annotated and curated relational database of glycan structures. Server http://glycosuitedb.expasy.org/ Cat PTM databases EDAM Carbohydrate structure database Link SP_explicit LinkNB None Query Unknown| HTML| ???| glycosuitedb.expasy.org/glycosuite/results?prot_swissprot=%s|results_index=protein|ig_hist=1 Contact Unknown Email Unknown Note HTML is unlikely to change in near future, but whole database might be supplanted. Status Referenced ID GO IDOther None Name Gene ontology Desc Controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members. THe aim is to standardize representations of gene and gene product attributes across species and databases. Server http://www.geneontology.org/ Cat Ontologies EDAM Ontology Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.ebi.ac.uk/ego/QuickGO?mode=display&entry=%s Contact Midori Harris Email midori@ebi.ac.uk Note Example cross-reference: /db_xref="GO:123" Status Referenced ID GOA-UniProt IDOther None Name Gene ontology annotation database for UniProt (GOA-UniProt) Desc Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). Server http://www.ebi.ac.uk/goa Cat None EDAM Proteome annotation database Link db_xref LinkNB None Query Unknown| Unknown | Gene Ontology Annotation Database Identifier| None Contact Emily Dimmer Email edimmer@ebi.ac.uk Note Example cross-reference: /db_xref=" GOA :P01100" Status None ID GOLD IDOther None Name Genomes database Desc Information on complete and ongoing genome projects, as well as metagenomes and metadata. Server http://www.genomesonline.org/ Cat None EDAM General genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Nikos Kyrpides Email nckyrpides@lbl.gov Note None Status None ID GOLDDB IDOther None Name GOLDDB database of genomics of lipid-associated disorders Desc GOLDDB integrates disparate information on the function and properties of genes and their protein products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders including non-insulin dependent diabetes, various hyperlipidemias, high blood pressure and atherosclerosis. Server https://gold.tugraz.at/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email zlatko.trajanoski@tugraz.at Note None Status None ID GoPubMed IDOther None Name GoPubMed ontology-based literature search Desc Ontology-based literature search. Server http://www.gopubmed.org Cat None EDAM Literature database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Schroeder Email ms@biotec.tu-dresden.de Note None Status None ID GPCRDB IDOther None Name Information system for G protein-coupled receptors (GPCRs) Desc GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases. Server http://www.gpcr.org/7tm/ Cat Protein family/group databases EDAM Membrane protein database; Protein-ligand interaction database Link SP_implicit LinkNB All Swiss-Prot entries that contains a CC line of the type "-!- SIMILARITY: Belongs to the G-protein coupled receptor ..." Query Unknown| HTML| ???| ??? Contact Unknown Email Unknown Note None Status Referenced ID GPCR_NaVa IDOther None Name GPCR natural variants database Desc Sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). Server http://nava.liacs.nl/index.html Cat None EDAM Membrane protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email j.kazius@lacdr.leidenuniv.nl Note None Status None ID gpDB IDOther None Name A database of G-proteins,GPCRs,effectors and their interactions Desc Relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search. Server http://bioinformatics.biol.uoa.gr/gpDB/ Cat None EDAM Membrane protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Margarita Theodoropoulou Email mtheodo@biol.uoa.gr Note None Status None ID Gramene IDOther None Name Gramene database for comparative grass genomics Desc Gramene adds value to public data sets of grass genomes and helps to compare, identify and understand genes, pathways and phenotypes from different grass species. Server http://www.gramene.org/ Cat Organism-specific databases EDAM Comparative genomics database; Genotype / phenotype database; Organism-specific database; Biological pathways database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.gramene.org//db/protein/protein_search?acc=%s Contact Unknown Email Unknown Note None Status Referenced ID GreenPhylDB IDOther None Name A phylogenomic database for plant comparative genomics Desc Database for comparative genomic analyses of Arabidopsis thaliana and Oryza sativa full genomes. Server http://greenphyl.cirad.fr/cgi-bin/greenphyl.cgi Cat None EDAM Comparative genomics database; Phylogenetic database; Arabidopsis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Perin Christophe Email perin@cirad.fr Note None Status None ID GRIN IDOther None Name Germplasm Resources Information Network (GRIN) Desc GRIN taxonomic data provide the structure and nomenclature for accessions of the National Plant Germplasm System (NPGS). All families and genera of vascular plants and species from throughout the world are represented, especially economic plants and their relatives. Information on scientific and common names, classification, distribution, references, and economic impacts are provided. Server http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl Cat Not available EDAM General plant database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="GRIN:1005973" Status Referenced ID GyDB IDOther None Name Gypsy database of mobile genetic elements Desc Molecular diversity and evolutionary relationships of mobile genetic elements, viruses and related host genes. Server http://gydb.uv.es/index.php/Main_Page Cat None EDAM Virus-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Carlos llorens Email carlos.llorens@uv.es Note None Status None ID H-InvDB IDOther None Name H-InvDB integrated database of human genes and transcripts Desc From extensive analyses of all human transcripts, H-InvDB provides curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. Server http://www.h-invitational.jp/ Cat Organism-specific databases EDAM Gene expression and microarray database; Polymorphism database; Metabolic pathways database; Human genes database; Organism-specific database; Functional RNA database; Gene structure database; Protein localization database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.jbirc.aist.go.jp/hinv/soup/pub_Locus.pl?locus_id=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="H-InvDB:HIT000000001", /db_xref="H-InvDB:HIX0000001" Status Referenced ID HaemB IDOther None Name Haemophilia B Mutation Database Desc point mutations and short additions and deletions in the factor IX gene Server http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Peter Green Email p.green@umds.ac.uk Note None Status None ID HAMAP IDOther None Name High-quality automated and manual annotation of microbial proteomes (HAMAP) Desc A system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins. Server http://www.expasy.org/sprot/hamap/ Cat Family and domain databases EDAM Proteome annotation database; Protein sequence classification database Link SP_explicit LinkNB None Query HAMAP family members| HTML| HAMAP ID| http://www.uniprot.org/uniprot/?query=%22hamap+MF_%s&format=tab&columns=id Query HAMAP family sequences| HTML| HAMAP ID| http://www.uniprot.org/uniprot/?query=%22hamap+MF_%s&format=txt Query HAMAP family rules| HTML| HAMAP ID| http://www.expasy.org/unirule/MF_%s Query HAMAP family rules| Text| HAMAP ID| http://www.expasy.org/unirule/MF_%s.txt Contact Unknown Email Unknown Note None Status Referenced ID HAMASTERS IDOther None Name Hemophila A FVIII mutation database (HAMASTERS) Desc Resources for Haemophilia A / factor VIII (FVIII) genetic variation at the DNA and protein level. Server http://europium.csc.mrc.ac.uk/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email geoffrey.kemball-cook@csc.mrc.ac.uk Note None Status None ID HCAD IDOther None Name Human chromosome aberration database (HCAD) Desc Human chromosome aberration database. Server http://www.pdg.cnb.uam.es/UniPub/HCAD/ Cat None EDAM Chromosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID HepSeq IDOther None Name HepSeq international repository for Hepatitis B virus strain data Desc Molecular, clinical and epidemiological database for hepatitis B infection. Server http://www.hpa-bioinfodatabases.org.uk/hepatitis_open/main.php Cat None EDAM General virus database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Saravanamuttu Gnaneshan Email saravanamuttu.gnaneshan@hpa.org.uk Note None Status None ID HERVd IDOther None Name Human endogenous retrovirus database (HERVd) Desc A database compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects, for screening human genome for HERVs. The HERV database now contains retroviruses from more than 90 % of the human genome. Server http://herv.img.cas.cz/ Cat None EDAM Virus-specific database; Nucleotide sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID HGDP-CEPH IDOther None Name HGDP-CEPH diversity panel database (HGDP-CEPH) Desc Polymorphic marker genotypes generated by users of the DNAs of the HGDP-CEPH Diversity Panel. Server http://www.cephb.fr/fr/hgdp/ Cat None EDAM Genetic map or linkage database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Emmanuel Tubacher Email hgdp-cephdb@cephb.fr Note None Status None ID HGMD IDOther None Name Human gene mutation database (HGMD) Desc Known (published) gene lesions responsible for human inherited disease. Server http://www.hgmd.org Cat None EDAM Human genes, mutation and disease database; Disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Peter Stenson Email stensonPD@cardiff.ac.uk Note None Status None ID HGNC IDOther Genew Name Human gene nomenclature database (HGNC) Desc Database of unique and meaningful names for all human genes. Server http://www.genenames.org/ Cat Organism-specific databases EDAM Organism-specific database; General genomics database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.genenames.org/data/hgnc_data.php?hgnc_id=%s Contact Elspeth Bruford Email elspeth@ebi.ac.uk Note Example cross-reference: /db_xref="HGNC:2041" Status Referenced ID HGT-DB IDOther None Name Horizontal gene transfer-database (HGT-DB) Desc Genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. Server http://genomes.urv.es/HGT-DB/ Cat None EDAM Phylogenetic database; Prokaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email vallve@quimica.urv.es Note None Status None ID HGVbaseG2P IDOther None Name Human Genome Variation database of Genotype-to-Phenotype information (HGVbaseG2P) Desc Centralized compilation of summary level findings from genetic association studies, both large and small. Server http://www.hgvbaseg2p.org Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Anthony Brookes Email ajb97@leicester.ac.uk Note None Status None ID HIC-Up IDOther None Name Hetero-compound information (HIC-Up) Desc Structural biology of hetero-compounds ("small molecules"). Server http://xray.bmc.uu.se/hicup/ Cat None EDAM Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email gerard@xray.bmc.uu.se Note None Status None ID HmtDB IDOther None Name Human mitochondrial genomic database (HmtDB) Desc Human mitochondrial genomic database based on variability studies supporting population genetics and biomedical research. Server http://www.hmtdb.uniba.it/ Cat None EDAM Mitochondrial genes and proteins database; Genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Marcella Antimonelli Email m.attimonelli@biologia.uniba.it Note None Status None ID HOGENOM IDOther None Name Database of homologous sequences from complete genomes (HOGENOM) Desc Homologous genes from fully sequenced organisms. It allows selection of sets of homologous genes among species, and visualisation of multiple alignments and phylogenetic trees. It is useful for comparative sequence analysis, phylogeny, molecular evolution studies and to get a view of what is known about a peculiar gene family. Server http://pbil.univ-lyon1.fr/databases/hogenom3.html Cat Phylogenomic databases EDAM Sequence alignment database; Genes database; Phylogenetic database; Comparative genomics database Link SP_explicit LinkNB None Query Unknown| HTML| ???| pbil.univ-lyon1.fr/cgi-bin/acnuc-ac2tree?query=%s&db=HOGENOM Contact Guy Perrière Email perriere@biomserv.univ-lyon1.fr Note None Status Referenced ID HOINVGEN IDOther None Name Homologous invertebrate genes database (HOINVGEN) Desc Homologous invertebrate genes. It allows selection of sets of homologous genes among invertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family. Server http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html Cat None EDAM Genes database; Sequence alignment database; Phylogenetic database; Comparative genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Arndt von Haeseler Email paulseni@uni-duesseldorf.de Note None Status None ID HOVERGEN IDOther None Name Homologous vertebrate genes database (HOVERGEN) Desc Homologous vertebrate genes. It allows selection of sets of homologous genes among vertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family. Server http://pbil.univ-lyon1.fr/databases/hovergen.html Cat Phylogenomic databases EDAM Genes database; Sequence alignment database; Phylogenetic database; Comparative genomics database Link SP_explicit LinkNB None Query Unknown| HTML| ???| pbil.univ-lyon1.fr/cgi-bin/acnuc-ac2tree?query=%s&db=HOVERGEN Contact Unknown Email Unknown Note None Status Referenced ID HomeoboxPage IDOther None Name HomeoboxPage homeobox gene page Desc Information relevant to homeobox genes, in particular about classification/evolution. Server http://www.biosci.ki.se/groups/tbu/homeo.html Cat None EDAM Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Thomas R. Bürglin Email burglin@ubaclu.unibas.ch Note None Status None ID HomoMINT IDOther None Name HomoMINT inferred human protein interaction network Desc Database for extending protein-protein interactions experimentally verified in models organisms, to the orthologous proteins in Homo sapiens. Server http://mint.bio.uniroma2.it/HomoMINT Cat None EDAM Protein-protein interaction database; Biological pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andrew Chatr-aryamontri Email aryamontri@hotmail.com Note None Status None ID HOMSTRAD IDOther None Name Homologous structure alignment database (HOMSTRAD) Desc A curated database of annotated, structure-based sequence alignments for homologous protein families, from all known protein structure. Server http://tardis.nibio.go.jp/homstrad/ Cat None EDAM Sequence alignment database; Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Tom Blundell Email tom@cryst.bioc.cam.ac.uk Note None Status None ID Hoppsigen IDOther None Name Homologous processed pseudogenes database (Hoppsigen) Desc Nucleic database of homologous processed pseudogenes. Server http://pbil.univ-lyon1.fr/databases/hoppsigen.html Cat None EDAM Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID HORDE IDOther None Name Human olfactory receptor data explorer (HORDE) Desc Database of human Olfactory Receptors (ORs), the largest multigene family in multicellular organisms. Information on the OR proteins, their gene structure and their genomic organization. Also available are OR repertoires of other mammalian species. Server http://bioportal.weizmann.ac.il/HORDE/ Cat None EDAM Specific protein database; Genes database; Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Tsviya Olender Email tsviya.olender@weizmann.ac.il Note None Status None ID HotSprint IDOther None Name Computational Hot Spots of Protein Interfaces (HotSprint) database Desc Information about the evolutionary history of the residues on the interface and represents which residues are highly conserved on the interface. In this way, functionally and structurally important residues on the interface can be distinguished. Server http://prism.ccbb.ku.edu.tr/hotsprint/ Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ozlem Keskin Email okeskin@eng.ku.edu.tr Note None Status None ID HPA IDOther None Name Human protein atlas (HPA) of expression and localization of proteins Desc Expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images. Server http://www.proteinatlas.org/ Cat Organism-specific databases EDAM Gene expression and microarray database; Cancer genes database; Electron microscopy database; Organism-specific database; Protein localization database Link SP_explicit LinkNB None Query Unknown| HTML| Ensembl identifier| http://www.proteinatlas.org/gene_info.php?ensembl_gene_id=%S Query Unknown| HTML| HGNC symbol | http://www.proteinatlas.org/gene_info.php?hugo_id=%S Query Unknown| HTML| HPA antibody id | http://www.proteinatlas.org/gene_info.php?antibody_id=%S Contact Erik Björling Email erik@biotech.kth.se Note None Status Referenced ID HS3D IDOther None Name Homo sapiens splice sites dataset (HS3D) Desc Homo Sapiens Exon, Intron and Splice regions extracted from GenBank. Server http://www.sci.unisannio.it/docenti/rampone/ Cat None EDAM Gene structure database; Splice sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Salvatore Rampone Email rampone@unisannio.it Note None Status None ID HSC-2DPAGE_HumanHeart IDOther None Name 2-DE gel protein databases at Harefield (HSC-2DPAGE) - Human Heart (Ventricle) Desc Database to retrieve spots from human heart (ventricle) databases. This includes facilities to select spots from the gel image, perform sophisticated searches and obtained sorted spot listings. Server http://www.doc.ic.ac.uk/vip/hsc-2dpage/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query HSC-2DPAGE entry| HTML| HSC-2DPAGE spot identifier| http://www.doc.ic.ac.uk/vip/hsc-2dpage/cgi/spot.cgi?file=hdvent&name=Human Heart (Ventricle)&spot=%s Contact Unknown Email Unknown Note None Status Referenced ID HSC-2DPAGE_HumanEndothelialCell IDOther None Name 2-DE gel protein databases at Harefield (HSC-2DPAGE) Desc Database to retrieve spots from human endothelial cell database. This includes facilities to select spots from the gel image, perform sophisticated searches and obtained sorted spot listings. Server http://www.doc.ic.ac.uk/vip/hsc-2dpage/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query HSC-2DPAGE entry| HTML| HSC-2DPAGE spot identifier| http://www.doc.ic.ac.uk/vip/hsc-2dpage/cgi/spot.cgi?file=eahy&name=Human endothelial cell (EA.hy 926)&spot=%s Contact Unknown Email Unknown Note None Status Referenced ID HSC-2DPAGE_RatHeart IDOther None Name 2-DE gel protein databases at Harefield (HSC-2DPAGE) Desc Database to retrieve spots from rat heart (ventricle) database. This includes facilities to select spots from the gel image, perform sophisticated searches and obtained sorted spot listings. Server http://www.doc.ic.ac.uk/vip/hsc-2dpage/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query HSC-2DPAGE entry| HTML| HSC-2DPAGE spot identifier| http://www.doc.ic.ac.uk/vip/hsc-2dpage/cgi/spot.cgi?file=ratvent&name=Rat Heart (Ventricle)&spot=%s Contact Unknown Email Unknown Note None Status Referenced ID HSC-2DPAGE_DogHeart IDOther None Name 2-DE gel protein databases at Harefield (HSC-2DPAGE) Desc Database to retrieve spots from dog heart (ventricle) database. This includes facilities to select spots from the gel image, perform sophisticated searches and obtained sorted spot listings. Server http://www.doc.ic.ac.uk/vip/hsc-2dpage/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query HSC-2DPAGE entry| HTML| HSC-2DPAGE spot identifier| http://www.doc.ic.ac.uk/vip/hsc-2dpage/cgi/spot.cgi?file=dogvent&name=Dog heart (ventricle)&spot=%s Contact Unknown Email Unknown Note None Status Referenced ID HSSP IDOther None Name Homology-derived secondary structure of proteins database (HSSP) Desc Homology-derived secondary structure of proteins database. Server http://swift.cmbi.kun.nl/swift/hssp/ Cat 3D structure databases EDAM Protein secondary structure and alignment database Link SP_explicit| db-xref LinkNB None Query HSSP entry| HTML| Protein accession number| http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[HSSP-ID:'%s'] Contact G Vriend Email Vriend@cmbi.ru.nl Note Alternative server: http://swift.cmbi.ru.nl/gv/hssp/. Example cross-reference: /db_xref="HSSP:12GS" Status Referenced ID HTPSELEX IDOther None Name HTPSELEX database of high-throughput SELEX libraries for transcription factor binding sites Desc Sets of invitro selected transcription factor binding site sequences obtained with SELEX and high-throughput SELEX method. Server http://www.isrec.isb-sib.ch/htpselex/ Cat None EDAM Transcription factor and binding site database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Philipp Bucher Email Philipp.Bucher@isrec.unil.ch Note None Status None ID HUGE IDOther None Name Human unidentified gene-encoded large proteins database (HUGE) Desc Database of the human cDNA project at the Kazusa DNA Research Institute, covering various sets of large human proteins of hitherto unidentified functions. Server http://www.kazusa.or.jp/huge/ Cat Organism-specific databases EDAM mRNA, EST or cDNA database; Organism-specific database Link SP_implicit LinkNB Human sequence entries with KIAAnnnn in a GN line Query Unknown| HTML| ???| ??? Contact Unknown Email Unknown Note None Status Referenced ID HumanPAX6 IDOther None Name Human PAX6 allelic variant database (HumanPAX6) Desc Human PAX6 allelic variant database. Server http://pax6.hgu.mrc.ac.uk/ Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact alastair.brown Email alastair.brown@hgu.mrc.ac.uk Note None Status None ID HumanMtDB IDOther None Name Human mitochondrial genome database (HumanMtDB) Desc Human mitochondrial genome database. Server http://www.genpat.uu.se/mtDB Cat None EDAM Mitochondrial genes and proteins database; Human genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Max Ingman Email Max.Ingman@genpat.uu.se Note None Status None ID HuSiDa IDOther None Name Human siRNA database Desc Depository for both sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. Server http://itb.biologie.hu-berlin.de/~nebulus/sirna/index.htm Cat None EDAM siRNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID HvrBase++ IDOther None Name HvrBase++ phylogenetic database for primate species Desc Hypervariable regions database. Server http://www.hvrbase.org Cat None EDAM Phylogenetic database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Arndt von Haeseler Email kohl@cs.uni-duesseldorf.de Note None Status None ID HyperCAT IDOther None Name Bacillus cereus group Typing Database (HyperCAT) Desc Typing databases for the Bacillus cereus group of bacteria, which includes B. cereus, B. anthracis, B. thuringiensis, B. mycoides, B. pseudomycoides, and B. weihenstephanensis. The databases contain MultiLocus Sequence Typing (MLST), MultiLocus Enzyme Electrophoresis (MLEE), and Amplified Fragment Length Polymorphism (AFLP) phylogenetic data. Server http://mlstoslo.uio.no/ Cat None EDAM Polymorphism database; Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Nicolas Tourasse Email nicolat@biotek.uio.no Note None Status None ID HyperCLDB IDOther None Name HyperCLDB cell Line database Desc Cell culture availability extracted from the cell line database of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue and PubMed database of bibliographic biomedical references. Server http://bioinformatics.istge.it/cldb/indexes.html Cat None EDAM Cell culture database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email paolo.romano@istge.it Note None Status None ID IARCTP53 IDOther None Name IARC TP53 mutation database Desc All TP53 gene variations identified in human populations and tumor samples. Data are compiled from the peer-reviewed literature and from generalist databases. Server http://www-p53.iarc.fr/ Cat None EDAM Cancer genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Magali OLIVIER Email molivier@iarc.fr Note None Status None ID IDbases IDOther None Name IDbases immunodeficiency mutation databases Desc Locus-specific databases for immunodeficiency-causing mutations. Server http://bioinf.uta.fi/base_root/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Mauno Vihinen Email mauno.vihinen@uta.fi, maunov@ebi.ac.uk Note None Status None ID IMGT IDOther None Name The international immunogenetics database (IMGT) Desc Database for the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species. Server http://imgt.cines.fr/ Cat Protein family/group databases EDAM Immunological genes or proteins database Link SP_implicit LinkNB All entries with a KW "Immunoglobulin [CV] region" and >=1 EMBL X-ref. Query Unknown| HTML| ???| imgt.cines.fr/cgi-bin/IMGTlect.jv?query=201+%s Contact Unknown Email lefranc@ligm.igh.cnrs.fr Note None Status Referenced ID IMGT/HLA IDOther None Name IMGT database of human MHC Desc 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. Server http://www.ebi.ac.uk/imgt/hla/ Cat None EDAM Immunological genes or proteins database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact James Robinson Email jrobinso@ebi.ac.uk Note Example cross-reference: /db_xref="IMGT/HLA:HLA00031" Status None ID IMGT/3Dstructure-DB IDOther None Name IMGT 3D structure database for immunoglobulins (IG), T cell receptors (TR), MHC and RPI Desc IMGT 3D structure database for immunoglobulins (IG), T cell receptors (TR), MHC and RPI. Server http://www.imgt.org/3Dstructure-DB/ Cat None EDAM Immunological genes or proteins database; Protein structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact François Ehrenmann Email Francois.Ehrenmann@igh.cnrs.fr Note None Status None ID IMGT/GENE-DB IDOther None Name IMGT gene database for immunoglobulins (IG) and T cell recetors (TR) Desc IMGT gene database for immunoglobulins (IG) and T cell recetors (TR). Server http://www.imgt.org/IMGT_GENE-DB/GENElect?livret=0 Cat None EDAM Immunological genes or proteins database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Véronique Giudicelli Email Veronique.Giudicelli@igh.cnrs.fr Note Example cross-reference: /db_xref="IMGT/GENE-DB:IGKC" Status None ID IMGT/LIGM-DB IDOther None Name IMGT nucleotide sequence database for immunoglobulins (IG) and T cell recetors (TR) Desc IMGT nucleotide sequence database for immunoglobulins (IG) and T cell recetors (TR). Server http://www.imgt.org/IMGTPrimerDB/ Cat None EDAM Immunological genes or proteins database; Protein sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Joumana Michaloud Email Joumana.Michaloud@igh.cnrs.fr Note Example cross-reference: /db_xref="IMGT/LIGM:U03895" Status None ID IMGT/PRIMER-DB IDOther None Name IMGT primer database for immunoglobulins (IG) and T cell recetors (TR) Desc IMGT primer database for immunoglobulins (IG) and T cell recetors (TR). Server http://www.imgt.org/cgi-bin/IMGTlect.jv?livret=0 Cat None EDAM Immunological database; Molecular probes or primers database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Géraldine Folch Email Geraldine.Folch@igh.cnrs.fr Note None Status None ID INFEVERS IDOther None Name Familial mediterranean fever (FMF) mutations database (INFEVERS) Desc The registry of familial mediterranean fever (FMF) and hereditary auto-inflammatory disorders mutations. Server http://fmf.igh.cnrs.fr/infevers Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID InParanoid IDOther None Name Inparanoid ortholgues database Desc Eukaryotic orthholog groups. Server http://InParanoid.sbc.su.se Cat None EDAM Nucleic acid sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Erik Sonnhammer Email Erik.Sonnhammer@sbc.su.se Note None Status None ID IntAct IDOther None Name IntAct protein interaction database and analysis system Desc Protein interaction database and analysis system. Server http://www.ebi.ac.uk/intact/ Cat Protein-protein interaction databases EDAM Protein-protein interaction database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.ebi.ac.uk/intact/binary-search/faces/search.xhtml?query=%s Contact Henning Hermjakob Email hhe@ebi.ac.uk Note None Status Referenced ID Integr8 IDOther None Name Integr8 genome and proteome database Desc Integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl)| protein sequences (from databases including the UniProt Knowledgebase and IPI)| statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA)| and information about orthology, paralogy, and synteny. Server http://www.ebi.ac.uk/integr8/ Cat None EDAM Proteome database; Genome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email pkersey@ebi.ac.uk Note None Status None ID INTEGRALL IDOther None Name INTEGRALL integron integrases and gene cassettes Desc Database of DNA sequences and genetic arrangements. Server http://integrall.bio.ua.pt/ Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Alexandra Moura Email amoura@ua.pt Note None Status None ID IntEnz IDOther None Name Integrated relational enzyme database (IntEnz) Desc IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. Server http://www.ebi.ac.uk/intenz Cat None EDAM Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Paula de Matos Email pmatos@ebi.ac.uk Note None Status None ID InterPro IDOther None Name InterPro integrated database of protein families, domains, regions, repeats and functional sites Desc Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences. Server http://www.ebi.ac.uk/interpro/ Cat Family and domain databases EDAM Protein sequence classification database; Protein functional sites database Link SP_explicit| db_xref LinkNB None Query InterPro entry| HTML| InterPro accession number| http://www.ebi.ac.uk/interpro/IEntry?ac=%s Contact Sarah Hunter Email hunter@ebi.ac.uk Note Example cross-reference: /db_xref="InterPro:IPR002928" Status Referenced ID ICDS IDOther None Name Interrupted coding sequences (ICDS) Desc Interrupted coding sequences. Server http://www-bio3d-igbmc.u-strasbg.fr/ICDS/ Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Olivier Poch Email poch@titus.u-strasbg.fr Note None Status None ID IPD IDOther None Name Immuno polymorphism database (IPD) Desc Database for the study of polymorphism in genes of the immune system. Server http://www.ebi.ac.uk/ipd/ Cat None EDAM Polymorphism database; Immunological genes or proteins database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email ipd@ebi.ac.uk Note None Status None ID IPD-ESTDAB IDOther None Name Immuno polymorphism EST database (IPD-ESTDAB) Desc Searchable database of tumour cell lines. Server http://www.ebi.ac.uk/ipd/estdab/index.html Cat None EDAM Cancer gene database; Polymorphism database; mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email ipd@ebi.ac.uk Note None Status None ID IPD-HPA IDOther None Name Immuno polymorphism human platelet antigens database (IPD-HPA) Desc Information on human platelet antigens (HPA). Server http://www.ebi.ac.uk/ipd/hpa/index.html Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email ipd@ebi.ac.uk Note None Status None ID IPD-KIR IDOther None Name Immuno polymorphism killer-cell Immunoglobulin-like receptor database (IPD-KIR) Desc Sequences of human Killer-cell Immunoglobulin-like Receptors (KIR). Server http://www.ebi.ac.uk/ipd/kir/index.html Cat None EDAM Polymorphism database; Immunological genes or proteins database; Protein sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email ipd@ebi.ac.uk Note None Status None ID IPD-MHC IDOther None Name Immuno polymorphism major histocompatibility complex database (IPD-MHC) Desc Sequences of the the major histocompatibility complex in a number of species. Server http://www.ebi.ac.uk/ipd/mhc Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email ipd@ebi.ac.uk Note None Status None ID IPI IDOther None Name International protein index (IPI) Desc Provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. Server http://www.ebi.ac.uk/IPI Cat Sequence databases EDAM Proteome database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=%s Contact Helpdesk Email ipi_help@ebi.ac.uk Note None Status Referenced ID iRefIndex IDOther None Name iRefIndex index of consolidated protein interactions Desc An index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods. Server http://irefindex.uio.no/wiki/iRefIndex Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ian Donaldson Email i.m.donaldson@biotek.uio.no Note None Status None ID IRESdb IDOther None Name Internal ribosome entry site database (IRESdb) Desc Internal ribosome entry sites. Server http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ Cat None EDAM Nucleic acid functional sites database; Ribosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email vagner@toulouse.inserm.fr Note None Status None ID IRESite IDOther None Name Database of experimentally verified IRES structures (IRESite) Desc Information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure. Server http://www.iresite.org Cat None EDAM Ribosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Martin Mokrejš Email mmokrejs@iresite.org Note None Status None ID ISfinder IDOther None Name Insertion sequence elements database (ISfinder) Desc A database of insertion sequences isolated from eubacteria and archae. It is organised into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Server http://www-is.biotoul.fr Cat None EDAM Mobile genetic elements database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Chandler Email Michael.Chandler@ibcg.biotoul.fr Note Example cross-reference: /db_xref="ISFinder:ISA1083-2" Status None ID ISOLA IDOther None Name Italian Solanaceae genome resource (ISOLA) Desc Solanaceae genome resource. Server http://biosrv.cab.unina.it/isola Cat None EDAM Plant genome database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Chiusano Maria Luisa Email chiusano@unina.it Note None Status None ID ITS2 IDOther None Name Internal transcribed spacer 2 sequences (ITS2) Desc Optimal global pairwise alignments from about 200,000 internal transcribed spacer 2 (ITS2) sequences - all against all - have been generated in order to model ITS2 secondary structures based on sequences with known structures. Server http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?about Cat None EDAM Sequence alignment database; RNA structure and alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Joerg Schultz Email Joerg.Schultz@biozentrum.uni-wuerzburg.de Note None Status None ID ITTACA IDOther None Name Integrated tumor transcriptome array and clinical data analysis (ITTACA) Desc Database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma. Server http://bioinfo-out.curie.fr/ittaca/ Cat None EDAM Gene expression and microarray database; Cancer genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Emmanuel Barillot Email ittaca@curie.fr Note None Status None ID IUPAC IDOther None Name IUPAC nomenclature database Desc Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc. Server http://www.chem.qmul.ac.uk/iupac/ Cat None EDAM Biochemical nomenclature database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email g.p.moss@qmul.ac.uk Note None Status None ID IUPHAR-DB IDOther None Name IUPHAR database Desc Official database of the IUPHAR Committee on Receptor Nomenclature and Drug Classification, incorporating the IUPHAR Database of G Protein-Coupled Receptors and the IUPHAR Database of Voltage-Gated and Ligand-Gated Ion Channels. Server http://www.iuphar-db.org Cat None EDAM Drug and drug design database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Anthony J Harmar Email tony.harmar@ed.ac.uk Note None Status None ID IXDB IDOther None Name Integrated X chromosome database (IXDB) Desc Integrated X chromosome database. Server http://ixdb.mpimg-berlin-dahlem.mpg.de Cat None EDAM Chromosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email sudbrak@mpimg-berlin-dahlem.mpg.de Note None Status None ID JAIL IDOther None Name JAIL structure-based interface library for macromolecules Desc JAIL classifies not only the interfaces between domain architectures but also those between protein chains and those between proteins and nucleic acids. Server http://bioinformatics.charite.de/jail/ Cat None EDAM Protein interaction database; Tertiary structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stefan Günther Email stefan.guenther@charite.de Note None Status None ID JASPAR IDOther None Name JASPAR eukaryotic transcription factor binding profiles Desc High-quality transcription factor binding profile database. Server http://jaspar.cgb.ki.se/ Cat None EDAM Transcription factor and binding site database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Boris Lenhard Email boris.lenhard@bccs.uib.no Note None Status None ID JCM IDOther None Name Japan collection of microorganisms (JCM) Desc Japan collection of microorganisms. Server http://www.jcm.riken.go.jp/JCM/catalogue.shtml Cat Not available EDAM Taxonomic database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="JCM:1339" Status Referenced ID JenaLib IDOther None Name Jena library of biological macromolecules (JenaLib) Desc Information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. JenaLib provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available. Server http://www.fli-leibniz.de/IMAGE.html Cat None EDAM Tertiary structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Rolf Huehne Email rhuehne@fli-leibniz.de Note None Status None ID JPGV IDOther None Name Jena prokaryotic genome viewer (JPGV) Desc Visualization and analysis of prokaryotic genomes. Server http://jpgv.fli-leibniz.de Cat None EDAM Genome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Marius Felder Email mfelder@fli-leibniz.de Note None Status None ID KaryotypeDB IDOther None Name Karyotype features from different animals and plants Desc Karyotype and chromosome information like chromosome number, length, karyotype features, idiograms, physical localizations of DNA sequences by fluorescence in situ hybridizion (FISH), and cell material for metaphase chromosomes and polytene chromosomes from different animal and plant species together with literature references and links. Server http://www.nenno.it/karyotypedb/ Cat None EDAM Chromosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Mario Nenno Email mario@nenno.it Note None Status None ID KEGG IDOther None Name Kyoto encyclopedia of genes and genomes (KEGG) Desc Encyclopedia of genes and genomes. Server http://www.genome.jp/kegg/ Cat Genome annotation databases EDAM Genome annotation database; Genes database; General genomics database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.genome.jp/dbget-bin/www_bget?%s Contact Unknown Email Unknown Note None Status Referenced ID KDD IDOther None Name Kidney development database Desc Data from a large number of developmental studies that have a bearing on the study of kidney development. Server http://golgi.ana.ed.ac.uk/kidhome.html Cat None EDAM Embryology and development database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jamie Davies Email jamie.davies@ed.ac.uk Note None Status None ID KinMutBase IDOther None Name KinMutBase registry of disease-causing mutations in protein kinase domains database Desc Disease-causing mutations in protein kinase domains. Server http://www.uta.fi/imt/bioinfo/KinMutBase/ Cat None EDAM Cancer gene database; Disease-associated protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Mauno Vihinen Email mauno.vihinen@uta.fi Note None Status None ID Kinomer IDOther None Name Kinomer database Desc A multilevel HMM library that models these protein kinase groups. It allows accurate identification of protein kinases and classification to the appropriate kinase group. Server http://www.compbio.dundee.ac.uk/kinomer Cat None EDAM Protein sequence motif or profile database; Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Geoff Barton Email g.j.barton@dundee.ac.uk Note None Status None ID KNOTTIN IDOther None Name KNOTTIN database Desc Database of knottins; intriguing miniproteins with strong potential in drug design. Server http://knottin.cbs.cnrs.fr Cat None EDAM Drug and drug design database; Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Laurent Chiche Email Laurent.Chiche@cbs.cnrs.fr Note None Status None ID L1Base IDOther None Name LINE-1 human and rodent Desc Putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included. Server http://line1.molgen.mpg.de Cat None EDAM Mobile genetic elements database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID LEGER IDOther None Name LEGER genome database for Listeria research Desc LEGER links requirements of listerial research projects with knowledge derived from functional genome studies. LEGER provides information on gene functions, protein expression levels, subcellular localization of proteins and the biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology. Server http://leger2.gbf.de/cgi-bin/expLeger.pl Cat None EDAM Prokaryote genome database; Gene expression and microarray database; Protein localization database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Guido Dieterich Email lja@gbf.de Note None Status None ID LegioList IDOther None Name Legionella pneumophila genome database Desc Legionella pneumophila genome database. Server http://genolist.pasteur.fr/LegioList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/LegioList/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID Leproma IDOther None Name Mycobacterium leprae genome database Desc Mycobacterium leprae genome database. Server http://genolist.pasteur.fr/Leproma/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/Leproma/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID LGICdb IDOther None Name Ligand-gated ion channel database (LGICdb) Desc Nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Server http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php Cat None EDAM Sequence alignment database; Phylogenetic database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Nicolas Le Novere Email lenov@ebi.ac.uk Note None Status None ID LigAsite IDOther None Name Ligand attachment site database (LigAsite) Desc A gold-standard dataset of biologically relevant binding sites in protein structures. Server http://www.scmbb.ulb.ac.be/Users/benoit/LigASite Cat None EDAM Protein functional sites database; Protein-ligand interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Shoshana Wosak Email shoshana.wodak@rogers.com Note None Status None ID LipaseEngineering IDOther None Name Lipase engineering database Desc Integrates information on sequence and structure of lipases and related proteins sharing the same a/b hydrolase fold to facilitate protein engineering. Server http://www.led.uni-stuttgart.de/ Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Juergen.Pleiss@po.uni-stuttgart.de Note None Status None ID ListiList IDOther None Name Listeria innocua and Listeria monocytogenes genomes database (ListiList) Desc Listeria innocua and Listeria monocytogenes genomes database. Server http://genolist.pasteur.fr/ListiList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/ListiList/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID LumbriBASE IDOther None Name Lumbricus rubellus genome project database Desc Genome database for the earthworm, Lumbricus rubellus. Server http://xyala.cap.ed.ac.uk/Lumbribase/index.shtml Cat None EDAM Invertebrate genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Mark Blaxter Email mark.blaxter@ed.ac.uk Note None Status None ID MaizeGDB IDOther MaizeDB Name Maize genetics and genomics database (MaizeGDB) Desc Biological information about the crop plant Zea mays ssp. mays. The following datatypes are accessible through this site: genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information. Server http://www.maizegdb.org/ Cat Organism-specific databases EDAM Plant-specific database; Organism-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.maizegdb.org/cgi-bin/id_search.cgi?id=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="MaizeGDB:635633" Status Referenced ID MAMEP IDOther None Name Molecular anatomy of mouse embryo project (MAMEP) Desc Functional analysis of pattern formation, tissue development and organogenesis in mouse. Server http://mamep.molgen.mpg.de/ Cat None EDAM Embryology and development database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Martin Werber Email werber@molgen.mpg.de Note None Status None ID MamPol IDOther None Name Mammalia polymorphism database (MamPol) Desc A collection of all the existing polymorphic sequences in the Mammalia group. Server http://mampol.uab.es Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sonia Casillas Email raquel.egea@uab.es Note None Status None ID MAPU IDOther None Name Max-Planck unified proteome database (MAPU) Desc Body fluid proteomes including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. Server http://www.mapuproteome.com/ Cat None EDAM Proteome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Matthias Mann Email mmann@biochem.mpg.de Note None Status None ID MAtDB IDOther None Name Arabadopsis genome database (MAtDB) Desc A repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project. Server http://mips.gsf.de/proj/thal/db Cat None EDAM Plant genome database; Arabidopsis database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email h.schoof@wzw.tum.de Note None Status None ID MACiE IDOther None Name Mechanism, annotation and classification in enzymes (MACiE) database Desc Mechanism, annotation and classification of enzymes. Server http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ Cat None EDAM Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact John Mitchell Email jbom1@cam.ac.uk Note None Status None ID MedOBIS IDOther None Name Mediterranean ocean biogeographic information system (MedOBIS) Desc Regional repository of marine biodiversity data. Server http://www.medobis.org Cat None EDAM Ecological database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sarah Faulwetter Email sarifa@her.hcmr.gr Note None Status None ID MeGX IDOther MegDB Name MeGX marine microbial ecological genomics database Desc Specialized database for genome-wide analysis of marine bacteria and metagenomics. Server http://www.megx.net Cat None EDAM Ecological database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Renzo Kottmann Email rkottman@mpi-bremen.de Note None Status None ID MEPD IDOther None Name Medaka expression pattern database (MEPD) Desc Medaka gene expression data examined through whole mount in situ hybridization. Server http://ani.embl.de:8080/mepd/ Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email henrich@dsp.jst.go.jp Note None Status None ID MEROPS IDOther None Name MEROPS peptidase database Desc Information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. Information includes the classification and nomenclature of the peptidase and links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. Server http://merops.sanger.ac.uk/ Cat Protein family/group databases EDAM Enzyme database Link SP_explicit LinkNB None Query Unknown| HTML| ???| merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s Contact Neil D. Rawlings Email ndr@sanger.ac.uk Note None Status Referenced ID MetaCrop IDOther None Name MetaCrop database of metabolic pathways in crop plants Desc Diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models. Server http://metacrop.ipk-gatersleben.de Cat None EDAM Metabolic pathways database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Falk Schreiber Email schreibe@ipk-gatersleben.de Note None Status None ID MetaGrowth IDOther None Name MetaGrowth database of culture conditions of obligate parasitic bacteria Desc Evidence and hypotheses for the study of culture conditions of obligate parasitic bacteria. Server http://www.igs.cnrs-mrs.fr/axenic/ Cat None EDAM Cell culture database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Karsten Suhre Email Hiroyuki.Ogata@igs.cnrs-mrs.fr Note None Status None ID Metal-MACiE IDOther None Name Metal-MACiE database of metals involved in biological catalysis Desc Properties and functions of the metal ions involved in the catalytic reactions of enzymes. Server http://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html Cat None EDAM Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Claudia Andreini Email andreini@cerm.unifi.it Note None Status None ID MethDB IDOther None Name MethDB DNA methylation database Desc DNA methylation and environmental epigenetic effects. Server http://www.methdb.de Cat None EDAM DNA methylation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christoph Grunau Email cgrunau@igh.cnrs.fr Note None Status None ID MfunGD IDOther None Name MIPS mouse functional genome database (MfunGD) Desc Mouse genome database including DNA and protein sequences, annotation, gene models and mapping etc. Server http://mips.gsf.de/genre/proj/mfungd/ Cat None EDAM Vertebrate genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andreas Ruepp Email andreas.ruepp@helmholtz-muenchen.de Note None Status None ID MGI IDOther MGD Name Mouse genome database (MGD) from Mouse Genome Informatics (MGI) Desc Integrated genetic, genomic, and biological data for mouse. Server http://www.informatics.jax.org/ Cat Organism-specific databases EDAM Vertebrate genome database; Organism-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.informatics.jax.org/searches/accession_report.cgi?id=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="MGI:1894891" Status Referenced ID Micado IDOther None Name Microbial advanced database organisation (Micado) Desc Microbial genome and functional analysis of Bacillus subtilis. Server http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_implicit LinkNB All Swiss-Prot entries with >=1 SubtiList Xref where the gene name does not start with "Y" Query Unknown| HTML| ???| genome.jouy.inra.fr/micado/gene.cgi?species=Bacillus+subtilis&gene=%2 Contact Unknown Email Unknown Note None Status Referenced ID MTRDB IDOther None Name Microorganisms tandem repeats database Desc Microorganisms tandem repeats database. Server http://minisatellites.u-psud.fr Cat None EDAM Repeat sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Vergnaud Email gilles.vergnaud@u-psud.fr Note None Status None ID MIM IDOther OMIM Name Online Mendelian inheritance in Man (OMIM) Desc Compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. Server http://www.ncbi.nlm.nih.gov/omim/ Cat Organism-specific databases EDAM Human genes, mutation and disease database; Organism-specific database; Genotype / phenotype database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=OMIM&dopt=Detailed&tmpl=dispomimTemplate&list_uids=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="MIM:123456" Status Referenced ID MINT IDOther None Name Molecular interaction Database (MINT) Desc Experimentally verified protein-protein interactions mined from the scientific literature by expert curators. Server http://mint.bio.uniroma2.it/mint/ Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gianni Cesareni Email cesareni@uniroma2.it Note None Status None ID MIPSPlantsDB IDOther None Name MIPS plants database Desc Data for individual plant species and a platform for integrative and comparative plant genome research. Server http://mips.gsf.de/proj/plant/jsf/genomes.jsp Cat None EDAM Plant genome database; Comparative genomics database; General plant database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Klaus Mayer Email K.mayer@helmholtz-muenchen.de Note None Status None ID miRBase IDOther None Name miRBase database Desc Database of all published miRNA sequences, genomic locations and associated annotation, predicted miRNA target genes and a confidential service assigning official names for novel miRNA genes prior to publication of their discovery. Server http://microrna.sanger.ac.uk/ Cat None EDAM miRNA database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sam Griffiths-Jones Email sam.griffiths-jones@manchester.ac.uk Note None Status None ID miriam IDOther None Name MIRIAM resources Desc Catalogue of data types (these can be controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP). Server http://www.ebi.ac.uk/miriam/ Cat None EDAM Data type, object or resource database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Camille Laibe Email laibe@ebi.ac.uk Note None Status None ID miROrtho IDOther None Name miROrtho animal microRNA database Desc Catalogue of animal microRNA genes. Server http://cegg.unige.ch/mirortho Cat None EDAM miRNA database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email evgeny.zdobnov@unige.ch Note None Status None ID MMRUV IDOther None Name MMR Gene Unclassified Variants Database Desc Database of mismatch repair gene unclassified variants: information from functional assays and other type of data to support the interpretation of MMR gene unclassified variants. Server http://www.mmrmissense.net/ Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email r.h.sijmons@medgen.umcg.nl Note None Status None ID MitoDrome IDOther None Name OXPHOS genes in Drosophila Desc Annotation for Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome. Server http://www2.ba.itb.cnr.it/MitoDrome/ Cat None EDAM Mitochondrial genes and proteins database; Genes database; mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email domenica.delia@ba.itb.cnr.it Note None Status None ID MITOP2 IDOther None Name Mitochondrial proteome database Desc Mitochondria-related genes, proteins and diseases. Server http://www.mitop.de:8080/mitop2/ Cat None EDAM Mitochondrial genes and proteins database; Proteome database; Disease-associated protein database; Disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Holger ProkischÊ Email thomas@pedgen.med.uni-muenchen.de Note None Status None ID MitoRes IDOther None Name MitoRes resource for mitochondria-related genes, transcripts and proteins Desc Mitochondria-related genes, transcripts and proteins Server http://www2.ba.itb.cnr.it/MitoNuc/ Cat None EDAM Mitochondrial genes and proteins database; Proteome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Domenica D'Elia Email domenica.delia@ba.itb.cnr.it Note None Status None ID MLVAbank IDOther None Name Bacterial MLVA-genotyping service (MLVAbank) Desc Bacterial MLVA-genotyping service. Server http://mlva.u-psud.fr/ Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Patrick Bouchon Email patrick_bouchon@yahoo.fr Note None Status None ID MMsINC IDOther None Name MMsINC chemoinformatics database Desc Chemoinformatics database. Server http://mms.dsfarm.unipd.it/MMsINC/search/ Cat None EDAM Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email stefano.moro@unipd.it Note None Status None ID MNCDB IDOther None Name MNCDB Neurospora crassa genome database Desc Molecular structure and functional network of the entirely sequenced, filamentous fungus Neurospora crassa. Server http://mips.gsf.de/genre/proj/ncrassa/ Cat None EDAM Biological pathways database; Fungal genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ulrich Gueldener Email u.gueldener@helmholtz-muenchen.de Note None Status None ID ModBase IDOther None Name ModBase database of comparative protein structure models Desc Three-dimensional protein models calculated by comparative modeling. Server http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi Cat 3D structure databases EDAM Protein structure database Link SP_implicit LinkNB All Swiss-Prot and TrEMBL entries Query Unknown| HTML| ???| ??? Contact Unknown Email Unknown Note None Status Referenced ID MODOMICS IDOther None Name Database of RNA modification pathways Desc Database of RNA modification pathways. Server http://www.genesilico.pl/modomics Cat None EDAM Biological pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Kristian Rother Email krother@genesilico.pl Note None Status None ID MoKA IDOther None Name MoKCa database of mutations of kinases in cancer Desc Structural and functional annotation on the phenotypic consequences of mutations in protein kinases implicated in cancer. Server http://strubiol.icr.ac.uk/extra/mokca/ Cat None EDAM Cancer gene database; Disease-associated protein database; Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dr Frances Pearl Email frances.pearl@icr.ac.uk Note None Status None ID MolliGen IDOther None Name MolliGen Mollicutes database Desc Comparative genomics of Mollicutes. Server http://cbi.labri.fr/outils/molligen/ Cat None EDAM Comparative genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Pascal Sirand Email sirand@bordeaux.inra.fr Note None Status None ID MOSAIC IDOther None Name MOSAIC bacterial genome comparison database Desc Comparison of closely related bacterial genomes. Server http://genome.jouy.inra.fr/mosaic/ Cat None EDAM Comparative genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email mosaic-db@jouy.inra.fr Note None Status None ID MOsDB IDOther None Name MOsDB rice genome database Desc Publicly available sequences of the rice (Oryza sativa L.) genome. Server http://mips.gsf.de/proj/plant/jsf/rice/index.jsp Cat None EDAM Plant genome database; Rice database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email manuel.spannagl@gsf.de Note None Status None ID MouseSAGE IDOther None Name MouseSAGE serial analysis of gene expression database Desc Collection of public available SAGE libraries generated from various mouse tissues and cell lines. The libraries were collected from GEO repository as well as from individual laboratories that made the libraries freely available on the Internet or in their publications. Server http://mouse.img.cas.cz/sage/ Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID MouseBook IDOther None Name MouseBook data from MRC Harwell Desc All the data from MRC Harwell. This includes mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies. Server http://www.mousebook.org Cat None EDAM Organism-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andrew Blake Email a.blake@har.mrc.ac.uk Note None Status None ID Mpact IDOther None Name MPact: Representation of Interaction Data at MIP Desc Protein interaction resources from MIPS, designed to support the PSI-MI standard. Server http://mips.gsf.de/genre/proj/mpact Cat None EDAM Protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ulrich GŸldener Email u.gueldener@gsf.de Note None Status None ID Mugen IDOther None Name MUGEN mouse database Desc Database of murine models of immune processes and immunological diseases. Server http://www.mugen-noe.org/database Cat None EDAM Immunological database; Disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Zouberakis Email zouberakis@fleming.gr Note None Status None ID MUMDB IDOther None Name MIPS Ustilago maydis Database (MUMDB) Desc Molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. Server http://mips.gsf.de/genre/proj/ustilago/ Cat None EDAM Biological pathways database; Fungal genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ulrich Gueldener Email u.gueldener@helmholtz-muenchen.de Note None Status None ID MyHits IDOther None Name MyHits protein domains database Desc Protein domain database for investigating the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models. Server http://myhits.isb-sib.ch/cgi-bin/index Cat None EDAM Protein sequence motif or profile database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Marco Pagni Email Marco.Pagni@isb-sib.ch Note None Status None ID MypuList IDOther None Name Mycoplasma pulmonis genome database Desc Mycoplasma pulmonis genome database. Server http://genolist.pasteur.fr/MypuList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/MypuList/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID NAPROC-13 IDOther None Name NAPROC-13 natural products 13C NMR database Desc Natural products 13C NMR, for the dereplication of natural product mixtures in bioassay-guided protocols. Server http://c13.usal.es Cat None EDAM Chemical and small molecule database; NMR database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Roberto Therón Email theron@usal.es Note None Status None ID Narcisse IDOther None Name Narcisse mirror view of conserved synteny Desc Mirror view of conserved synteny. Server http://narcisse.toulouse.inra.fr Cat None EDAM Genetic map or linkage database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Thomas Faraut Email Thomas.Faraut@toulouse.inra.fr Note None Status None ID NBRC IDOther NITE-BRC Name NITE biological resource center Desc Microbial culture catalogue. Server http://www.nbrc.nite.go.jp/e/index.html Cat Not available EDAM Cell culture database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="NBRC:3189" Status Referenced ID NCL IDOther None Name NCL Mutation Database Desc Published mutations and polymorphisms in the NCL genes together with unpublished data included with permission. Server http://www.ucl.ac.uk/ncl/mutation.shtml Cat None EDAM Genes database; Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sara Mole Email S.Mole@ucl.ac.uk Note None Status None ID ncRNAs IDOther None Name ncRNAs database Desc Sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Server http://biobases.ibch.poznan.pl/ncRNA/ Cat None EDAM Gene regulation database; Functional RNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Maciej Szymanski Email jbarcisz@ibch.poznan.pl Note None Status None ID NEMBASE IDOther None Name NEMBASE database for analysis of nematode ESTs Desc Nematode EST datasets. Server http://www.nematodes.org/nembase3/index.shtml Cat None EDAM mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ralf Schmid Email R.Schmid@ed.ac.uk Note None Status None ID NESbase IDOther None Name NESbase database of leucine-rich nuclear export signals Desc Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature. Server http://www.cbs.dtu.dk/databases/NESbase Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email tanja@cbs.dtu.dk Note None Status None ID NextBio IDOther None Name NextBio gene-centric data for human, mouse, rat, fly, worm and yeast Desc Gene-centric data for human, mouse, rat, fly, worm and yeast. Server http://www.nextbio.com/ Cat Other EDAM Genes database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.nextbio.com/b/home/home.nb?id=%s&type=feature Contact Unknown Email Unknown Note None Status Referenced ID NextDB IDOther None Name Nematode expression pattern dataBase (NextDB) Desc Nematode expression pattern dataBase. Server http://nematode.lab.nig.ac.jp/ Cat Not available EDAM Gene expression and microarray database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="NextDB:CELK01662" Status Referenced ID niaEST IDOther None Name NIA mouse cDNA project Desc NIA mouse cDNA project Server http://lgsun.grc.nia.nih.gov/cDNA/ Cat Not available EDAM mRNA, EST or cDNA database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="niaEST:L0304H12-3" Status Referenced ID NMPDR IDOther None Name National microbial pathogen data resource Desc Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio| as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. Server http://www.nmpdr.org Cat Genome annotation databases EDAM Genome annotation database; Pathogen database; Comparative genomics database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.nmpdr.org/linkin.cgi?id=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="NMPDR:fig|306254.1.peg.183" Status Referenced ID NMRShift IDOther None Name NMRShift database of organic structure nmr spectra Desc An NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. It features peer-reviewed submission of datasets by its users. Server http://nmrshiftdb.ice.mpg.de/ Cat None EDAM NMR database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email stefan.kuhn@uni-koeln.de Note None Status None ID NOPdb IDOther None Name Nucleolar proteome database (NOPdb) Desc Data from LamondLab proteomic analysis of human nucleoli. High sensitivity mass spectrometry and stringent criteria is used to identify peptides from human proteins from purified nucleoli. Server http://www.lamondlab.com/NOPdb3.0/ Cat None EDAM Mass spectromery database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email angus@lifesci.dundee.ac.uk Note None Status None ID NORINE IDOther None Name NORINE database of nonribosomal peptides Desc Database of nonribosomal peptides. Server http://bioinfo.lifl.fr/norine/ Cat None EDAM General peptides database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Segolene Caboche Email caboche@lifl.fr Note None Status None ID NPC-db IDOther None Name Niemann-Pick Type C mutations Desc Niemann-Pick type C disease gene variation database (NPC-db). Server http://npc.fzk.de/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Heiko.Runz@med.uni-heidelberg.de Note None Status None ID NPD IDOther None Name Nuclear protein database (NPD) Desc Information on vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms. Server http://npd.hgu.mrc.ac.uk Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email euchromatin@hotmail.com Note None Status None ID NRESTdb IDOther None Name Natural rubber EST database (NRESTdb) Desc Natural rubber EST database. Server http://genome.ukm.my/nrestdb/ Cat Not available EDAM mRNA, EST or cDNA database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="NRESTdb:Y01A01" Status Referenced ID NRSub IDOther None Name Non-Redundant B.subtilis database (NRSub) Desc Complete genome of Bacillus subtilis, plus additional data on gene mapping and codon usage. Server http://pbil.univ-lyon1.fr/nrsub/nrsub.html Cat None EDAM Genome map database; Prokaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email perriere@biomserv.univ-lyon1.fr Note None Status None ID NUREBASE IDOther None Name Nuclear receptor database (NUREBASE) Desc Nuclear receptor database Server http://www.ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email nurebase@listes.ens-lyon.fr Note None Status None ID OGLYCBASE IDOther None Name O-GlycBase database Desc Database of O- and C-glycosylated proteins. The criteria for inclusion are at least one experimentally verified O- or C-glycosylation site. The terminal sugar linked to serine or threonine is cited when known. The database is non-redundant in the sense that it contains no identical sequences, unless there is conflicting glycosylation data. Mucins have tandem repeat sequences, which are O-glycosylated. This result in some redundancy of the O-glycosylation sites. Server http://www.cbs.dtu.dk/databases/OGLYCBASE/ Cat None EDAM Protein functional sites database; Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ramneek Gupta Email ramneek@cbs.dtu.dk Note None Status None ID OGP IDOther None Name Oxford glycoProteomics 2-DE database (OGP) Desc Two-dimensional polyacrylamide gel electrophoresis database. Server http://proteomewww.bioch.ox.ac.uk/2d/2d.html Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query OGP entry| HTML| Sequence accession number| http://proteomewww.glycob.ox.ac.uk/cgi-bin/2d-search-ac?%s Contact Unknown Email Unknown Note None Status Referenced ID OMA IDOther None Name Identification of orthologs from complete genome data (OMA database) Desc Identification of orthologs from complete genome data. Server http://www.omabrowser.org Cat Phylogenomic databases EDAM Nucleic acid sequence classification database; Phylogenetic database; Link SP_explicit LinkNB None Query Unknown| HTML| ???| omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=%s Contact Unknown Email Unknown Note None Status Referenced ID OPTIC IDOther None Name Orthologous and paralogous transcripts in clades (OPTIC) database Desc Orthologous and paralogous transcripts in clades, from anaylsis of complete genomes (flies, nematodes, amniota, yeasts) in several clades. Server http://genserv.anat.ox.ac.uk/ Cat None EDAM Nucleic acid sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Andreas Heger Email andreas.heger@anat.ox.ac.uk Note None Status None ID ORENZA IDOther None Name Database of orphan enzyme activities (ORENZA) Desc Enzyme Activities for which no sequences are available in the main sequence protein databases. Server http://www.orenza.u-psud.fr/ Cat None EDAM Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Lespinet Email olivier.lespinet@igmors.u-psud.fr Note None Status None ID Orphanet IDOther None Name Orphanet portal for rare diseases and orphan drug Desc Information on rare diseases and orphan drugs. Server http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB Cat Organism-specific databases EDAM Drug and drug design database; Disease database Link SP_explicit LinkNB None Query Unknown| HTML| ???| http://www.orpha.net//consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=%s Contact Unknown Email Unknown Note None Status Referenced ID OrthoDB IDOther None Name Orthologous groups database (OrthoDB) Desc Orthologous groups database. Server hhttp://cegg.unige.ch/orthodb2 Cat None EDAM Nucleic acid sequence classification database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Evgeny Zdobnov Email zdobnov@medecine.unige.ch Note None Status None ID OryGenesDB IDOther None Name Database for rice reverse genetics (OryGenesDB) Desc Oryza sativa database of sequence information, such as the T-DNA and Ds flanking sequence tags (FSTs), plus related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data etc). Server http://orygenesdb.cirad.fr/ Cat None EDAM mRNA, EST or cDNA database; Nucleotide sequence database; Rice database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christophe PŽrin Email orygenesdb@cirad.fr Note None Status None ID Oryza IDOther None Name Oryza tag line Desc Database for the functional analyis of the rice genome. Phenotypic data from evaluation of the Génoplante rice insertion line library. Sequence information (Flanking Sequence Tags) from the molecular characterization of the mutagen insertion sites. Server http://urgi.versailles.inra.fr/OryzaTagLine/ Cat None EDAM Genotype / phenotype database; Rice database; Genome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Pierre Larmande Email larmande@cirad.fr Note None Status None ID Osteogenesis IDOther None Name Osteogenesis imperfecta and type III collagen mutations Desc All published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP and LEPRE1 genes. Server http://www.le.ac.uk/ge/collagen/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Raymond Dalgleish Email ray@le.ac.uk Note None Status None ID p53FamTaG IDOther None Name p53FamTaG direct target genes Desc A resource of human p53, p63, p73 direct target genes combining in silico prediction and microarray analysis. Server http://www2.ba.itb.cnr.it/p53FamTaG/ Cat None EDAM Genes database; Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email elisabetta.sbisa@ba.itb.cnr.it Note None Status None ID PairsDB IDOther None Name PairsDB BLAST and PSI-BLAST alignments Desc Collection of protein sequences and the BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually, results can be retrieved from a database of pre-computed alignments. Server http://pairsdb.csc.fi Cat None EDAM Sequence alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Kimmo Mattila Email Kimmo.Mattila@csc.fi Note None Status None ID PANDIT IDOther None Name Protein and associated nucleotide domains with inferred trees (PANDIT) Desc Protein and associated nucleotide domains with inferred trees. Server http://www.ebi.ac.uk/goldman-srv/pandit/ Cat None EDAM Protein functional sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Nick Goldman Email pandit@ebi.ac.uk Note None Status None ID PANDORA IDOther None Name PANDORA visualization and annotation for protein sets Desc Keyword-based analysis of protein sets by integration of annotation sources. Server http://www.pandora.cs.huji.ac.il Cat None EDAM General protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michal Linial Email michall@cc.huji.ac.il Note None Status None ID PANTHER IDOther None Name Protein analysis through evolutionary relationships (PANTHER) Desc Classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms. PANTHER includes "PANTHER Genes" (genes, transcripts and proteins in Human, Mouse, Rat, and Drosophila melanogaster), PANTHER Families (Protein families and subfamilies and associated data such as phylogenetic trees, multiple sequence alignments and HMMs), "PANTHER Pathways" (expert-curated signaling and metabolic pathways mapped to protein sequences in PANTHER Library) and "PANTHER Ontologies". Server http://www.pantherdb.org/ Cat Family and domain databases; Protein sequence classification database EDAM Biological pathways database; Protein sequence classification database; Genes database; Phylogenetic database Link SP_explicit LinkNB None Query PANTHER Gene| HTML| Panther Gene ID| http://www.pantherdb.org/genes/gene.do?acc=%s Query PANTHER Family| HTML| Panther family ID| http://www.pantherdb.org/panther/family.do?clsAccession=%s Query PANTHER Pathway| HTML| Panther pathway ID| http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=%s Contact Unknown Email Unknown Note None Status Referenced ID ParameciumDB IDOther None Name Database for the model organism Paramecium tetraurelia (ParameciumDB) Desc Macronuclear genome sequence and annotations, linked to available genetic data (RNA interference data and stock collection) for the model organism, Paramecium tetraurelia. Server http://paramecium.cgm.cnrs-gif.fr Cat None EDAM Unicellular eukaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Linda Sperling Email sperling@cgm.cnrs-gif.fr Note None Status None ID Pathema IDOther None Name Pathema: a clade-specific bioinformatics resource Desc Genome database for six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica. Server http://www.jcvi.org/cms/research/projects/pathema/overview/ Cat Not available EDAM Prokaryote genome database; Pathogen database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="Pathema:BA_4405", /db_xref="Pathema:191218" Status Referenced ID PathoPlant IDOther None Name PathoPlant database of plant-pathogen interactions and Arabidopsis expression Desc Plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. Also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment. Server http://www.pathoplant.de Cat None EDAM Gene expression and microarray database; Arabidopsis database; Signalling pathways database; Plant-specific database; Pathogen database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Lorenz Buelow Email l.buelow@tu-braunschweig.de Note None Status None ID PathwayInteractionDatabase IDOther None Name NCI-Nature pathway interaction database Desc Biomolecular interactions and cellular processes assembled into human signaling pathways. Server http://pid.nci.nih.gov/ Cat Enzyme and pathway databases EDAM Signalling pathways database Link SP_explicit LinkNB None Query Pathway| HTML| NCI-Nature Pathway ID| http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=%s&source=NATURE&what=graphic&jpg=on&ppage=1 Contact Unknown Email Unknown Note None Status Referenced ID PDB IDOther None Name The RCSB Protein Data Bank Desc A repository for 3D biological macromolecular structure data. Server http://www.rcsb.org/pdb/ Cat 3D structure databases EDAM Tertiary structure database Link SP_explicit| db_xref LinkNB None Query PDB entry| Text| PDB ID| srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e Contact Unknown Email Unknown Note /dbxref="PDB:12GS" Status Referenced ID PDBe IDOther None Name PDBe protein structure database in Europe Desc PDBe protein structure database in Europe Server http://www.ebi.ac.uk/pdbe/ Cat None EDAM Tertiary structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Kim Henrick Email henrick@ebi.ac.uk Note None Status None ID PDBFINDER IDOther None Name PDBFINDER reformatted PDB files Desc The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates| it is meant to ad searches in the administrative records of PDB files. Server http://swift.cmbi.ru.nl/gv/pdbfinder/ Cat None EDAM Protein structure annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact G Vriend Email vriend@cmbi.ru.nl Note None Status None ID pdbfun IDOther None Name pdbfun annotated protein structures Desc Database of annotated residues in proteins from PDB. Server http://pdbfun.uniroma2.it Cat None EDAM Protein structure annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Manuela Helmer-Citterich Email citterich@uniroma2.it Note None Status None ID PDB-redo IDOther None Name PDB-redo database of re-refined PDB entries Desc Re-refined macromolecular X-ray diffraction structures. Server http://swift.cmbi.ru.nl/pdbredo/index.html Cat None EDAM Tertiary structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact gert Vriend Email vriend@cmbi.ru.nl Note None Status None ID PDBREPORT IDOther None Name Structure validation reports for PDB entries (PDBREPORT) Desc Reports describing structural problems in PDB entries that have been determined using X-ray diffraction or NMR techniques. There are many more than ten million diagnostics. Server http://swift.cmbi.ru.nl/gv/pdbreport/ Cat None EDAM Protein structure annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gert Vriend Email vriend@cmbi.ru.nl Note None Status None ID PDBselect IDOther None Name PDBselect database of representative PDB chains Desc Selection of a representative set of PDB chains. Server http://bioinfo.tg.fh-giessen.de/pdbselect/ Cat None EDAM Protein structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Uwe Hobohm Email uwe.hobohm@tg.fh-giessen.de Note None Status None ID PDBsum IDOther None Name PDBsum overview of macromolecular structures Desc At-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them. Server http://www.ebi.ac.uk/pdbsum Cat 3D structure databases EDAM Protein structure annotation database Link SP_explicit LinkNB None Query PDBSum entry| HTML| PDB ID| http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e Contact Roman Laskowski Email roman@ebi.ac.uk Note None Status Referenced ID PDBTM IDOther None Name Transmembrane proteins from PDB (PDBTM) Desc Transmembrane protein selection of the Protein Data Bank (PDB). Server http://pdbtm.enzim.hu/ Cat None EDAM Membrane protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email tusi@enzim.hu Note None Status None ID PED IDOther None Name Pancreatic expression database (PED) Desc Database for cancer pathogenesis, allowing query by cancer tissue and type, a wide range of sequence types, SNP selection for candidate gene screening and disease links, as well as cross-species analyses. . Server http://www.pancreasexpression.org Cat None EDAM Cancer genes database; Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Claude Chelala Email Claude.Chelala@cancer.org.uk Note None Status None ID PEDANT IDOther None Name PEDANT3 protein extraction, description and analysis tool Desc Automatic analysis of genomic sequences by a large variety of bioinformatics tools. For example the following pre-computed analyses are available to analyse protein function: Blast similarity searches against the non-redundant protein sequence database, motif searches against the Pfam, BLOCKS and PROSITE databases. Prediction of cellular roles and functions are made based on high stringency BLAST searches against protein sequences with manually assigned functional categories according to the Functional Catalogue (FunCat) developed by MIPS and Biomax AG. Protein structure analysis includes the similarity-based identification of known 3D structures and structural domains, by searching against the PDB and SCOP databases, and predictions of transmembrane regions, low similarity regions and non-globular domains. Server http://pedant.gsf.de Cat None EDAM Genome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dmitrij Frishman Email d.frishman@wzw.tum.de Note None Status None ID PepSeeker IDOther None Name PepSeeker database of proteome peptide identifications for investigating fragmentation patterns Desc Proteome peptide identifications for investigating fragmentation patterns. Server http://www.ispider.manchester.ac.uk/pepseeker/ Cat None EDAM Peptide identification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Simon Hubbard Email simon.hubbard@manchester.ac.uk Note None Status None ID Peptaibol IDOther None Name Peptaibol database of natural fungal peptides Desc Natural fungal peptides. Server http://peptaibol.cryst.bbk.ac.uk Cat None EDAM General peptides database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dr. Lee Whitmore Email l.whitmore@bbk.ac.uk Note None Status None ID PeptideAtlas IDOther None Name PeptideAtlas peptide database Desc A multi-organism compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. Server http://www.peptideatlas.org Cat Proteomic databases; Peptide identification database; Mass spectromery database EDAM General peptides database Link SP_explicit LinkNB None Query Unknown| HTML| ???| https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=%s Contact Unknown Email Unknown Note None Status Referenced ID PeptideDB IDOther None Name PeptideDB database of bioactive signaling peptides Desc Naturally occurring signalling peptides from animal source, which are derived by cleavage from prepropeptide precursor proteins. It includes cytokine and growth factor, peptide hormones, antimicrobial peptides, toxins and venom peptides, and antifreeze proteins. Server http://www.peptides.be/ Cat None EDAM Specific protein database; General peptides database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email liliane.schoofs@bio.kuleuven.be Note None Status None ID PeroxiBase IDOther None Name PeroxiBase peroxidase family database Desc Sequences from peroxidase superfamilies with annotation on putative functions and transcription regulation. Server http://peroxibase.isb-sib.ch/index.php Cat Protein family/group databases EDAM Specific protein database Link SP_explicit LinkNB None Query Unknown| HTML| ???| peroxibase.isb-sib.ch/listing.php?action=view&id=%s Contact Unknown Email dunand@scsv.ups-tlse.fr Note None Status Referenced ID PeroxisomeDB IDOther None Name Peroxisome database (PeroxisomeDB) Desc Curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccaromyces cerevisiae (encoded by 61 genes). Server http://www.peroxisomeDB.org Cat None EDAM Metabolic pathways database; Specific protein database; Proteome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Aurora Pujol Email apujol@iro.es Note None Status None ID PespotDB IDOther None Name Pepspot database (PespotDB) of peptide chip data Desc Repository for the storage and the analysis of data coming from interaction assays exploiting peptide chip technology. Server http://mint.bio.uniroma2.it/PepspotDB Cat None EDAM Peptide identification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stefano Costa Email stefano.costa@uniroma2.it Note None Status None ID Pfam IDOther None Name Pfam protein domain database Desc Large colleciton of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Server http://pfam.sanger.ac.uk/ Cat Family and domain databases EDAM Protein sequence classification database; Sequence alignment database; Sequence motif or profile database Link SP_explicit| db_xref LinkNB None Query Pfam entry| HTML| Sequence accession number| http://pfam.sanger.ac.uk/protein/acc=%s Query Pfam entry| HTML| Pfam family accession number| http://pfam.sanger.ac.uk/family?acc=%s Query Pfam entry| HTML| Pfam clan ID| http://pfam.sanger.ac.uk/clan?acc=%s Query Pfam entry| HTML| NCBI taxonomic ID| http://pfam.sanger.ac.uk/proteome?taxId=%s Contact Alex Bateman Email agb@sanger.ac.uk Note Example cross-reference: /db_xref="PFAM:PF00003" Status Referenced ID PGN IDOther None Name Plant Genome Network (PGN) Desc A general purpose EST analysis pipeline/website that can be readily used as a "front end" for EST sequencing projects. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. Server http://pgn.cornell.edu/ Cat Not available EDAM mRNA, EST or cDNA database; Plant-specific database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="PGN:aam01-1ms3-a05" Status Referenced ID PharmGKB IDOther None Name The pharmacogenetics and pharmacogenomics knowledge base (PharmGKB) Desc Database on the impact of human genetic variations on drug response. PharmGKB curates primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. Server http://www.pharmgkb.org Cat Organism-specific databases EDAM Genotype / phenotype database; Drug and drug design database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.pharmgkb.org/do/serve?objId=%s&objCls=Gene Contact Unknown Email Unknown Note None Status Referenced ID PhenomicDB IDOther None Name PhenomicDB cross-species genotype/phenotype database Desc A multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indeces (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. Server http://www.phenomicdb.de Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Bertram Weiss Email bertram.weiss@bayerhealthcare.com Note None Status None ID PHCI-2DPAGE IDOther None Name Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE) Desc Two-dimensional polyacrylamide gel electrophoresis database. Server http://www.gram.au.dk/2d/2d.html Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query PHCI-2DPAGE entry| HTML| Sequence accession number| http://www.gram.au.dk/cgi-bin/get-2d-entry?%s Contact Unknown Email Unknown Note None Status Referenced ID PHI-base IDOther None Name PHI-base pathogen host interactions database Desc Curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries. Server http://www.phibase.org Cat None EDAM Genes database; Pathogen database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Martin Urban Email phi-base@bbsrc.ac.uk Note None Status None ID PhosPhAt IDOther None Name Arabidopsis experimental phosphorylation sites database (PhosPhAt) Desc Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. Server http://phosphat.mpimp-golm.mpg.de/app.html Cat None EDAM Phosphorylation sites database; Arabidopsis database; Mass spectromery database; Peptide identification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Waltraud Schulze Email WSchulze@mpimp-golm.mpg.de Note None Status None ID PhosphoELM IDOther None Name PhosphoELM database of S/T/Y phosphorlation sites Desc Experimentally verified phosphorylation sites in eukaryotic proteins. Server http://phospho.elm.eu.org/ Cat None EDAM Phosphorylation sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Toby Gibson Email toby.gibson@embl.de Note None Status None ID PHOSPHO3D IDOther None Name PHOSPHO3D structures of phosphorylation sites Desc Three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites. Server http://bioinformatica.uniroma2.it/phospho3d Cat None EDAM Phosphorylation sites database; Protein structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Manuela Helmer-Citterich Email citterich@uniroma2.it Note None Status None ID PhosphoPep IDOther None Name PhosphoPep database of MS-derived phosphorylation data from 4 organisms Desc MS-derived phosphorylation data from 4 different organisms: the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae). Server http://www.phosphopep.org/ Cat None EDAM Phosphorylation sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ruedi Aebersold Email aebersold@imsb.biol.ethz.ch Note None Status None ID PhosphoSite IDOther None Name Phosphorylation site database Desc A curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites. Information in PhosphoSite version 1.0 includes the phosphorylated residue and its surrounding sequence, orthologous sites in other species, the location within domains and motifs, links to other online resources and literature references. Server http://www.phosphosite.org Cat PTM databases EDAM Phosphorylation sites database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.phosphosite.org/uniprotAccAction.do?id=%s Contact Unknown Email Unknown Note None Status Referenced ID PhosSite IDOther None Name PhosSite phosphorylation site database for Archaea and bacteria Desc Phosphorylation sites for Archaea and bacteria. Server http://vigen.biochem.vt.edu/xpd/xpd.htm Cat PTM databases EDAM Phosphorylation sites database Link SP_explicit LinkNB None Query Unknown| HTML| ???| vigen.biochem.vt.edu/xpd/xpd2.cfm?extf=uniprot&extref=%s Contact Unknown Email Unknown Note None Status Referenced ID PhotoList IDOther None Name PhotoList Photorhabdus luminescens genome database Desc Photorhabdus luminescens genome database. Server http://genolist.pasteur.fr/PhotoList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/PhotoList/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID PhylomeDB IDOther None Name PhylomeDB database of phylogenetic trees for all proteins Desc A collection of gene phylogenies (phylomes) including phylogenetic trees, multiple sequence alignments and genome-wide orthology and paralogy predictions based on the analysis of the phylogenetic trees. Server http://phylomedb.bioinfo.cipf.es Cat None EDAM Sequence alignment database; Phylogenetic database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Toni Gabaldon Email tgabaldon@cipf.es Note None Status None ID PhyloPat IDOther None Name PhyloPat database of phylogenetic patterns Desc Database for the analysis of where in evolution some phylogenetic lineages were started and over which species they were contained. PhyloPat uses the latest release of EnsMartand their one-to-one, one-to-many and many-to-many orthologies. Server http://www.cmbi.ru.nl/phylopat Cat None EDAM Phylogenetic database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email t.hulsen@cmbi.ru.nl Note None Status None ID PhytoProt IDOther None Name PhytoProt protein clusters database Desc Database built from "all-by-all" comparison of (putative) protein sequences and sequence clustering. Relationships between sequences in a cluster and help identify annotation errors (fused genes, missing exons, frameshifts, etc). Server http://urgi.versailles.inra.fr/phytoprot/ Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID PIPs IDOther None Name Human protein-protein interaction prediction (PIPs) Desc Predicted human protein interactions. Server http://www.compbio.dundee.ac.uk/www-pips Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email geoff@compbio.dundee.ac.uk Note None Status None ID PIR IDOther None Name Protein sequence database of the Protein Information Resource (PIR) Desc Integrated protein informatics resource for genomic, proteomic and systems biology research. Server http://pir.georgetown.edu/ Cat Sequence databases EDAM Protein sequence database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| pir.georgetown.edu/cgi-bin/nbrfget?uid=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="PIR:S12345" Status Referenced ID PIRSF IDOther None Name PIRSF whole-protein classification database Desc Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. Server http://pir.georgetown.edu/pirsf/ Cat Family and domain databases EDAM Protein sequence classification database Link SP_explicit LinkNB None Query PIRSF entry| HTML| PIRSF Number| pir.georgetown.edu/cgi-bin/ipcSF?id=%s Contact Unknown Email Unknown Note None Status Referenced ID PlantDNAC-values IDOther None Name Plant DNA C-values database (PlantDNAC-values) Desc The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for different plant species. It combines data from the Angiosperm DNA C-values Database, Gymnosperm DNA C-values Database, the Pteridophyte DNA C-values Database, the Bryophyte DNA C-values Database, together with the addition of the Algae DNA C-values database. Server http://data.kew.org/cvalues/ Cat None EDAM Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ilia Leitch Email i.leitch@kew.org Note None Status None ID PlantsnoRNA IDOther None Name Plant snoRNA database Desc Plant snoRNA database. Server http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home Cat None EDAM snoRNA database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID PlantCARE IDOther None Name Plant cis acting element Desc A database of different names of plant transcription sites (monocots, dicots and other) describing plant promoters, with plant transcription sites, consensus sequences and matrices. Server http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ Cat None EDAM Transcription regulatory sites database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stephane rombauts Email stephane.rombauts@psb.ugent.be Note None Status None ID PlantMarkers IDOther None Name PlantMarkers database of predicted molecular markers from plants Desc Predicted molecular markers from plants. Server http://markers.btk.fi Cat None EDAM Genetic map or linkage database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stephen Rudd Email stephen.rudd@btk.utu.fi Note None Status None ID PLANT-Pis IDOther None Name PLANT-Pis database for protease inhibitors and their genes in higher plants Desc Information on the distribution and functional properties of protease inhibitors (PIs) in higher plants. Server http://bighost.area.ba.cnr.it/PLANT-Pis Cat None EDAM Specific protein database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Luigi Ceci Email luigi.ceci@area.ba.cnr.it Note None Status None ID PlantProm IDOther None Name PlantProm database of experimental plant promoter and transcription start site Desc An annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species. Server http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom Cat None EDAM Transcription regulatory sites database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID PlasmoDraft IDOther None Name Predictions of Plasmodium falciparum gene function Desc Gene Ontology (GO) annotation predictions for the genes of Plasmodium falciparum. It involves both the ~60% of genes that lake GO annotation, and the genes that are already annotated in GeneDB. Predictions of PlasmoDraft are based on transcriptome, proteome, and interactome data, and are thus complementary to predictions achieved by sequence homology. Server http://www.atgc-montpellier.fr/PlasmoDraft/ Cat None EDAM Genome annotation database Link Genome annotation database LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Laurent Bréhélin Email brehelin@lirmm.fr Note None Status None ID PLMItRNA IDOther None Name PLMItRNA database of tRNAs in plant mitochondria Desc A database for tRNA molecules and genes in mitochondria of photosynthetic eukaryotes. Server http://www.ba.itb.cnr.it/PLMItRNA/ Cat None EDAM Mitochondrial genes and proteins database; tRNA database; Genes database; Plant-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Luigi Ceci Email luigi.ceci@area.ba.cnr.it Note None Status None ID Plprot IDOther None Name Plastid proteins database (Plprot) Desc Integrates data from large scale proteome analyses of different plastid types. These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison yields a core proteome common to all plastid types and provides furthermore information about plastid type-specific functions. Server http://www.plprot.ethz.ch/ Cat None EDAM Specific protein database; Proteome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sacha Baginsky Email sacha.baginsky@ipw.biol.ethz.ch Note None Status None ID PMAP-CutDB IDOther None Name PMAP-CutDB proteolytic event database Desc Curated proteolytic events and pathways from the literature. Server http://www.proteolysis.org/ Cat Other EDAM Biological pathways database Link SP_explicit LinkNB None Query Unknown| HTML| ???| http://substrate.burnham.org/lookup/uniprot/%s Contact Unknown Email Unknown Note None Status Referenced ID PMDB IDOther None Name Protein model database (PMDB) Desc Three dimensional protein models from structure prediction methods. The database currently stores all models submitted to the last four editions of the CASP experiment. Server http://www.caspur.it/PMDB/ Cat None EDAM Protein structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Anna Tramontano Email pmdb@caspur.it Note None Status None ID Polymorphix IDOther None Name Polymorphix intraspecific sequence polymorphism database Desc Families of polymorphic sequences. Server http://pbil.univ-lyon1.fr/polymorphix/query.php Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID PoMaMo IDOther None Name PoMaMo potato maps database Desc Potato sequences, mapping info, SNPs etc. Server https://gabi.rzpd.de/PoMaMo.html Cat None EDAM Genome map database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email svenja@rzpd.de Note None Status None ID PPD IDOther None Name PPD protein pKa values database Desc Protein pKa values. Server http://www.jenner.ac.uk/PPD/pKahomepage.htm Cat None EDAM Protein physicochemical properties database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Darren Flower Email Darren.Flower@jenner.ac.uk Note None Status None ID PPNEMA IDOther None Name rRNA genes from plant-parasitic nematodes (PPNEMA) Desc Plant-parasitic nematodes multialigned ribosomal cistrons. Server http://www.ppnema.uniba.it/ Cat None EDAM rRNA database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email m.attimonelli@biologia.uniba.it Note None Status None ID PptaseDB IDOther None Name Prokaryotic protein phosphatase database (PptaseDB) Desc Prokaryotic protein phosphatases. Server http://www.ebi.ac.uk/uniprot/remotingAPI/javadoc/domain/api/uk/ac/ebi/kraken/interfaces/uniprot/dbx/pptasedb/PptaseDB.html Cat Protein family/group databases EDAM Specific protein database Link SP_explicit LinkNB None Query Unknown| HTML| ???| http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=accession&extref=%s Contact Unknown Email Unknown Note None Status Referenced ID preDiCT IDOther None Name preDiCT database of drug effects on the heart Desc Drug effects on the heart. Server http://www.vph-predict.eu/ Cat None EDAM Drug and drug design database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email katherine.fletcher@dpag.ox.ac.uk Note None Status None ID PRIDE IDOther None Name PRIDE proteomics identifications database Desc Standards compliant, public data repository for proteomics data, protein and peptide identifications together with the evidence supporting these identifications. Server http://www.ebi.ac.uk/pride Cat Proteomic databases EDAM Peptide identification database; General proteomics database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=%s Contact Juan Antonio Vizcaino Email juan@ebi.ac.uk Note None Status Referenced ID PRINTS IDOther None Name PRINTS protein motif fingerprint database Desc A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family. Server http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ Cat Family and domain databases EDAM Protein sequence classification database; Protein sequence motif or profile database Link SP_explicit LinkNB None Query PRINTS entry| HTML| PRINTS accession number| http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=pr00018 Contact Terri Atwood Email teresa.k.attwood@manchester.ac.uk Note Obsolete abbreviation: PRINT Status Referenced ID Prism IDOther None Name Prism protein interaction by structural matching Desc Database to explore protein interfaces and predict protein-protein interactions. Server http://prism.ccbb.ku.edu.tr/prism Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ozlem Keskin Email okeskin@ku.edu.tr Note None Status None ID probeBase IDOther None Name probeBase database of rRNA-targeted oligonucleotide probes Desc rRNA-targeted oligonucleotide probes. Server http://www.microbial-ecology.net/probebase Cat None EDAM Molecular probes or primers database; rRNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Matthias Horn Email probeBase@microbial-ecology.net Note None Status None ID ProCMD IDOther None Name ProCMD 3D protein C mutations database Desc Database for molecular aspects of thrombophilic disease. It integrates clinical and phenotypical descriptions with functional and structural data obtained by computational approach to help to elucidate the chain of events leading from the molecular defect to disease. Server http://www.itb.cnr.it/procmd/ Cat None EDAM Human genes, mutation and disease database; Disease database; Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email pasqualina.dursi@itb.cnr.it Note None Status None ID PROCOGNATE IDOther None Name PROCOGNATE ligand domain mapping for enzymes Desc Cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers. Server http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html Cat None EDAM Enzyme database; Protein-ligand interaction database; Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Matthew Bashton Email bashton@ebi.ac.uk Note None Status None ID ProDom IDOther None Name ProDom protein domain database Desc A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database. Server http://prodom.prabi.fr/prodom/current/html/home.php Cat Family and domain databases EDAM Protein sequence classification database Link SP_explicit LinkNB None Query ProDom entry| HTML| ProDom family ID| http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=%s Query ProDom family alignment| HTML| ProDom family ID| http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent1=%s&wanted=align Query ProDom phylogenetic tree| HTML| ProDom family ID| http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent1=%s&wanted=tree Query ProDom domain image| HTML| ProDom family ID| http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?CG=0&question=DBLI&query=%s Query ProDom family alignment| Text| ProDom family ID| http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent0=%s Contact Unknown Email emmanuel.courcelle@toulouse.inra.fr Note None Status Referenced ID PRODORIC IDOther None Name PRODORIC prokaryotic database of gene regulation Desc Comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites. Server http://www.prodoric.de Cat None EDAM Gene regulation database; Gene expression and microarray database; Transcription factor and binding site database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Richard Muench Email r.muench@tu-bs.de Note None Status None ID PromEC IDOther None Name PromEC verified E. coli promoters Desc E. coli mRNA promoters with experimentally identified transcriptional start sites. Server http://margalit.huji.ac.il/promec/ Cat None EDAM Transcription regulatory sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Hanna Margalit Email hanah@md2.huji.ac.il Note None Status None ID ProMEX IDOther None Name ProMEX protein mass spectral library Desc A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS). Developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification by ProMEX is linked to other molecular levels of biological organization such as metabolite, pathway and transcript data. Server http://promex.mpimp-golm.mpg.de/ Cat Proteomic databases EDAM Peptide identification database; Mass spectromery database; Arabidopsis database Link SP_explicit LinkNB None Query Unknown| HTML| ???| promex.mpimp-golm.mpg.de/cgi-bin/peplib.pl?action=11&txt_query=%s Contact Unknown Email weckwerth@mpimp-golm.mpg.de Note None Status Referenced ID PROPHECY IDOther None Name PROPHECY profiling of phenotypic characteristics in yeast Desc Quantitative information about phenotypes for the complete collection of deletion strains in yeast (Saccharomyces cerevisiae). Server http://prophecy.lundberg.gu.se Cat None EDAM Genotype / phenotype database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Anders Blomberg Email anders.blomberg@gmm.gu.se Note None Status None ID ProRule IDOther None Name ProRule collection of rules based on PROSITE predictors Desc ProRule section of PROSITE is constituted of manually created rules that increase the discriminatory power of PROSITE motifs (generally profiles) by providing additional information about functionally and/or structurally critical amino acids and can automatically generate annotation based on PROSITE motifs in the UniProtKB/Swiss-Prot format. Each ProRule is defined in the UniRule format. Server http://www.expasy.org/prosite/prorule.html Cat None EDAM Protein sequence motif or profile database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christian Sigrist Email christian.sigrist@isb-sib.ch Note None Status None ID ProSAS IDOther None Name Protein Structure and Alternative Splicing database (ProSAS) Desc Unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. Annotates protein structures for several Ensembl genomes. Alternative transcripts can be analyzed on the protein structure and protein function level. Server http://www.bio.ifi.lmu.de/ProSAS/ Cat None EDAM Gene structure database; Protein structure annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Fabian Birzele Email fabian.birzele@bio.ifi.lmu.de Note None Status None ID PROSAT2 IDOther None Name PROSAT2 protein structure annotation tool Desc Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein. Server http://projects.villa-bosch.de/dbase/pdba/ Cat None EDAM Protein structure annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stefan Richter Email Stefan.Richter@eml-r.villa-bosch.de Note None Status None ID PROSITE IDOther None Name A Database of protein domains, families and functional sites Desc Documentation for protein domains, families and functional sites as well as associated patterns and profiles to identify them. Server http://www.expasy.org/prosite/ Cat Family and domain databases EDAM Protein sequence classification database; Protein functional sites database; Protein sequence motif or profile database Link SP_explicit LinkNB None Query PROSITE entry| Text| ProSite ID| http://www.expasy.org/cgi-bin/get-prosite-raw.pl?%s Query PROSITE entry| HTML| ProSite ID| http://www.expasy.org/cgi-bin/prosite-search-ac?%s Contact Hulo Nicolas Email nicolas.hulo@isb-sib.ch Note None Status Referenced ID ProtoNet IDOther None Name ProtoNet automatic hierarchical classification of proteins Desc Automatic hierarchical classification of protein sequences. Server http://www.protonet.cs.huji.ac.il/ Cat Other EDAM Protein sequence classification database Link SP_implicit LinkNB All UniProtKB entries Query Unknown| HTML| ???| www.protonet.cs.huji.ac.il/sp.php?prot=%s Contact Michal Linial Email proto@cs.huji.ac.il Note None Status Referenced ID Protepedia IDOther None Name Protepedia collaborative 3D protein encyclopedia Desc Free, collaborative 3D encyclopedia of proteins & other molecules. Server http://www.proteopedia.org/wiki/index.php/Main_Page Cat None EDAM General protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email jaime.prilusky@weizman.ac.il Note None Status None ID ProTeus IDOther None Name Protein terminus short linear sequences Desc Tool for identification of short linear signatures in protein termini, based on a positional-based search method for revealing short significant signatures in termini of proteins. Server http://www.proteus.cs.huji.ac.il Cat None EDAM Protein sequence motif or profile database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Mathieu Blanchette Email blanchem@mcb.mcgill.ca Note None Status None ID PseudoBase IDOther None Name PseudoBase RNA pseudoknots database Desc Collection of RNA pseudoknots. Server http://www.ekevanbatenburg.nl/PKBASE/PKB.HTML Cat None EDAM RNA structure and alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Batenburg@rulsfb.leidenuniv.nl Note None Status None ID PseudoCAP IDOther None Name PseudoCAP pseudomonas genome database Desc Pseudomonas genome database. Server http://www.pseudomonas.com/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ??? | www.pseudomonas.com/getAnnotation.do?locusID=%s Query Unknown| HTML| GI number| http://www.pseudomonas.com/getAnnotation.do?gi=%s Contact Unknown Email Unknown Note None Status Referenced ID pSTIING IDOther None Name Protein, signalling, transcriptional interactions and inflammation networks gateway (pSTIING) Desc Protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. Server http://pstiing.licr.org/ Cat None EDAM Protein interaction database; Biological pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Marketa Zvelebil Email marketa@ludwig.ucl.ac.uk Note None Status None ID PTCH IDOther None Name PTCH mutation database Desc Information on mutations and polymorphisms in the PTCH1 gene. The human homologue of Drosophila patched, PTCH1, has been identified as the gene underlying the cancer predisposition syndrome Nevoid Basal Cell Carcinoma Syndrome (NBCCS, OMIM 109400). This syndrome is also known as Gorlin's syndrome or Basal Cell Nevus Syndrome. Server http://www.cybergene.se/cgi-bin/w3-msql/ptchbase/index.html Cat None EDAM Polymorphism database; Cancer genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email jano@cybergene.se Note None Status None ID PubMeth IDOther None Name PubMeth reviewed methylation database in cancer Desc An annotated and reviewed database of methylation in cancer. It is based on automated textmining of literature and is afterwards manually curated and annotated. Server http://www.pubmeth.org Cat None EDAM Cancer genes database; DNA methylation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Maté Ongenaert Email mate.ongenaert@ugent.be Note None Status None ID RATMAP IDOther None Name RATMAP rat genome database Desc Rat genome database. Server http://ratmap.gen.gu.se/ Cat Not available EDAM Vertebrate genome database; Genome map database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="RATMAP:5" Status Referenced ID RDG IDOther None Name Rat genome database (RDG) Desc Rat genome database. Server http://rgd.mcw.edu/ Cat Not available EDAM Vertebrate genome database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status Referenced ID RB1GeneMutation IDOther None Name RB1 gene mutation database (RB1GeneMutation) Desc Retinoblastoma genetics database. Server http://www.verandi.de/joomla/ Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dietmar Lohmann Email dr.lohmann@uni-essen.de Note None Status None ID Reactome IDOther None Name Reactome knowledgebase of biological pathways Desc Curated knowledgebase of biological pathways and processes. Server http://www.reactome.org/ Cat Enzyme and pathway databases EDAM Biological pathways database Link SP_explicit LinkNB None Query Pathway| HTML| Reactome pathway ID| http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%s&ZOOM=2 Query Pathway| XML| Reactome pathway ID| http://www.reactome.org/cgi-bin/sbml_export?DB=gk_current&ID=%s Contact Esther Schmidt Email eschmidt@ebi.ac.uk Note Obsolete abbreviation: GK Status Referenced ID REBASE IDOther None Name REBASE restriction enzymes and methylases database Desc Restriction enzymes and methylases database. Server http://rebase.neb.com/ Cat Protein family/group databases EDAM Enzyme database Link SP_explicit LinkNB None Query Unknown| HTML| ???| rebase.neb.com/rebase/enz/%s.html Contact Unknown Email Unknown Note None Status Referenced ID REDIdb IDOther None Name RNA editing database (REDIdb) Desc Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored. Server http://biologia.unical.it/py_script/overview.html Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Carla Quagliariello Email c.quagliariello@unical.it Note None Status None ID RefSeq IDOther None Name NCBI reference sequences Desc A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. Provides a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses. Server http://www.ncbi.nlm.nih.gov/RefSeq/ Cat Sequence databases EDAM Sequence database; Comparative genomics database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=%s Contact Unknown Email Unknown Note None Status Referenced ID REPAIRtoire IDOther None Name REPAIRtoire DNA repair pathways Desc Components involved in the repair mechanisms for all kinds of cellular DNA lesions. Four repair pathways (from H.sapiens, E.coli and S.cerevisiae) are contained, together with their protein components and molecular events that trigger those pathways. Server http://repairtoire.genesilico.pl/ Cat None EDAM Biological pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Grzegorz Papaj Email grzesiek@genesilico.pl Note None Status None ID REPRODUCTION-2DPAGE IDOther REPRODUCTION2DPAGE Name REPRODUCTION-2DPAGE database Desc REPRODUCTION-2DPAGE 2D gel protein database. Server http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query REPRODUCTION-2DPAGE entry| HTML| Sequence accession number| http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s&format=text Query REPRODUCTION-2DPAGE entry| Text| Sequence accession number| http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s Contact Unknown Email Unknown Note None Status Referenced ID RepSeq IDOther None Name RepSeq repeat-containing proteins Desc Facility for detecting and analysing the occurence of amino acid repeat-containing proteins within sequenced proteomes. Server http://www.repseq.org/ Cat None EDAM Repeat sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email dd505@york.ac.uk Note None Status None ID RESID IDOther None Name RESID database of protein modifications Desc A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. Server http://www.ebi.ac.uk/RESID/ IDOther None Name Protein Modification Cat None EDAM General protein modifications database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email john.garavelli@ebi.ac.uk Note None Status None ID RetrOryza IDOther None Name RetrOryza database of rice LTR retrotransposons Desc Information and resources related to LTR-retrotransposons in rice genome. Server http://www.retroryza.org Cat None EDAM Mobile genetic elements database; Rice database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Olivier Panaud Email panaud@univ-perp.fr Note None Status None ID RFAM IDOther None Name RNA families database of alignments and CMs (RFAM) Desc Collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. The main use of Rfam is as a source of RNA multiple alignments with consensus secondary structure annotation in a consistent format. Server http://rfam.janelia.org/ Cat Not available EDAM Sequence alignment database; RNA structure and alignment database Link db_xref LinkNB None Query RFAM RNA family| HTML| Sequence accession number| http://rfam.sanger.ac.uk/family?acc=%s Query RFAM RNA family| HTML| Sequence identifier| http://rfam.sanger.ac.uk/family?acc=%s Query RFAM RNA family| XML| Sequence accession number| http://rfam.sanger.ac.uk/family?acc=%s&output=xml Query RFAM RNA family| XML| Sequence identifier| http://rfam.sanger.ac.uk/family?acc=%s&output=xml Contact Unknown Email Unknown Note Example cross-reference: /db_xref="RFAM:RF00230" Status Referenced ID RGD IDOther None Name Rat genome database (RGD) Desc Rat genome database. Server http://rgd.mcw.edu/ Cat Organism-specific databases EDAM Vertebrate genome database; Organism-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| rgd.mcw.edu/tools/genes/genes_view.cgi?id=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="RGD:620528" Status Referenced ID RiceGenes IDOther None Name RiceGenes database Desc A repository of Rice strain, pathology and genetic mapping information. It also contains numerous maps that compare the rice genome to those of related grasses. Server http://stein.cshl.org/ricegenes.html Cat Not available EDAM Genome map database; Rice database; Genome annotation database; Comparative genomics database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="RiceGenes:AA231856" Status Referenced ID Rouge IDOther None Name Rodent unidentified gene-encoded large proteins database (Rouge) Desc A sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs). Server http://www.kazusa.or.jp/rouge/ Cat Organism-specific databases EDAM Protein sequence database; Organism-specific database Link SP_implicit LinkNB Mouse sequence entries with KIAAnnnn in a GN line Query Unknown| HTML| ???| ??? Contact Unknown Email Unknown Note None Status Referenced ID Rfam IDOther None Name Rfam RNA families database Desc Collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). Server http://rfam.sanger.ac.uk/ Cat None EDAM Sequence alignment database; RNA structure and alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Paul Gardner Email pg5@sanger.ac.uk Note None Status None ID RISSC IDOther None Name Ribosomal internal spacer sequence collection (RISSC) Desc Ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics. Server http://egg.umh.es/rissc Cat None EDAM Ribosome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Rodriguez Valera, Francisco Eduardo Email frvalera@umh.es Note None Status None ID RNAD IDOther None Name European ribosomal RNA database (RNAD) Desc Compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available. Server http://www.psb.ugent.be/rRNA/ Cat None EDAM rRNA database; Sequence alignment database; RNA structure and alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID RNA-FRABASE IDOther None Name RNA FRABASE database Desc Database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation. Server http://rnafrabase.ibch.poznan.pl/ Cat None EDAM RNA structure and alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Ryszard W. Adamiak Email adamiakr@ibch.poznan.pl Note None Status None ID RNAVirusDB IDOther None Name RNA virus genome database (RNAVirusDB) Desc RNA virus genome database. Server http://tree.bio.ed.ac.uk/rnavirusdb Cat None EDAM Viral genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email robert.belshaw@zoo.ox.ac.uk Note None Status None ID RNRdb IDOther None Name Ribonucleotide reductase database (RNRdb) Desc Compilation of all published 3D structures of different RNR proteins as well as a compilation of all mutant proteins constructed including links to the relevant publication(s). It is used to retrieve RNR protein sequences from any organism that have been either experimentally characterised or predicted from genome sequence data. Server http://rnrdb.molbio.su.se/ Cat None EDAM Specific protein database; Protein structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Britt-Marie Sjoberg Email rnrdb@molbio.su.se Note None Status None ID RsiteDB IDOther None Name RNA binding site database (RsiteDB) Desc Interactions of extruded, unpaired RNA nucleotide bases. It presents and classifies the protein binding pockets that accommodate them. It allows the recognition of similar protein binding patterns involved in interactions with different RNA molecules. Given an unbound structure of a target protein it allows the prediction of its RNA nucleotide binding sites. Server http://bioinfo3d.cs.tau.ac.il/RsiteDB/ Cat None EDAM Nucleic acid functional sites database; Protein-nucleic acid interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email shulmana@post.tau.ac.il Note None Status None ID RTKdb IDOther None Name Receptor tyrosine kinase database (RTKdb) Desc Receptor tyrosine kinase database. Server http://pbil.univ-lyon1.fr/RTKdb/ Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID RTPrimerDB IDOther None Name PCR primers and probes database (RTPrimerDB) Desc Database of primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories. Server http://medgen.ugent.be/rtprimerdb/ Cat None EDAM Molecular probes or primers database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Filip Pattyn Email joke.vandesompele@rug.ac.be Note None Status None ID S/MARtDB IDOther None Name The S/MAR transaction database (S/MARtDB) Desc Information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human. Server http://smartdb.bioinf.med.uni-goettingen.de/ Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email smartdb@bioinf.med.uni-goettingen.de Note None Status None ID S4 IDOther None Name S4 structure-based sequence alignments of SCOP superfamilies Desc An automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database. Server http://compbio.mds.qmw.ac.uk/S4.html Cat None EDAM Sequence alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Mansoor Saqi Email m.saqi@qmul.ac.uk Note None Status None ID SABIO-RK IDOther None Name System for the analysis of biochemical pathways - reaction kinetics (SABIO-RK) Desc Biochemical pathways and reaction kinetics. Server http://sabio.villa-bosch.de/SABIORK Cat None EDAM Biological pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Martin Golebiewski Email martin.golebiewski@eml-r.villa-bosch.de Note None Status None ID Saffron Genes IDOther None Name Saffron genes database Desc EST sequences from saffron (Crocus sativus) stigmas. Server http://www.saffrongenes.org Cat None EDAM mRNA, EST or cDNA database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Maria Luisa Chiusano Email chiusano@unina.it Note None Status None ID SagaList IDOther None Name Streptococcus agalactiae NEM316 / serotype III genome database Desc Streptococcus agalactiae NEM316 / serotype III genome database. Server http://genolist.pasteur.fr/SagaList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/SagaList/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID SCOP IDOther None Name Structural classification of proteins (SCOP) database Desc The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification. Server http://scop.mrc-lmb.cam.ac.uk/scop Cat None EDAM Protein domain classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Alexey Murzin Email scop@mrc-lmb.cam.ac.uk Note None Status None ID SCOPPI IDOther None Name Structural Classification of Protein-Protein Interfaces (SCOPPI) Desc Domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain associations and are annotated with various interaction characteristics. Server http://www.scoppi.org Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Schroeder Email ms@biotec.tu-dresden.de Note None Status None ID SCOWL IDOther None Name Structural characterization of water, ligands and proteins (SCOWL) Desc PDB interface interactions at atom, residue and domain level. The database contains protein interfaces and residue-residue interactions formed by structural units and interacting solvent. Server http://www.scowlp.org Cat None EDAM Protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email paszkows@mpi-cbg.de Note None Status None ID SeattleSNPs IDOther None Name SeattleSNPs variation discovery resource Desc Database for identifying, genotyping, and modeling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans. Server http://pga.gs.washington.edu/ Cat Polymorphism databases EDAM Polymorphism database; Biological pathways database; Genotype / phenotype database Link SP_implicit LinkNB All entries with >= HGNC X-ref and an RT line starting with "SeattleSNPs" Query Unknown| HTML| ???| pga.gs.washington.edu/data/%s/ Contact Unknown Email Unknown Note None Status Referenced ID Sebida IDOther None Name Sebida sex-biased genes Desc Functional and evolutionary analysis of sex-biased genes. Sebida integrates data from multiple microarray studies comparing male versus female gene expression in D. melanogaster, D. simulans, and A. gambiae. Server http://www.sebida.de Cat None EDAM Genes database; Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Florian Gnad Email gnad@biochem.mpg.de Note None Status None ID SEED IDOther None Name The SEED genome comparison environment Desc Environment for comparative genome analysis. Server http://www.theseed.org/ Cat Not available EDAM Comparative genomics database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="SEED:fig|83331.1.peg.1" Status Referenced ID Selectome IDOther None Name Selectome database of positive selection Desc Database of positive selection based on a rigorous branch-site specific likelihood test. Server http://bioinfo.unil.ch/selectome/ Cat None EDAM Phylogenetic database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Marc Robinson-Rechavi Email Marc.Robinson-Rechavi@unil.ch Note None Status None ID SGD IDOther None Name Saccharomyces genome database (SGD) Desc Database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. Server http://www.yeastgenome.org/ Cat Organism-specific databases EDAM Yeast genome database; Fungi-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.yeastgenome.org/cgi-bin/locus.fpl?dbid=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="SGD:L0000470" Status Referenced ID SILVA IDOther None Name SILVA ribosomal RNA sequence data Desc SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Server http://www.arb-silva.de Cat None EDAM rRNA database; Nucleotide sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Frank Oliver Glöckner Email fog@mpi-bremen.de Note None Status None ID SIMAP IDOther None Name Similarity matrix of proteins (SIMAP) Desc Pre-calculated protein similarities. It contains published protein sequences and is continuously updated. Server http://boinc.bio.wzw.tum.de/boincsimap/ Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Thomas Rattei Email t.rattei@wzw.tum.de Note None Status None ID siRNAdb IDOther None Name siRNAdb database Desc siRNAdb database Server http://sirna.sbc.su.se/sirnadb_050915.txt Cat None EDAM siRNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email alistair.chalk@cgb.ki.se Note None Status None ID SISYPHUS IDOther None Name SISYPHUS database of protein structure alignments Desc Structural alignments for proteins with non-trivial relationships. Server http://sisyphus.mrc-cpe.cam.ac.uk Cat None EDAM Structure alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Antonina Andreeva Email sisyphus@mrc-lmb.cam.ac.uk Note None Status None ID SitesBase IDOther None Name SitesBase database Desc Known ligand binding sites within PDB navigable by PDB identifier or ligand 3 letter code e.g. NAD. Each binding site has a frequently updated register of structurally similar binding sites sharing atomic similarity detected by geometric hashing. Multiple alignments, structural superpositions and links to other structural databases are also available enabling further analysis. Server http://www.modelling.leeds.ac.uk/sb/ Cat None EDAM Protein functional sites database; Protein-ligand interaction database; Sequence alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Nicola Gold Email n.d.gold@leeds.ac.uk Note None Status None ID SMART IDOther None Name Simple modular architecture research tool (SMART) Desc SMART protein domain database. Server http://smart.embl.de/ Cat Family and domain databases EDAM Protein sequence classification database Link SP_explicit LinkNB None Query SMART entry| HTML| SMART domain name| http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY Query SMART entry| HTML| SMART accession number| http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY Contact Peer Bork Email Ivica.Letunic@EMBL-Heidelberg.DE Note None Status Referenced ID SMR IDOther None Name A database of annotated 3D protein structure models Desc Annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. Server http://swissmodel.expasy.org/repository/ Cat 3D structure databases EDAM Protein structure database Link SP_explicit LinkNB None Query SMR entry| HTML| SwissProt accession number| http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s Contact Torsten Schwede Email Torsten.Schwede@unibas.ch Note None Status Referenced ID SNAP IDOther None Name SNAP database of human gene variations Desc Human gene variations. Server http://platform.humgen.au.dk/ Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jun Wang Email wangj@genomics.org.cn Note None Status None ID SNAPPI IDOther None Name SNAPPI database of structures, interfaces and alignments for protein-protein interactions Desc Structures, interfaces and alignments for protein-protein interactions. Server http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp Cat None EDAM Protein-protein interaction database; Protein structure database; Alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Emily Jefferson Email emily@compbio.dundee.ac.uk Note None Status None ID Sno/scaRNAbase IDOther None Name Small nucleolar RNA and small cajal body-specific RNA database (sno/scaRNAbase) Desc sno/scaRNA-associated genetic and functional data, from several database sources via web-accessible search interfaces. Server http://gene.fudan.sh.cn/snoRNAbase.nsf Cat None EDAM snRNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Weilin Wu Email xiejun@fudan.edu.cn Note None Status None ID snoRNABase IDOther snoRNA-LBME-db Name snoRNABase database of human H/ACA and C/D box snoRNAs Desc Human H/ACA and C/D box snoRNAs. Server http://www-snorna.biotoul.fr/ Cat None EDAM snoRNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michel Weber Email weber@ibcg.boiotoul.fr Note None Status None ID SNPeffect IDOther None Name SNPeffect database of molecular phenotyping of human SNPs and disease mutations Desc Molecular phenotyping of human SNPs and disease mutations. Server http://snpeffect.vib.be Cat None EDAM Polymorphism database; Human genes, mutation and disease database; Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Joke Reumers Email joke.reumers@gmail.com Note None Status None ID SNPnexus IDOther None Name SNPnexus database for SNP selection Desc SNP selection database. Server http://www.snp-nexus.org Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Claude.Chelala@cancer.org.uk Note None Status None ID SNPSTR IDOther None Name SNPSTR databasee Desc Database of compound genetic marker called SNPSTR which combines a STR marker with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 base pairs apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers. Server http://www.sbg.bio.ic.ac.uk/~ino/cgi-bin/SNPSTRdatabase.html Cat None EDAM Genetic map or linkage database; Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Stumpf Email ino.agrafioti@imperial.ac.uk Note None Status None ID SOURCE IDOther None Name The Stanford online universal resource for Clones and ESTs (SOURCE) Desc A unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports. Server http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch Cat Other EDAM mRNA, EST or cDNA database Link SP_implicit LinkNB All human and mouse entries with >=1 gene name and >= 1 MIM or MGI X-ref. Query Unknown| HTML| ???| ??? Contact Unknown Email Unknown Note None Status Referenced ID SoyBase IDOther None Name SoyBase soybean genome database Desc Database of soybean genetics and molecular biology. Server http://soybase.agron.iastate.edu/ Cat Not available EDAM Plant genome database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="SoyBase:Satt005" Status Referenced ID SubtiList IDOther None Name Bacillus subtilis genome sequencing project Desc Bacillus subtilis genome sequencing project Server http://genolist.pasteur.fr/SubtiList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/SubtiList/genome.cgi?external_query+%s Contact Unknown Email moszer@pasteur.fr Note Example cross-reference: /db_xref="SubtiList:BG10001" Status Referenced ID SpliceAid IDOther None Name SpliceAid database of strictly experimentally assessed target RNA sequences in humans Desc Experimental RNA target motifs bound by splicing proteins in humans. Server http://www.introni.it/splicing.html Cat None EDAM Gene structure database Link Gene structure database; Splice sites database; Nucleotide sequence motif or profile database LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Piva Francesco Email f.piva@univpm.it Note None Status None ID SpliceNest IDOther None Name SpliceNest database Desc Visualizing splicing of genes from EST Data, based on mappings of the GeneNest EST Contigs to genomic sequence. Server http://splicenest.molgen.mpg.de/ Cat None EDAM mRNA, EST or cDNA database; Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID SpodoBase IDOther None Name Spodoptera frugiperda database (SpodoBase) Desc An integrated database for the genomics of the Lepidoptera Spodoptera frugiperda. Server http://bioweb.ensam.inra.fr/spodobase/ Cat None EDAM Organism-specific database; Invertebrate genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID STCDB IDOther None Name Signal transduction classification database (STCDB) Desc Signal transduction classification. Server http://bibiserv.techfak.uni-bielefeld.de/stcdb/ Cat None EDAM Signalling pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email mchen@techfak.uni-bielefeld.de Note None Status None ID STITCH IDOther None Name STITCH chemical-protein interactions Desc A resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. Server http://stitch.embl.de Cat None EDAM Protein-ligand interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Peer Bork Email bork@embl.de Note None Status None ID StrainInfo.net IDOther None Name StrainInfo.net bioportal Desc Search the holdings of multiple biological resource centres (BRCs) through a single web interface. Server http://www.straininfo.net Cat None EDAM Biological resource database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Bert Verslyppe Email Bert.Verslyppe Note None Status None ID Strepto-DB IDOther None Name Strepto-DB comparative genomics of group A and group B streptococci Desc Database for comparative genome analyses of group A and group B streptococci. Server http://www.oger.tu-bs.de/strepto_db/ Cat None EDAM Comparative genomics database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Johannes Klein Email johannes.klein@tu-bs.de Note None Status None ID STRING IDOther None Name STRING protein-protein interaction database Desc Known and predicted protein-protein interactions. Server http://string-db.org/ Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Christian von Mering Email mering@molbio.uzh.ch Note None Status None ID StructurallyConservedInterfaces IDOther None Name Structurally conserved interfaces Desc Structures of protein-protein interfaces from PDB. Server http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html Cat None EDAM Protein-protein interaction database; Protein structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID Sulfolobus IDOther None Name Sulfolobus genome database Desc The three sequenced Sulfolobus genomes. Server http://www.sulfolobus.org Cat None EDAM Prokaryote genome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Kim Brugger Email brugger@mermaid.molbio.ku.dk Note None Status None ID SuperDrug IDOther None Name SuperDrug drug database Desc Drug compounds with conformers. Server http://bioinformatics.charite.de/superdrug Cat None EDAM Drug and drug design database; Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Robert Preissner Email robert.preissner@charite.de Note None Status None ID SUPERFAMILY IDOther None Name SUPERFAMILY HMM library and genome assignments Desc Structural and functional protein annotations for all completely sequenced organisms. Server http://supfam.org Cat None EDAM Protein sequence classification database; Proteome annotation database; Sequence motif or profile database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Julian Gough Email gough@supfam.org Note None Status None ID SuperHapten IDOther None Name SuperHapten immunogenic compound database Desc Database of haptens, related antibodies and carriers. Server http://bioinformatics.charite.de/superhapten Cat None EDAM Immunological database; Immunological genes or proteins database; Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stefan Guenther Email stefan.guenther@charite.de Note None Status None ID SuperNatural IDOther None Name SuperNatural natural compound database Desc A searchable database of natural compounds. Server http://bioinformatics.charite.de/supernatural Cat None EDAM Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dunkel, Mathias Email mathias.dunkel@charite.de Note None Status None ID Superscent IDOther None Name Superscent database of scents Desc Database of scent molecules. Server http://bioinformatics.charite.de/superscent Cat None EDAM Scents database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Robert Preissner Email robert.preissner@charite.de Note None Status None ID SuperSite IDOther None Name SuperSite dictionary of metabolite and drug binding sites in proteins Desc A ligand and binding site oriented view of the protein structural space. SuperSite integrates evolutionary information in the proteins as well as predicted binding sites from LigsiteCSC. Server http://bioinf-services.charite.de/supersite/ Cat None EDAM Drug and drug design database; Protein functional sites database; Protein-ligand interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Dominic Jansen Email dominic_jansen@web.de Note None Status None ID SuperTarget-Matador IDOther None Name SuperTarget and Matador database Desc Enzyme, drug and pathways database. Server http://insilico.charite.de/supertarget Cat None EDAM Biological pathways database; Drug and drug design database; Enzyme database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Robert Preissner Email robert@drug-redesign.de Note None Status None ID Supertoxic IDOther None Name Supertoxic toxic compounds database Desc Database of toxic compounds with synonyms. Server http://bioinformatics.charite.de/supertoxic Cat None EDAM Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Robert Preissner Email robert.preissner@charite.de Note None Status None ID SURFACE IDOther None Name SURFACE database of protein surface patches Desc Surface residues and functions, annotated, compared and evaluated. Server http://cbm.bio.uniroma2.it/surface Cat None EDAM Protein functional sites database; Protein structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID SWEET-DB glycans IDOther None Name SWEET-DB glycans database Desc Glycans database. Server http://www.dkfz-heidelberg.de/spec2/sweetdb/ Cat None EDAM Carbohydrate structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email w.vonderlieth@dkfz.de Note None Status None ID WORLD-2DPAGE(CGL14067-2DPAGE) IDOther CGL14067-2DPAGE Name World-wide gel-based proteomics database (CGL14067-2DPAGE) Desc World-wide gel-based proteomics database (CGL14067-2DPAGE) Server http://www.expasy.org/world-2dpage/ Cat None EDAM Two-dimensional gel electrophoresis database Link None LinkNB None Query World-2DPAGE entry| HTML| Sequence accession number| http://world-2dpage.expasy.org/repository/ac=%s&database=cgl14067-2dpage Contact frederique lisacek Email frederique.lisacek@isb-sib.ch Note None Status None ID WORLD-2DPAGE(NIBR 2D-PAGE) IDOther NIBR 2D-PAGE Name World-wide gel-based proteomics database (NIBR 2D-PAGE) Desc World-wide gel-based proteomics database (NIBR 2D-PAGE) Server http://www.expasy.org/world-2dpage/ Cat None EDAM Two-dimensional gel electrophoresis database Link None LinkNB None Query World-2DPAGE entry| HTML| Sequence accession number| http://world-2dpage.expasy.org/repository/ac=%s&database=nibr_2d-page Contact frederique lisacek Email frederique.lisacek@isb-sib.ch Note None Status None ID WORLD-2DPAGE(0003) IDOther 0003 Name World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome Desc World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome. Server http://www.expasy.org/world-2dpage/ Cat None EDAM Two-dimensional gel electrophoresis database; Arabidopsis database Link None LinkNB None Query World-2DPAGE entry| HTML| Sequence accession number| http://world-2dpage.expasy.org/repository/ac=%s&database=0003 Contact frederique lisacek Email frederique.lisacek@isb-sib.ch Note None Status None ID WORLD-2DPAGE(0004) IDOther 0004 Name World-wide gel-based proteomics database (0004) for mature rat olfactory bulb Desc World-wide gel-based proteomics database (0004) for mature rat olfactory bulb. Server http://www.expasy.org/world-2dpage/ Cat None EDAM Two-dimensional gel electrophoresis database Link None LinkNB None Query World-2DPAGE entry| HTML| Sequence accession number| http://world-2dpage.expasy.org/repository/ac=%s&database=0004 Contact frederique lisacek Email frederique.lisacek@isb-sib.ch Note None Status None ID WORLD-2DPAGE(0005) IDOther 0005 Name World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose Desc World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose. Server http://www.expasy.org/world-2dpage/ Cat None EDAM Two-dimensional gel electrophoresis database Link None LinkNB None Query World-2DPAGE entry| HTML| Sequence accession number| http://world-2dpage.expasy.org/repository/ac=%s&database=0005 Contact frederique lisacek Email frederique.lisacek@isb-sib.ch Note None Status None ID WORLD-2DPAGE(0006) IDOther 0006 Name World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee Desc World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee. Server http://www.expasy.org/world-2dpage/ Cat None EDAM Two-dimensional gel electrophoresis database Link None LinkNB None Query World-2DPAGE entry| HTML| Sequence accession number| http://world-2dpage.expasy.org/repository/ac=%s.1&database=0006 Contact frederique lisacek Email frederique.lisacek@isb-sib.ch Note None Status None ID SWISS-2DPAGE IDOther None Name Two-dimensional polyacrylamide gel electrophoresis database (SWISS-2DPAGE) Desc Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps. Server http://www.expasy.org/ch2d/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query Protein entry| HTML| SWISS-2DPAGE protein entry name| http://www.expasy.org/swiss-2dpage/%s Query Protein entry| HTML| Sequence accession number| http://www.expasy.org/swiss-2dpage/%s Query Protein entry| Text| Sequence accession number| http://www.expasy.org/swiss-2dpage/format=raw&extract&ac=%s Query SWISS-2DPAGE spot| HTML| SWISS-2DPAGE spot serial number| http://www.expasy.org/swiss-2dpage/spot=%s Query SWISS-2DPAGE protein list| HTML| Reference map name| http://www.expasy.org/swiss-2dpage/map=%s Query SWISS-2DPAGE reference map| HTML| Reference map name| http://www.expasy.org/swiss-2dpage/viewer&ac=all&map=%s Contact Unknown Email Unknown Note None Status Referenced ID SwissRegulon IDOther None Name SwissRegulon database of regulatory site annotations Desc Genome-wide annotations of regulatory sites. Server http://www.swissregulon.unibas.ch Cat None EDAM Transcription regulatory sites database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Erik van Nimwegen Email Erik.Vannimwegen@unibas.ch Note None Status None ID SYSTERS IDOther None Name SYSTERS protein family database Desc Large-scale protein clustering based on sequence similarity. Server http://systers.molgen.mpg.de/ Cat None EDAM Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email krause_a@molgen.mpg.de Note None Status None ID Systomonas IDOther None Name Systomonas database for systems biology of Systomonas Desc Molecular networks in pseudomonads with focus on Pseudomonas aeruginosa. Server http://www.systomonas.de/ Cat None EDAM Biological pathways database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Richard Münch Email r.muench@tu-bs.de Note None Status None ID SysZNFC2H2 IDOther None Name C2H2 zinc finger gene database (SysZNFC2H2) Desc An information resource for C2H2 Zinc Finger genes in human and mouse. Server http://epgd.biosino.org/SysZNF Cat None EDAM Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email hans-juergen.thiesen@med.uni-rostock.de Note None Status None ID T1Dbase IDOther None Name Type 1 diabetes database (T1Dbase) Desc Database for type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology. Server http://www.t1dbase.org/page/Welcome/display Cat None EDAM Disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Luc Smink Email Luc.Smink@cimr.cam.ac.uk Note None Status None ID TAED IDOther None Name The adaptive evolution database (TAED) Desc Protein-encoding gene families. Server http://www.bioinfo.no/tools/TAED Cat None EDAM Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID TAIR IDOther None Name The Arabidopsis information resource (TAIR) Desc Comprehensive information resources for Arabidopsis. Server http://www.arabidopsis.org/ Cat Organism-specific databases EDAM Arabidopsis database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.arabidopsis.org/servlets/TairObject?type=locus&name=%s Contact Unknown Email Unknown Note None Status Referenced ID TarBase IDOther None Name miRNA target database (TarBase) Desc The database of experimentally supported targets. Server http://microrna.gr/tarbase Cat None EDAM miRNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email gipapado@fleming.gr Note None Status None ID TassDB IDOther None Name Tandem splice site database Desc TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Server http://helios.informatik.uni-freiburg.de/TassDB/ Cat None EDAM Splice sites database; Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Michael Hiller Email tassdb@informatik.uni-freiburg.de Note None Status None ID taxon IDOther None Name NCBI's taxonomic identifier Desc NCBI's taxonomic identifier Server http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html Cat None EDAM Taxonomic database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="taxon:4932" Status Referenced ID TBMap IDOther None Name Mapping names in TreeBASE Desc TBMap is a project to map names in the the phylogenetic database TreeBASE to names in taxonomic databases, such as uBio, ITIS, IPNI, and the NCBI taxonomy database. Server http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap Cat None EDAM Taxonomic database; Phylogenetic database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email r.page@bio.gla.ac.uk Note None Status None ID TCACycle IDOther None Name TCA cycle gene mutation database Desc TCA cycle gene mutation database. Server http://chromium.liacs.nl/lovd_sdh/home.php Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jean-Pierre Bayley Email J.P.L.Bayley@lumc.nl Note None Status None ID TCDB IDOther None Name Transport classification database Desc A comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. Server http://www.tcdb.org/ Cat Protein family/group databases EDAM Membrane protein database; Protein sequence classification database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.tcdb.org/tcdb/transporter.php?tc=%s Contact Unknown Email Unknown Note None Status Referenced ID TDR IDOther None Name TDR targets database Desc Identification and ranking of targets against neglected tropical diseases. Server http://tdrtargets.org/ Cat None EDAM Drug and drug design database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email tdr-targetgroup@sanger.ac.uk Note None Status None ID 1000Genomes IDOther None Name The 1000 Genomes project Desc Database of human genetic variation. Server http://1000genomes.org/page.php Cat None EDAM Polymorphism database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Laura Clarke Email laura@ebi.ac.uk Note None Status None ID TIGR IDOther None Name The bacterial database(s) of The Institute of Genome Research Desc The TIGR Arabidopsis thaliana Genome Annotation Database. Server http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml Cat Genome annotation databases EDAM Genome annotation database; Arabidopsis database Link SP_explicit LinkNB None Query Unknown| HTML| ???| cmr.tigr.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s Contact Unknown Email Unknown Note None Status Referenced ID TIGRFAM IDOther None Name A protein family database Desc Protein families based on hidden Markov models (HMMs). Server http://www.tigr.org/TIGRFAMs/ Cat Family and domain databases EDAM Protein sequence classification database; Sequence motif or profile database Link SP_explicit LinkNB None Query TIGRFAM entry| HTML| TIGRFAM ID| http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi?hmm_acc=%s Contact Unknown Email Unknown Note None Status Referenced ID TmaDB IDOther None Name Tissue microarray database Desc Tissue microarray (TMA) database for archiving all aspects of data associated with TMAs. Server http://www.bioinformatics.leeds.ac.uk/tmadb/ Cat None EDAM Gene expression and microarray database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Archana Sharma-Oates Email a.sharmaoates@leeds.ac.uk Note None Status None ID Tomatestdb IDOther None Name An EST database from multiple Tomato species Desc A collection of tomato EST sequences downloaded from dbEST. Server http://biosrv.cab.unina.it/tomatestdb/ Cat None EDAM mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Chiusano Maria Luisa Email chiusano@unina.it Note None Status None ID TopDB IDOther None Name Topology of transmembrane proteins Desc Transmembrane protein datasets containing experimentally derived topology information. Server http://topdb.enzim.hu Cat None EDAM Membrane protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Istvan Simon Email simon@enzim.hu Note None Status None ID TOPDOM IDOther None Name Transmembrane domains and motifs Desc A collection of domains and sequence motifs located conservatively in one side of transmembrane proteins. Server http://topdom.enzim.hu Cat None EDAM Membrane protein database; Nucleotide sequence motif or profile database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email tusi@enzim.hu Note None Status None ID TOPS IDOther None Name Topology of protein structures Desc Topology of protein structures Server http://www.tops.leeds.ac.uk Cat None EDAM Protein secondary structure and alignment database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID ToxWiz IDOther None Name Target mechanisms of action of compounds Desc Database for predicting toxic endpoints and for elucidating mechanisms of toxicity. Server http://www.camcellnet.com/products.php?id=1 Cat None EDAM Chemical and small molecule database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email info@camcellnet.com Note None Status None ID Transdab IDOther None Name Database of transglutaminase substrate proteins Desc Database of transglutaminase substrate proteins. Server http://genomics.dote.hu/wiki Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Eva Csosz Email cseva(at)med.unideb.hu Note None Status None ID TRANSPATH IDOther None Name TRANSPATH database Desc Information on signaling molecules, metabolic enzymes, second messengers, endogenous metabolites, miRNAs and the reactions they are involved in, resulting in a complex network of interconnected chains of reactions and pathways. Server http://www.biobase.de/index.php?id=transpathdatabases Cat None EDAM Signalling pathways database; Enzyme database; Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email mkl@biobase.de Note None Status None ID TranspoGene IDOther None Name Transposed elements in proteins for 7 organisms Desc Data on the influence of Transposed Elements (TEs) on the transcriptome of 7 species. Server http://transpogene.tau.ac.il/ Cat None EDAM Mobile genetic elements database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Asaf Levy Email asaflev1@post.tau.ac.il Note None Status None ID TRBase IDOther None Name Tandem repeats database Desc Tandem repeats in the human genome. Server http://trbase.ex.ac.uk/ Cat None EDAM Repeat sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Stephen Aves Email S.J.Aves@exeter.ac.uk Note None Status None ID TreeFam IDOther None Name Phylogenetic trees of animal genes Desc Phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. Server http://www.treefam.org Cat None EDAM Phylogenetic database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Richard Durbin Email rd@sanger.ac.uk Note None Status None ID tRNASequences IDOther None Name tRNA sequences database Desc Compilation of tRNA sequences and sequence of tRNA genes. Server http://www.staff.uni-bayreuth.de/~btc914/search/index.html Cat None EDAM Nucleotide sequence database; tRNA database; Genes database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Mathias.Sprinzl@uni­bayreuth.de Note None Status None ID TropGENE-DB IDOther None Name TropGENE database Desc Genetic and genomic information about tropical crops studied by Cirad. Server http://tropgenedb.cirad.fr/ Cat None EDAM Genome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Manuel Ruiz Email ruiz@cirad.fr Note None Status None ID TrSDB IDOther None Name TrSDB transcription factors Desc Biological Proteome KnowledgeBase linking IPI and SPTR-NR based Proteome analyses with TranScout, TransMem and ProtLoc and offering crosslinks with other relevant biodatabases such as SWISS-PROT, NCBI Refseq, Ensembl, InterPro or Gene Ontology Annotation. Server http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl Cat None EDAM Transcription factor and binding site database; Proteome database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note None Status None ID TubercuList IDOther None Name Mycobacterium tuberculosis strain H37Rv genome database Desc Mycobacterium tuberculosis strain H37Rv genome database Server http://genolist.pasteur.fr/TubercuList/ Cat Organism-specific databases EDAM Prokaryote genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| genolist.pasteur.fr/TubercuList/genome.cgi?external_query+%s Contact Unknown Email Unknown Note None Status Referenced ID U12DB IDOther None Name U12-type intron database Desc U12-type intron database Server http://genome.imim.es/cgi-bin/u12db/u12db.cgi Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Tyler Alioto Email talioto@imim.es Note None Status None ID UMD-DMD IDOther None Name UMD-DMD France genotype-phenotype dystrophinopathy patients Desc Knowledgebase related to mutations of the DMD gene. Server http://www.umd.be/DMD/ Cat None EDAM Genotype / phenotype database; Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Sylvie Tuffery-Giraud Email sylvie.tuffery@inserm.fr Note None Status None ID UniGene IDOther None Name UniGene gene-oriented nucleotide sequence clusters Desc Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. Server http://www.ncbi.nlm.nih.gov/sites/entrez?db=UniGene Cat Sequence databases EDAM mRNA, EST or cDNA database; Nucleic acid sequence classification database; Gene expression and microarray database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s1&CID=%s2 Contact Unknown Email Unknown Note None Status Referenced ID UniHI IDOther None Name Unified human interactome database Desc Protein interaction analysis. Server http://www.mdc-berlin.de/unihi Cat None EDAM Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Matthias Futschik Email m.futschik@biologie.hu-berlin.de Note None Status None ID UNILIB IDOther None Name Unified library database Desc A library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap. Server http://binfo.ym.edu.tw/edu/seminars/clho/UniLib Browser_kidney.htm Cat None EDAM mRNA, EST or cDNA database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="UNILIB:1002" Status Referenced ID UniSave IDOther None Name Uniprot version archive Desc A repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. Server http://www.ebi.ac.uk/uniprot/unisave/ Cat None EDAM Protein sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Rolf Apweiler Email apweiler@ebi.ac.uk Note None Status None ID UNITE IDOther None Name UNITE rDNA sequences from ectomycorrhizal asco- and basidiomycetes Desc UNITE is a rDNA sequence database focused on ectomycorrhizal asco- and basidiomycetes. Server http://unite.ut.ee/ Cat None EDAM rDNA sequence database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Urmas Kõljalg Email koljalg@ut.ee Note None Status None ID UniTrap IDOther None Name UniTrap gene trap clones Desc Tools for the biologist enabling optimized use of gene trap clones. Server http://unitrap.cbm.fvg.it/ Cat None EDAM Gene structure database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Guglielmo Roma Email guglielmo.roma@gmail.com Note None Status None ID UMD IDOther None Name Universal mutation database Desc Collection of mutations in human genes associated with genetic diseases. Server http://umd.be Cat None EDAM Human genes, mutation and disease database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email g.collod-beroud@inserm.montp.fr Note None Status None ID UniProt IDOther SwissProt Name Universal protein resource Desc A comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Server http://www.uniprot.org/ Cat None EDAM Protein sequence database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Rolf Apweiler Email apweiler@ebi.ac.uk Note None Status None ID UniProtKB/Swiss-Prot IDOther SwissProt Name Universal protein resource knowledge base / Swiss-Prot Desc Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature Server http://www.uniprot.org Cat None EDAM Protein sequence database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Lydie Bougueleret Email Lydie.bougueleret@sib-isb.ch Note Example cross-reference: /db_xref="UniProtKB/Swiss-Prot:P12345" Status None ID UniProtKB/TrEMBL IDOther None Name Universal protein resource knowledge base / Swiss-Prot Desc Section of the UniProt knowledgebase, containing computationally analysed records waiting for full manual annotation Server http://www.uniprot.org/ Cat None EDAM Protein sequence database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Lydie Bougueleret Email Lydie.bougueleret@sib-isb.ch Note Example cross-reference: /db_xref=" UniProtKB/TrEMBL:Q00177" Status None ID UniRef IDOther None Name Non-redundant reference (UniRef) databases Desc Clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view. Server http://www.uniprot.org/help/uniref Cat Other EDAM Protein sequence classification database Link SP_implicit LinkNB All Swiss-Prot and TrEMBL (UniProt knowledgebase) entries Query Unknown| HTML| ???| ??? Contact Unknown Email Unknown Note None Status Referenced ID UTILLdb IDOther None Name URGV TILLING platform databases Desc Lines, phenotype categories, sequences and mutations for pea and tomatoe. Server http://urgv.evry.inra.fr/UTILLdb Cat None EDAM Genotype / phenotype database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Brunaud Email brunaud@evry.inra.fr Note None Status None ID UTRdb IDOther None Name Regulatory motifs in eukaryotic UTRs Desc UTResource collect data and analysis tool for the functional classification of 5' and 3'UTRs of eukaryotic mRNAs. Server http://www.ba.itb.cnr.it/UTR/ Cat None EDAM Transcription regulatory sites database; Nucleotide sequence motif or profile database; mRNA, EST or cDNA database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Graziano Pesole Email graziano.pesole@biologia.uniba.it Note None Status None ID UTRsite IDOther None Name Regulatory motifs in eukaryotic UTRs Desc UTRSite is a collection of functional sequence patterns located in 5' or 3' UTR sequences. Server http://www.ba.itb.cnr.it/UTR/ Cat None EDAM Transcription regulatory sites database; Nucleotide sequence motif or profile database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Graziano Pesole Email graziano.pesole@biologia.uniba.it Note None Status None ID VBASE2 IDOther None Name Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse Desc An integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank. Server http://www.vbase2.org/ Cat None EDAM Immunological genes or proteins database Link db_xref LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown Note Example cross-reference: /db_xref="VBASE2:humIGKV165" Status Referenced ID VectorBase IDOther None Name Invertebrate vectors of human pathogens Desc Invertebrate vectors of human pathogens. Server http://www.vectorbase.org/ Cat Genome annotation databases EDAM Pathogen database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.vectorbase.org/Genome/BRCGene/?gene=%s Contact Daniel Lawson Email lawson@ebi.ac.uk Note Example cross-reference: db_xref="VectorBase:ENSANGG00000007825" Status Referenced ID VEGA IDOther None Name Vertebrate Genome Annotation (VEGA) database Desc A central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence. Server http://vega.sanger.ac.uk/ Cat None EDAM Genome annotation database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Jen Harrow Email jla1@sanger.ac.uk Note None Status None ID VIDA IDOther None Name Virus Database at University College London Desc VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, you can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures. Server http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA3/VIDA.html Cat None EDAM Virus-specific database; Sequence alignment database; Protein sequence classification database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email m.alba@ucl.ac.uk Note None Status None ID VirusMINT IDOther None Name Viral protein interaction Desc VirusMINT aims at collecting and annotating in a structured format all the interactions between human and viral proteins and to integrate this information in the human protein interaction network. Server http://mint.bio.uniroma2.it/virusmint/ Cat None EDAM Virus-specific database; Protein-protein interaction database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Gianni Cesareni Email cesareni@uniroma2.it Note None Status None ID VSGdb IDOther None Name A database of trypanosomal variant surface glycoproteins Desc A database of trypanosomal variant surface glycoproteins. Server http://leishman.cent.gla.ac.uk/pward001/vsgdb/kook_index.html Cat None EDAM Specific protein database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact John Wilkes Email l.marcello.1@research.gla.ac.uk Note None Status None ID WorfDB IDOther None Name The C.elegans ORFeome cloning project Desc The C.elegans ORFeome cloning project Server http://worfdb.dfci.harvard.edu/ Cat Organism-specific databases EDAM Organism-specific database Link SP_implicit LinkNB All C.elegans entries with an explicit cross-reference to WormPep Query Unknown| HTML| ???| worfdb.dfci.harvard.edu/searchallwormorfs.pl?by=name&sid=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="WorfDB:pos-1" Status Referenced ID World-2DPAGE IDOther None Name The world-2DPAGE database Desc A public repository, standards compliant, for proteomics image data published in the literature. Server http://world-2dpage.expasy.org/repository/ Cat 2D gel databases EDAM Two-dimensional gel electrophoresis database Link SP_explicit LinkNB None Query Unknown| HTML| ???| world-2dpage.expasy.org/repository/%s Contact Unknown Email Unknown Note None Status Referenced ID WormBase IDOther None Name Caenorhabditis elegans genome database Desc Caenorhabditis elegans genome database Server http://www.wormbase.org/ Cat Organism-specific databases EDAM Invertebrate genome database; Organism-specific database Link SP_explicit| db_xref LinkNB None Query Unknown| HTML| ???| www.wormbase.org/db/gene/gene?name=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="WormBase:R13H7" Status Referenced ID Xenbase IDOther None Name Xenopus laevis and tropicalis biology and genomics resource Desc Xenopus laevis and tropicalis biology and genomics resource Server http://www.xenbase.org/ Cat Organism-specific databases EDAM Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| www.xenbase.org/gene/showgene.do?method=display&geneId=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref=Xenbase:XB-GENE-1019547 Status Referenced ID Yeast complexes IDOther None Name Yeast complexes database Desc Information on protein-protein interactions and protein complexes in yeast. Server http://yeast-complexes.embl.de/ Cat None EDAM Protein-protein interaction database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Rob Russel Email complexes@embl.de Note None Status None ID Yeast-GFP IDOther None Name Yeast GFP fusion localization database Desc Yeast GFP fusion localization database Server http://yeastgfp.ucsf.edu Cat Organism-specific databases EDAM Organism-specific database; Gene structure database; Fungi-specific database Link SP_implicit LinkNB All Swiss-Prot entries from Saccharomyces cerevisiae with Y[A-Z]{2}[0-9]{3}[A-Z] in the GN line Query Unknown| HTML| ???| yeastgfp.ucsf.edu/getOrf.php?orf=%s Contact Unknown Email Unknown Note None Status Referenced ID YEASTRACT IDOther None Name Transcriptional regulators database Desc A curated repository of more than 34469 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1000 bibliographic references. It also includes the description of 291 specific DNA binding sites for more than a hundred characterized TFs. Server http://www.yeastract.com Cat None EDAM Transcription regulatory sites database; Transcription factor and binding site database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Isabel S‡ Correia Email isacorreia@ist.utl.pt Note None Status None ID YGOB IDOther None Name Yeast gene order browser Desc Tool for visualising the syntenic context of any gene from several yeast genomes. Server http://wolfe.gen.tcd.ie/ygob Cat None EDAM Genetic map or linkage database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Kevin Byrne Email kevin.byrne@tcd.ie Note None Status None ID yMGV IDOther None Name Yeast microarray global viewer Desc Transcriptional expression profiles of yeast genes among most of the published expression datasets. Server http://transcriptome.ens.fr/ymgv/ Cat None EDAM Gene expression and microarray database; Fungi-specific database Link None LinkNB None Query Unknown| Unknown| Unknown| Unknown Contact Unknown Email Unknown ID ZFIN IDOther None Name Zebrafish information network genome database Desc Zebrafish information network genome database Server http://zfin.org/ Cat Organism-specific databases EDAM Vertebrate genome database; Organism-specific database Link SP_explicit LinkNB None Query Unknown| HTML| ???| zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=%s Contact Unknown Email Unknown Note Example cross-reference: /db_xref="ZFIN:ZDB-GENE-011205-17" Status Referenced