# DRCAT.dat
# Data Resource Catalogue
#
# Date:    21:06:2011 14:47
# Version: alpha 1 (DRCAT_alpha1)
# Created: June 2009 (Jon Ison)
# Updated: June 2011 (Jon Ison & Peter Rice)

ID      1000Genomes
Name    The 1000 Genomes project
Desc    Database of human genetic variation.
URL     http://1000genomes.org/page.php
Taxon   9606 | Homo sapiens
EDAMtpc 0199 | Genetic variation

ID      2dpage
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.
URL     http://www.mpiib-berlin.mpg.de/2D-PAGE
Taxon   1 | all
EDAMtpc 0121 | Proteomics


ID      3Dgenomics
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.
URL     http://www.sbg.bio.ic.ac.uk/3dgenomics
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 3040 | Protein structure

ID      3did
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.
URL     http://3did.irbbarcelona.org/
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0166 | Protein structural motifs and surfaces
EDAMdat 2377 | Protein structure report (domain)
EDAMdat 2359 | Domain-domain interaction
EDAMdat 2378 | Protein-motif interaction
EDAMid  1138 | Pfam accession number
EDAMid  2757 | Pfam domain name
EDAMid  1116 | ELM ID
EDAMfmt 2331 | HTML
Query   Protein structure report (domain) | HTML | Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_domain_cgi.pl?draw=graph&domain=%s
Query   Protein structure report (domain) | HTML | Pfam accession number | http://3did.irbbarcelona.org/cgi-bin/query_pfamID_cgi.pl?draw=graph&id=%s
Query   Domain-domain interaction | HTML | Pfam domain name;Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_interaction_cgi.pl?domain1=%s1&db=Pfam&domain2=%s2
Query   Domain-domain interaction | HTML | Pfam domain name;Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_path_cgi.pl?domain1=%s1&domain2=%s2
Query   Protein structure report (domain) | HTML | ELM ID | http://3did.irbbarcelona.org/cgi-bin/query_peptide_cgi.pl?draw=graph&peptide=%s
Query   Protein-motif interaction | HTML | Pfam domain name;ELM ID | http://3did.irbbarcelona.org//cgi-bin/query_dmi_cgi.pl?domain=%s1&ddb=%&peptide=%s2&mdb=ELM
Example Pfam domain name | SH3_1
Example Pfam accession number | PF00018
Example Pfam domain name | Ank
Example Pfam domain name | SH3_1
Example Pfam domain name | SH2
Example Pfam domain name | efhand
Example ELM ID | LIG_SH3_1
Example ELM ID | LIG_SH3_1

ID      3DMET
Name    3DMET
Desc    Three-dimensional structures of natural metabolites.
URL     http://www.3dmet.dna.affrc.go.jp/
Taxon   1 | all
EDAMtpc 0154 | Small molecules
EDAMtpc 0079 | Metabolites

ID      4dxpress
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.
URL     http://4dx.embl.de/4DXpress
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMid  1033 | Gene ID (Ensembl)
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Query   Gene annotation | HTML | Gene ID (Ensembl) | http://4dx.embl.de/4DXpress/reg/all/search/bquery.do?id=%s
Example Gene ID (Ensembl) | ENSMUSG00000036026

ID      5srrna
Name    5S rRNA database
Desc    Information on nucleotide sequences of 5S rRNAs and their genes.
URL     http://biobases.ibch.poznan.pl/5SData/
Taxon   1 | all
EDAMtpc 0660 | rRNA
EDAMtpc 0623 | Genes, gene family or system

ID      a1atvar
Name    A1ATVar A1-antitrypsin database
Desc    Database of human SERPINA1 gene variants leading to alpha1-antitrypsin deficiency
URL     http://www.goldenhelix.org/a1atvar/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      Aarhus_Ghent-2DPAGE
Acc     DB-0114
Name    Human keratinocyte 2D gel protein database from Aarhus and Ghent universities
Desc    Human keratinocyte 2D gel protein database from Aarhus and Ghent universities
Cat     2D gel databases
URL     None
Taxon   9606 | Homo sapiens
EDAMtpc 0767 | Protein and peptide identification
EDAMid  0842 | Identifier
Xref    SP_explicit | Identifier {Aarhus/Ghent-2DPAGE}
Example Identifier {Aarhus/Ghent-2DPAGE} | 9109

ID      abcdb
Name    Archaeal and bacterial ABC transporter database (ABCdb)
Desc    Archaeal and bacterial ABC transporter database.
URL     http://www-abcdb.biotoul.fr
Taxon   2 | Bacteria
Taxon   2157 | Archaea
EDAMtpc 0820 | Membrane proteins

ID      abs
Name    ABS database of binding sites from orthologous promoters
Desc    Annotated regulatory binding sites from orthologous promoters.
URL     http://genome.imim.es/datasets/abs2005/
Taxon   1 | all
! EDAMtpc 0111 | Promoters
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMdat 1312 | Gene features (promoter)
EDAMid  2741 | ABS ID
EDAMfmt 2331 | HTML
Query   Gene features (promoter) | HTML | ABS ID | http://genome.crg.es/datasets/abs2005/entries/%s.html
Example ABS ID | A0001

ID      aceview
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).
URL     http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
URLlink http://www.ncbi.nlm.nih.gov/ieb/research/acembly/AboutAceView.v69.html#quote
Cat     Not available
Taxon   3702 | Arabidopsis thaliana
Taxon   6239 | Caenorhabditis elegans
Taxon   9606 | Homo sapiens
Taxon   10088 | Mus
Taxon   10114 | Rattus
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0623 | Genes, gene family or system
EDAMdat 0916 | Gene annotation
EDAMdat 0929 | Gene annotation (expression)
EDAMdat 2394 | Gene annotation (functional)
EDAMdat 1300 | Nucleic acid features (gene structure)
EDAMdat 2703 | Gene annotation (clone or EST)
EDAMid  1045 | Species name
EDAMid  1108 | GenBank accession
EDAMid  2296 | Gene name (AceView)
EDAMid  1027 | Gene ID (NCBI)
EDAMid  2704 | Clone ID (IMAGE)
EDAMid  2803 | Clone ID (RefSeq)
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Species name;Gene name (AceView) | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Query   Gene annotation (expression) | HTML | Species name;Gene name (AceView) | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fexp
Query   Gene annotation (functional) | HTML | Species name;Gene name (AceView) | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=ffunc
Query   Nucleic acid features (gene structure) | HTML {AceView alternative} | Species name;Gene name (AceView) | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fmol
Query   Nucleic acid features (gene structure) | HTML {AceView single} | Species name;Gene name (AceView) | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fiche
Query   Gene annotation | HTML | Species name;Gene ID (NCBI) | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Query   Gene annotation | HTML | Species name;Clone ID (RefSeq) | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Query   Gene annotation | HTML | Species name;Clone ID (IMAGE) {GenBank cDNA ID} | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Query   Gene annotation (clone or EST) {Genbank to human AceView} | HTML | Species name;GenBank accession | http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2
Example Species name | human
Example Gene name (AceView) | pten
Example Gene ID (NCBI) | 266
Example Clone ID (RefSeq) | NM_000014.3
Example Clone ID (IMAGE) | image:4838723
Example GenBank accession | AY487421

ID      ACLAME
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.
URL     http://aclame.ulb.ac.be
Taxon   1 | all
EDAMtpc 0798 | Mobile genetic elements

ID      AffinDB
Name    Affinity database (AffinDB) for protein–ligand complexes
Desc    Affinity database for protein–ligand complexes
URL     http://www.agklebe.de/affinity
Taxon   1 | all
EDAMtpc 0148 | Protein-ligand interactions

ID      AFTOL
Name    Assembling the Fungal Tree of Life (AFTOL) database
Desc    Fungal structural and biochemical database.
URL     http://www.aftol.org/index.php
Cat     Not available
Taxon   4751 | Fungi
EDAMtpc 0782 | Fungi
EDAMid  1045 | Species name
EDAMid  1870 | Genus name
EDAMdat 2395 | Fungi annotation
EDAMdat 2396 | Fungi annotation (anamorph)
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Fungi annotation | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2
Query   Fungi annotation (anamorph) | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2__(anamorph)
Example Genus name | Aspergillus
Example Species name | giganteus

ID      AGD
Acc     DB-0001
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.
URL     http://agd.vital-it.ch/
Cat     Organism-specific databases
Taxon   33169 | Eremothecium gossypii
EDAMtpc 0782 | Fungi
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0197 | Gene expression resources
EDAMid  1026 | Gene symbol
EDAMid  1045 | Species name
EDAMdat 0916 | Gene annotation
EDAMdat 2397 | Gene features (exon)
EDAMdat 0896 | Protein report
EDAMdat 2399 | Gene annotation (transcript)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene symbol
Query   Gene annotation | HTML | Gene symbol | http://agd.vital-it.ch/Ashbya_gossypii/geneview?db=core;gene=%s
Query   Gene annotation (transcript) | HTML | Gene symbol | http://agd.vital-it.ch/Ashbya_gossypii/transview?db=core;transcript=%s
Query   Gene features (exon) | HTML | Gene symbol | http://agd.vital-it.ch/Ashbya_gossypii/exonview?db=core;transcript=%s
Query   Protein report | HTML | Gene symbol | http://agd.vital-it.ch/Ashbya_gossypii/protview?db=core;peptide=%s
Query   Gene annotation | HTML | Species name;Gene symbol | http://agd.vital-it.ch/%s1/geneview?gene=%s2
Example Species name | Ashbya_gossypii
Example Gene symbol | AAL011C
Example Gene symbol | ACL127W
Example Gene symbol | RLP7

ID      Allergome
Acc     DB-0160
Name    Allergome; a platform for allergen knowledge
Desc    Allergome; a platform for allergen knowledge
URL     http://www.allergome.org/
Cat     Protein family/group databases
Taxon   9606 | Homo sapiens
EDAMtpc 0804 | Immunoinformatics
EDAMdat 2018 | Annotation
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {Allergome}
Query   Annotation | HTML | Identifier {Allergome} | http://www.allergome.org/script/dettaglio.php?id_molecule=%s
Example Identifier {Allergome} | 2681

ID      AMYPDB
Name    Amyloid precursor proteins database (AMYPDB)
Desc    Amyloid precursor families and their amino acid sequence signatures.
URL     http://amyPDB.univ-rennes1.fr/
Taxon   9606 | Homo sapiens
EDAMtpc 2813 | Disease genes and proteins

ID      ANPR
Name    Arabidopsis nucleolar protein database (ANPR)
Desc    Comparative analysis of human and Arabidopsis nucleolar proteomes
URL     http://bioinf.scri.sari.ac.uk/cgi-bin/atnoPDB/proteome_comparison
Taxon   3701 | Arabidopsis
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0780 | Plants
EDAMtpc 0797 | Comparative genomics

ID      Antibodypedia
Name    Antibodypedia database of antibodies to human proteins
Desc    Application-specific validation of publicly available antibodies to human protein targets.
URL     http://www.antibodypedia.org
Taxon   9606 | Homo sapiens
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens

ID      AntiJen
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.
URL     http://www.darrenflower.info/AntiJen
Taxon   7711 | Chordata
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0613 | Peptides and amino acids

ID      ANU-2DPAGE
Acc     DB-0002
Name    Australian National University 2-DE database (ANU-2DPAGE)
Desc    2-DE PAGE database.
URL     http://semele.anu.edu.au
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMid  3021 | UniProt accession
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://semele.anu.edu.au/cgi-bin/get-2d-entry?%s
Example UniProt accession | P02930
Example UniProt accession | Q9SIB9

ID      AphidBase
Name    Aphid genome database (AphidBase)
Desc    Aphid genome database
URL     http://www.aphidbase.com/aphidbase/
Taxon   27482 | Aphididae
EDAMtpc 2819 | Invertebrates


ID      APID
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).
URL     http://bioinfow.dep.usal.es/apid/index.htm
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions

ID      EuPathDB
IDalt   ApiDB
Acc     DB-0153
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).
URL     http://eupathdb.org/eupathdb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5794 | Apicomplexa
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene symbol
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene symbol | http://www.eupathdb.org/gene/%s
Example Gene symbol | cgd1_1090

ID      ApiDB_CryptoDB
IDalt   CryptoDB
Name    Cryptosporidium genome resources (CryptoDB)
Desc    Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium.
URL     http://cryptodb.org/cryptodb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5806 | Cryptosporidium
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID | http://cryptodb.org/gene/%s
Example Gene ID | cgd7_20

ID      ApiDB_PlasmoDB
IDalt   PlasmoDB
Name    Plasmodium genome resources (PlasmoDB)
Desc    Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium.
URL     http://plasmodb.org/plasmo/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5820 | Plasmodium
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID | http://plasmodb.org/gene/%s
Example Gene ID | PF11_0344

ID      ApiDB_ToxoDB
IDalt   ToxoDB
Name    Toxoplasma genome resources (ToxoDB)
Desc    Genomic-scale datasets associated with the eukaryotic pathogens Toxoplasma.
URL     http://toxodb.org/toxo/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5810 | Toxoplasma
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID | http://toxodb.org/gene/%s
Example Gene ID | 49.m00014

ID      ApiDB_TrichDB
IDalt   TrichDB
Name    Trichomonas genome resources (TrichDB)
Desc    Genomic-scale datasets associated with the eukaryotic Trichomonas.
URL     http://trichdb.org/trichdb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5721 | Trichomonas
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID | http://trichdb.org/gene/%s
Example Gene ID | TVAG_386080

ID      ApiDB_TriTryPDB
IDalt   TritryPDB
Name    Kinetoplastid genome resources (TritryPDB)
Desc    Kinetoplastid genome resources.
URL     http://tritryPDB.org/tritryPDB/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5653 | Kinetoplastida
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID | http://tritryPDB.org/gene/%s
Example Gene ID | Tb927.8.620

ID      ApiDB_GiardiaDB
IDalt   GiardiaDB
Name    Giardia genome resources (GiardiaDB)
Desc    Genomic-scale datasets for the eukaryotic pathogen Giardia.
URL     http://giardiadb.org/giardiadb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5740 | Giardia
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID | http://giardiadb.org/gene/%s
Example Gene ID | GL50803_102438

ID      AppaDB
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.
URL     http://www.pristionchus.org
Taxon   54126 | Pristionchus pacificus
EDAMtpc 2820 | Vertebrates
EDAMtpc 0796 | Genetic mapping and linkage
EDAMtpc 0655 | mRNA, EST or cDNA

ID      ArachnoServer
Acc     DB-0145
Name    ArachnoServer
Desc    Spider toxin database
URL     http://www.arachnoserver.org
Cat     Organism-specific databases
Taxon   6845 | Arachnida
EDAMtpc 2661 | Toxins and targets
EDAMdat 2400 | Toxin annotation
EDAMid  2578 | ArachnoServer ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | ArachnoServer ID;Toxin name
Query   Toxin annotation | HTML | ArachnoServer ID | http://www.arachnoserver.org/toxincard.html?id=%s
Example ArachnoServer ID | AS000014

ID      AraC-XylS
Acc     DB-0003
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.
URL     http://www.eez.csic.es/arac-xyls/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMdat 2147 | Protein report (transcription factor)
EDAMid  2742 | AraC-XylS ID
EDAMfmt 2331 | HTML
Xref    SP_implicit | AraC-XylS ID
Query   Protein report (transcription factor) {AraC-XylS entry} | HTML | AraC-XylS ID | http://www.eez.csic.es/arac-xyls/wfichas/%s.HTM
Example AraC-XylS ID | HpaA

ID      ARAMEMNON
Name    ARAMEMNON database of plant membrane proteins
Desc    Plant membrane proteins.
URL     http://aramemnon.botanik.uni-koeln.de/
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0820 | Membrane proteins
EDAMtpc 0780 | Plants
EDAMdat 1456 | Protein report (membrane protein)
EDAMid  1895 | Locus ID (AGI)
EDAMfmt 2331 | HTML
Query   Protein report (membrane protein) | HTML | Locus ID (AGI) | http://aramemnon.uni-koeln.de/seq_view.ep?search=%s
Example Locus ID (AGI) | At1g10970

ID      ArchDB
Name    ArchDB database of loop structures
Desc    ArchDB database of loop structures.
URL     http://sbi.imim.es/cgi-bin/archdb/loops.pl
Taxon   1 | all
EDAMtpc 0166 | Protein structural motifs and surfaces
EDAMdat 0899 | Protein structure report (3D motif)
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Query   Protein structure report (3D motif) {Loop structure annotation} | HTML | PDB ID | http://sbi.imim.es/cgi-bin/archdb//loops.pl?PDB=%s
Example PDB ID | 1iiu

ID      Argonaute
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.
URL     http://argonaute.uni-hd.de
Taxon   40674 | Mammalia
! EDAMtpc 0661 | miRNA
EDAMtpc 3060 | Regulatory RNA
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 2846 | Gene regulatory networks

ID      ArrayExpress
Acc     DB-0004
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.
URL     http://www.ebi.ac.uk/arrayexpress/
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMtpc 0200 | Microarrays
EDAMdat 0931 | Experiment annotation (microarray)
EDAMdat 0929 | Gene annotation (expression)
EDAMid  0989 | Protein identifier
EDAMid  1144 | ArrayExpress accession number
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier
Query   Gene annotation (expression) {ArrayExpress gene expression summary} | HTML | Protein identifier | http://www.ebi.ac.uk/arrayexpress/genes/uniprot/%s
Query   Experiment annotation (microarray) {ArrayExpress entry} | HTML | ArrayExpress accession number | http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=%s
Example Protein identifier | P15455
Example ArrayExpress accession number | E-MEXP-700

ID      ASAP
Name    Systematic annotation package for community analysis of genomes (ASAP)
Desc    Genome sequences, associated annotations and functional characterization data for E. coli K-12.
URL     http://www.genome.wisc.edu/tools/asap.htm
Cat     Not available
Taxon   562 | Escherichia coli
EDAMtpc 1811 | Prokaryotes and archae
Xref    SP_FT | None
Example Identifier | ABE-0000006

ID      ASC
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.
URL     http://bioinformatica.isa.cnr.it/ASC/
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMtpc 0613 | Peptides and amino acids

ID      ASPICdb
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.
URL     http://t.caspur.it/ASPicDB/
Taxon   9606 | Homo sapiens
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMdat 2399 | Gene annotation (transcript)
EDAMdat 0896 | Protein report
EDAMid  1026 | Gene symbol
EDAMfmt 2331 | HTML
Query   Gene annotation (transcript) | HTML | Gene symbol | http://www.caspur.it/ASPicDB/resultsj.php?table=Transcript&organism=human&accession=Hugo&gene_name=%s
Query   Protein report | HTML | Gene symbol | http://www.caspur.it/ASPicDB/resultsj.php?table=Protein&organism=human&accession=Hugo&gene_name=%s
Example Gene symbol | tp53

ID      ASTD
Name    Alternative splicing and transcript diversity (ASTD) database
Desc    Alternative splice events and the resultant isoform splice patterns of genes from human and other model species. Three databases are available: AltSplice, AltExtron, and AEdb. AltSplice and AltExtron provide information on alternative intron/exons, alternative splice events, and isoform splice patterns.  AEdb contains: AEdb-Sequence (sequence and properties of alternatively splice exons), AEdb-Function (data on functional aspects of alternative splicing), AEdb-motif (data and sequence of known splice regulatory motifs), and AEdb-minigene (a collection of known minigene constructs for alternative splice events).
URL     http://www.ebi.ac.uk/astd/
NARid   28
NARCat  /nar/database/cat/1 | Nucleotide Sequence Databases
NARSub  /nar/database/subcat/1/3 | Gene structure, introns and exons, splice sites
Abstrct http://nar.oupjournals.org/cgi/content/abstract/34/suppl_1/D46
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMid  2367 | ASTD ID
EDAMid  2368 | ASTD ID (exon)
EDAMid  2369 | ASTD ID (intron)
EDAMid  2370 | ASTD ID (polya)
EDAMid  2371 | ASTD ID (tss)
EDAMdat 2397 | Gene features (exon)
EDAMdat 0896 | Protein report
EDAMdat 2399 | Gene annotation (transcript)
EDAMdat 0916 | Gene annotation
EDAMdat 1312 | Gene features (promoter)
EDAMdat 2397 | Gene features (exon)
EDAMdat 2754 | Gene features (intron)
EDAMdat 1302 | Nucleic acid features (PolyA signal)
EDAMid  1033 | Gene ID (Ensembl)
EDAMid  2398 | Protein ID (Ensembl)
EDAMfmt 1927 | EMBL format
EDAMfmt 2305 | GFF
EDAMfmt 2306 | GTF
EDAMfmt 1929 | FASTA format
EDAMfmt 2331 | HTML
Query   Gene annotation | HTML | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s
Query   Gene annotation | EMBL format | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=embl
Query   Gene annotation | FASTA format | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=fasta
Query   Gene annotation | GFF | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=gff
Query   Gene annotation | GTF | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=gtf
Query   Gene annotation (transcript) | HTML | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s
Query   Gene annotation (transcript) | EMBL format | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=embl
Query   Gene annotation (transcript) | GFF | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gff
Query   Gene annotation (transcript) | GTF | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gtf
Query   Protein report | HTML | Protein ID (Ensembl) | http://www.ebi.ac.uk/astd/peptideview.html?acc=%s
Query   Protein report | FASTA format | Protein ID (Ensembl) | http://www.ebi.ac.uk/astd/peptideview.html?acc=%s&export=fasta
Query   Gene features (exon) | HTML | ASTD ID (exon);ASTD ID | http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2
Query   Gene features (intron) | HTML | ASTD ID (intron);ASTD ID | http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2
Query   Gene features (promoter) {TSS} | HTML | ASTD ID (tss);ASTD ID | http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2
Query   Nucleic acid features (PolyA signal) | HTML | ASTD ID (polya) | http://www.ebi.ac.uk/astd/featureview.html?acc=%s
Example ASTD ID (exon);ASTD ID | EXON00000830017;TRAN00000134394
Example ASTD ID (intron);ASTD ID | INTR00000830053;TRAN00000134394
Example ASTD ID | TRAN00000134394
Example Gene ID (Ensembl) | ENSG00000148680
Example Protein ID (Ensembl) | PEPT00000029170
Example Transcript ID (Ensembl) | ENST00000229239

ID      ATCC
Name    American type culture collection database (ATCC)
Desc    ATCC cultures and bioproducts.
URL     http://www.lgcstandards-atcc.org/
Cat     Not available
Taxon   1 | all
EDAMtpc 0608 | Cell culture resources
EDAMdat 0963 | Cell line annotation
EDAMid  0842 | Identifier
Query   Cell line annotation | HTML | Identifier {Strain ID} | http://www.lgcstandards-atcc.org/SearchCatalogs/LinkIn?id=BAA-2146
Example Identifier | BAA-2146

ID      ATCC_in_host
Name    American type culture collection database (ATCC)
Desc    ATCC cultures and bioproducts
URL     http://www.lgcstandards-atcc.org/
Cat     Not available
Taxon   1 | all
EDAMtpc 0608 | Cell culture resources

ID      ATCC_dna
Name    American type culture collection database (ATCC)
Desc    ATCC cultures and bioproducts.
URL     http://www.lgcstandards-atcc.org/
Cat     Not available
Taxon   1 | all
EDAMtpc 0608 | Cell culture resources

ID      ATSD
Name    Aminoacyl-tRNA synthetases database (ATSD)
Desc    Aminoacyl-tRNA synthetases database.
URL     http://rose.man.poznan.pl/aars/index.html
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources

ID      AthaMap
Name    AthaMap database of Arabidopsis TFBS predictions
Desc    Genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana.
URL     http://www.athamap.de/
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0780 | Plants

ID      AutoPSI
Name    AutoPSI database of predicted SCOP classifications
Desc    Predicted SCOP classifications.
URL     http://services.bio.ifi.lmu.de:1046/AutoPSIDB/
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0736 | Protein domains and folds

ID      Axeldb
Name    Axeldb
Desc    Gene expression patterns and DNA sequences identified from Xenopus laevis embryos. Images of expression patterns for any given set of genes may be compared. Informations on literature, cDNA clones, nucleotidic sequences, expression pattern and accompanying pictures are available.
URL     http://www.dkfz.de/en/mol_embryology/axeldb.html
NARid   11
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/28/1/139
Taxon   8355 | Xenopus laevis
EDAMtpc 0197 | Gene expression resources
Xref    SP_FT | None

ID      BAliBASE
Name    BAliBASE benchmark alignment database
Desc    A benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations.
URL     http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment

ID      BCSDB
Name    BCSDB database of bacterial carbohydrate structures
Desc    Bacterial carbohydrate structures.
URL     http://www.glyco.ac.ru/bcsdb/start.shtml
Taxon   2 | Bacteria
EDAMtpc 0152 | Carbohydrates

ID      BDGP_EST
Name    Berkeley Drosophila genome project EST database (BDGP_EST)
Desc    Berkeley Drosophila genome project EST database.
URL     http://www.fruitfly.org/
Cat     Not available
Taxon   7215 | Drosophila
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0211 | Flies
Xref    SP_FT | None

ID      BDGP_INS
Name    Berkeley Drosophila genome project database: insertion (BDGP_INS)
Desc    Berkeley Drosophila genome project database: insertion
URL     http://www.fruitfly.org/
Cat     Not available
Taxon   7215 | Drosophila
EDAMtpc 0211 | Flies
Xref    SP_FT | None

ID      Bgee
Acc     DB-0133
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.
URL     http://bgee.unil.ch
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMdat 0929 | Gene annotation (expression)
EDAMdat 0928 | Gene expression profile
EDAMdat 0916 | Gene annotation
EDAMdat 2579 | Gene annotation (expressed gene list)
EDAMid  3021 | UniProt accession
EDAMid  1033 | Gene ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Gene annotation | HTML | UniProt accession | http://bgee.unil.ch/bgee/bgee?uniprot_id=%s
Query   Gene annotation | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Query   Gene expression profile | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Query   Gene annotation (expression) | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=data&gene_id=%s
Query   Gene annotation (expressed gene list) {Bgee ID file} | Text | Gene ID (Ensembl) | 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   Gene annotation (expressed gene list) {Bgee ID file with expression data} | Text | Gene ID (Ensembl) | 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   Gene annotation (expressed gene list) {Bgee ID file with expression data count} | Text | Gene ID (Ensembl) | 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   Gene annotation (expressed gene list) {Bgee ID file} | HTML | Gene ID (Ensembl) | 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   Gene annotation (expressed gene list) {Bgee ID file with expression data} | HTML | Gene ID (Ensembl) | 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   Gene annotation (expressed gene list) {Bgee ID file with expression data count} | HTML | Gene ID (Ensembl) | 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
Example Gene ID (Ensembl) | ENSG00000091831
Example UniProt accession | P32234

ID      BindingDB
Acc     DB-0127
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.
URL     http://www.bindingdb.org/
URLlink http://www.bindingdb.org/bind/SearchTemplates.jsp
Cat     Other
Taxon   1 | all
EDAMtpc 0148 | Protein-ligand interactions
EDAMtpc 0620 | Drugs and targets
EDAMdat 0962 | Small molecule report
EDAMdat 2402 | Protein-drug interaction
EDAMdat 0857 | Database hits (sequence)
EDAMdat 2726 | Inhibitor annotation
EDAMid  0842 | Identifier
EDAMid  1127 | PDB ID
EDAMid  1187 | PubMed ID
EDAMid  3021 | UniProt accession
EDAMid  2580 | BindingDB Monomer ID
EDAMid  1009 | Protein name
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Protein-drug interaction | HTML | UniProt accession | http://www.bindingdb.org/uniprot/%s
Query   Inhibitor annotation | HTML | Protein name {BindingDB target name} | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?tag=tg&kiunit=nM&icunit=nM&column=ki&submit=Search&energyterm=kJ%2Fmole&target=%s
Query   Small molecule report {ITC data} | HTML | Protein name {BindingDB target name} | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_itc.jsp?tag=tg&column=delta_G0&energyterm=kJ%2Fmole&startPg=0&Increment=50&submit=Search&target=%s
Query   Database hits (sequence) {BindingDB entries} | HTML | Identifier {Protein sequence} | http://www.bindingdb.org/bind/blastResult.jsp?DATASOURCE=protein&Search=B2&blastSeq=%s
Query   Small molecule report | HTML | BindingDB Monomer ID | http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=%s
Query   Small molecule report | HTML | Identifier {SMILES string} | http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=4&submit=Search&smilesStr=%s
Query   Protein-drug interaction | HTML | PDB ID | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_PDBids.jsp?PDBids_submit=Search&PDBids=%s
Query   Protein-drug interaction | HTML | PubMed ID | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=%s
Example UniProt accession | Q29005
Example Protein name | ABL
Example Protein name | Ab N1G9
Example Identifier {Protein sequence} | VKCGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLD
Example BindingDB Monomer ID | 100
Example Identifier {SMILES string} | CC%28C%29C1%28C%29SC%28Nc2ccccc2C%28F%29%28F%29F%29%3DNC1%3DO+%7Cc%3A18%7C
Example PDB ID | 1OKZ
Example PubMed ID | 17408953

ID      BioCyc
Acc     DB-0005
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)
URL     http://www.biocyc.org/
URLlink http://biocyc.org/linking.shtml
Cat     Enzyme and pathway databases; Metabolic pathways database
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 0753 | Metabolic pathways
EDAMdat 2018 | Annotation
EDAMdat 1509 | Protein report (enzyme)
EDAMdat 1288 | Genome map
EDAMdat 1283 | Cytogenetic map
EDAMdat 0962 | Small molecule report
EDAMdat 2984 | Pathway or network report
EDAMdat 0908 | Reaction annotation
EDAMid  1795 | Gene ID (EcoGene)
EDAMid  2106 | Reaction ID (BioCyc)
EDAMid  2107 | Enzyme ID (BioCyc)
EDAMid  2105 | Compound ID (BioCyc)
EDAMid  1157 | Pathway ID (BioCyc)
EDAMid  0987 | Chromosome name
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {BioCyc}
Query   Annotation | HTML | Identifier {BioCyc} | http://biocyc.org/getid?id=%s
Query   Pathway or network report | HTML | Pathway ID (BioCyc) | http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=%s
Query   Small molecule report | HTML | Compound ID (BioCyc) | http://biocyc.org/ECOLI/NEW-IMAGE?type=COMPOUND&object=%s
Query   Reaction annotation | HTML | Reaction ID (BioCyc) | http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=%s
Query   Protein report (enzyme) | HTML | Enzyme ID (BioCyc) | http://biocyc.org/ECOLI/new-image?type=ENZYME&object=%s
Query   Cytogenetic map | HTML | Chromosome name | http://biocyc.org/ECOLI/substring-search?type=%s
Query   Genome map | HTML | Gene ID (EcoGene) | http://biocyc.org/ECOLI/new-image?type=LOCUS-POSITION&object=%s
Query   Genome map | HTML | Identifier {Map position} | http://biocyc.org/ECOLI/substring-search?type=MAPTICK&object=%s
Example Pathway ID (BioCyc) | GLYCOLYSIS
Example Compound ID (BioCyc) | FRUCTOSE-6P
Example Reaction ID (BioCyc) | PGLUCISOM-RXN
Example Enzyme ID (BioCyc) | PGLUCISOM
Example Chromosome name | COLI-K12
Example Gene ID (EcoGene) | EG11024
Example Identifier {Map position} | None

ID      BioGRID
Name    BioGRID
Desc    Physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe
URL     http://thebiogrid.org/
Taxon   4932 | Saccharomyces cerevisiae
Taxon   9606 | Homo sapiens
Taxon   6239 | Caenorhabditis elegans
Taxon   7215 | Drosophila
Taxon   9606 | Homo sapiens
Taxon   4896 | Schizosaccharomyces pombe
EDAMtpc 0128 | Protein interactions
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0204 | Gene regulation resources

ID      biomodels
Name    BioModels database of annotated published models
Desc    A that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevants, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
URL     http://www.ebi.ac.uk/biomodels-main/
Taxon   1 | all
EDAMtpc 0771 | Biological models
EDAMdat 0950 | Biological model
EDAMid  1171 | BioModel ID
EDAMfmt 2585 | SBML
EDAMfmt 2331 | HTML
Query   Biological model | HTML | BioModel ID | http://www.ebi.ac.uk/biomodels-main/%s
Query   Biological model | SBML | BioModel ID | http://www.ebi.ac.uk/biomodels/models-main/publ/%s.xml
Example BioModel ID | BIOMD0000000001

ID      BioNumbers
Name    BioNumbers
Desc    A database of key numbers in molecular biology, along with relevant references to the original literature, useful comments, and related numbers.
URL     http://www.bionumbers.hms.harvard.edu/
Taxon   1 | all
EDAMtpc 3047 | Molecular biology reference


ID      BioSystems
Name    BioSystems
Desc    BioSystems is a composite biological pathway and disease database and aims to: (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biological systems data.
URL     http://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0634 | Disease resources

ID      BIPA
Name    BIPA database for interaction between protein and nucleic acid
Desc    Protein-nucleic acid interactions, with various features of protein-nuleic acid interfaces.
URL     http://www-cryst.bioc.cam.ac.uk/bipa
Taxon   1 | all
EDAMtpc 0149 | Protein-nucleic acid interactions
EDAMdat 1567 | Protein-nucleic acid interaction
EDAMdat 2358 | Domain-nucleic acid interaction
EDAMid  1042 | SCOP sunid
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Query   Protein-nucleic acid interaction | HTML | PDB ID | http://mordred.bioc.cam.ac.uk/bipa/structures/%s
Query   Domain-nucleic acid interaction | HTML | SCOP sunid | http://mordred.bioc.cam.ac.uk/bipa/scops/%s
Example PDB ID | 10MH
Example SCOP sunid | 120412

ID      BloodExpress
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.
URL     http://hscl.cimr.cam.ac.uk/bloodexpress/
Taxon   10088 | Mus
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0200 | Microarrays

ID      BlotBase
Name    BlotBase Northern blots database
Desc    Northern blots database.
URL     http://www.medicalgenomics.org/Databases/BlotBase
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMdat 2586 | Northern blot image
EDAMid  1026 | Gene symbol
EDAMid  2588 | BlotBase blot ID
EDAMfmt 2331 | HTML
Query   Northern blot image {BlotBase Blot Entry} | HTML | BlotBase blot ID | http://www.medicalgenomics.org/databases/blotbase/search?action=show_details&blot_id=%s
Query   Northern blot image {BlotBase Blot Listing by Gene} | HTML | Gene symbol | http://www.medicalgenomics.org/databases/blotbase/search?action=query&filter=genes&exact_match=yes&query=%s
Example Gene symbol | ace
Example BlotBase blot ID | 524

ID      BNDB
Name    Biochemical network database (BNDB)
Desc    Biochemical network database for analyzing and visualizing complex biochemical networks and processes.
URL     http://www.bndb.org/index.php?idx=main
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models

ID      BodyMap
Name    BodyMap
Desc    A human and mouse gene expression database based on ESTs collected from non-biased cDNA libraries. BodyMap allows unequivocal grouping of tags representing the same transcript and provides information for each transcript in different parts of the body. 
URL     http://bodymap.ims.u-tokyo.ac.jp/
NARid   12
NARCat  /nar/database/cat/7 | Human and other Vertebrate Genomes
NARSub  /nar/database/subcat/7/28 | Model organisms, comparative genomics
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/29/1/156

ID      BOLD
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.
URL     http://www.barcodinglife.org/views/login.php
Cat     Not available
Taxon   1 | all
EDAMtpc 0625 | Genotype and phenotype resources
Xref    SP_FT | None
Example Identifier | EPAF263

ID      BRENDA
Acc     DB-0131
Name    BRENDA comprehensive enzyme information system
Desc    Comprehensive enzyme information.
URL     http://www.brenda-enzymes.org
URLsoap http://www.brenda-enzymes.org/soap2
Cat     Enzyme and pathway databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMdat 1509 | Protein report (enzyme)
EDAMid  3021 | UniProt accession
EDAMid  1011 | EC number
EDAMid  2593 | BRENDA organism ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | EC number;BRENDA organism ID
Query   Protein report (enzyme) {BRENDA entry} | HTML | EC number | http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s
Query   Protein report (enzyme) {BRENDA entry} | HTML | EC number;BRENDA organism ID | http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s1&&OrganismID=&s3&ShowAll=True
Query   Protein report (enzyme) {BRENDA entry} | HTML | EC number;UniProt accession;BRENDA organism ID | http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s1&UniProtAcc=%s2&OrganismID=&s3&ShowAll=True
Example EC number | 1.1.5.82
Example EC number;UniProt accession | 1.1.5.82;P15719
Example EC number;UniProt accession;BRENDA organism ID | 1.1.5.82;P15719;4577

ID      BriX
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.
URL     http://brix.vub.ac.be/
Taxon   1 | all
EDAMtpc 0166 | Protein structural motifs and surfaces

ID      BuchneraBase
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.
URL     http://www.buchnera.org/
Taxon   32199 | Buchnera
EDAMtpc 1811 | Prokaryotes and archae

ID      ButterflyBase
Name    ButterflyBase database of comparative Genomics of Lepidoptera
Desc    Gene database for butterflies and moths.
URL     http://www.butterflybase.org
Taxon   7088 | Lepidoptera
EDAMtpc 2819 | Invertebrates
EDAMtpc 0797 | Comparative genomics

ID      CABRI
Name    Common Access to Biotechnological Resources and Information (CABRI)
Desc    A collection of European Biological Resource Centre catalogues.
URL     http://www.cabri.org/
Taxon   None
EDAMtpc 0607 | Laboratory resources
EDAMtpc 0608 | Cell culture resources
EDAMdat 0963 | Cell line annotation
EDAMid  2380 | CABRI accession
EDAMid  2597 | CABRI catalogue name
Xref    EMBL_explicit | CABRI catalogue name;CABRI accession
Query   Cell line annotation | Text | CABRI catalogue name;CABRI accession | http://www.cabri.org/CABRI/srs-bin/wgetz?-newId+-ascii+-e+[%s1:%s1 %s2]
Example CABRI catalogue name | ICLC
Example CABRI catalogue name | LMBP
Example CABRI accession | AL00001
Example CABRI accession | 2208

ID      CADRE
Name    Central aspergillus data repository (CADRE)
Desc    Central aspergillus data repository (CADRE).
URL     http://www.cadre-genomes.org.uk/Aspergillus_fumigatus/
Taxon   5042 | Eurotiales
EDAMtpc 0782 | Fungi


ID      CanGEM
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.
URL     http://www.cangem.org/
Taxon   9606 | Homo sapiens
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0200 | Microarrays
EDAMtpc 2640 | Cancer resources

ID      CATdb
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.
URL     http://urgv.evry.inra.fr/CATdb
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0780 | Plants
EDAMdat 0916 | Gene annotation
EDAMdat 0929 | Gene annotation (expression)
EDAMdat 2093 | Data reference
EDAMid  2388 | TAIR accession (At gene)
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Query   Gene annotation (expression) | HTML | TAIR accession (At gene) | http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_diff_id.pl?idnum=%s
Query   Gene annotation {CATdb Gene and Probe info} | HTML | TAIR accession (At gene) | http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/seq_info.pl?ident=%s
Query   Data reference {CATdb Search by keyword} | HTML | Identifier {Keyword} | http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_proj_kw.pl?kwrd=%s
Query   Gene annotation (expression) | HTML | TAIR accession (At gene) | http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_diff_id.pl?idnum=AT1G69880
Query   Gene annotation {CATdb Gene and Probe info} | HTML | TAIR accession (At gene) | http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/seq_info.pl?ident=AT1G69880
Query   Data reference {CATdb Search by keyword} | HTML | Identifier {Keyword} | http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_proj_kw.pl?kwrd=%s
Example Identifier {Keyword} | nitrogen

ID      CATH
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.
URL     http://www.cathdb.info/
URLsoap http://api.cathdb.info/api/soap/dataservices/wsdl
Taxon   1 | all
EDAMtpc 0736 | Protein domains and folds
EDAMtpc 3052 | Sequence clusters and classification
EDAMdat 0901 | Protein features (domains)
EDAMdat 1553 | CATH node
EDAMdat 1762 | CATH domain report
EDAMid  1040 | CATH domain ID
EDAMid  1008 | Polypeptide chain ID
EDAMid  1127 | PDB ID
EDAMid  1043 | CATH node ID
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Query   CATH domain report | HTML | CATH domain ID | http://www.cathdb.info/domain/%s
Query   CATH domain report | XML | CATH domain ID | http://www.cathdb.info/domain/%s?view=xml
Query   Protein features (domains) {CATH chain} | HTML | Polypeptide chain ID | http://www.cathdb.info/chain/%s
Query   Protein features (domains) {PDB} | HTML | PDB ID | http://www.cathdb.info/PDB/%s
Query   Protein features (domains) {PDB} | XML | PDB ID | http://www.cathdb.info/PDB/%s?view=xml
Query   CATH node | HTML | CATH node ID | http://www.cathdb.info/cathnode/%s
Example CATH domain ID | 1cukA01
Example Polypeptide chain ID | 1cukA
Example PDB ID | 1cuk
Example CATH node ID | 1.10.10.10

ID      CATMA
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.
URL     http://www.catma.org/
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0200 | Microarrays
EDAMtpc 0780 | Plants

ID      CAZy
Acc     DB-0136
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.
URL     http://www.cazy.org/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMdat 1509 | Protein report (enzyme)
EDAMid  2702 | Enzyme ID (CAZy)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Enzyme ID (CAZy)
Query   Protein report (enzyme) {CAZy entry} | HTML | Enzyme ID (CAZy) | http://www.cazy.org/fam/%s.html
Example Enzyme ID (CAZy) | GT2

ID      CBS
Name    Genome atlas database (CBS)
Desc    Summary of genomic information currently available for various organisms.
URL     http://www.cbs.dtu.dk/services/GenomeAtlas/
Taxon   1 | all
EDAMtpc 0622 | Genomics

ID      CC+
Name    CC+ database of coiled-coil structures
Desc    A relational database of coiled-coil structures.
URL     http://coiledcoils.chm.bris.ac.uk/ccplus
Taxon   1 | all
EDAMtpc 0166 | Protein structural motifs and surfaces

ID      CCAP
Name    Culture collection of algae and protozoa (CCAP)
Desc    Culture collection of algae and protozoa
URL     http://www.ccap.ac.uk/index.htm
Taxon   1 | all
EDAMtpc 0608 | Cell culture resources
EDAMdat 0963 | Cell line annotation
EDAMid  2778 | CCAP strain number
EDAMfmt 2331 | HTML
Query   Cell line annotation {Strain information} | HTML | CCAP strain number | http://www.ccap.ac.uk/strain_info.php?Strain_No=%s
Example CCAP strain number | 211/11B

ID      CellCycleDB
Name    Cell cycle database (CellCycleDB)
Desc    A collection of genes and proteins involved in human and yeast cell cycle.
URL     http://www.itb.cnr.it/cellcycle/index.html
Taxon   4932 | Saccharomyces cerevisiae
Taxon   9606 | Homo sapiens
EDAMtpc 0635 | Specific protein resources
EDAMtpc 2229 | Cell biology resources
EDAMtpc 0782 | Fungi
EDAMdat 0896 | Protein report
EDAMdat 0916 | Gene annotation
EDAMid  2764 | Protein name (UniProt)
EDAMid  2300 | Gene name (NCBI)
EDAMfmt 2331 | HTML
Query   Gene annotation | HTML | Gene name (NCBI) | http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=%s
Query   Protein report | HTML | Protein name (UniProt) | http://www.itb.cnr.it/cellcycle/protein_rep.php?protein_name=%s
Example Gene name (NCBI) | CCND1
Example Protein name (UniProt) | P53

ID      CellLineDB
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.
URL     http://bioinformatics.istge.it/interlab/cldb.html
Taxon   33208 | Metazoa
EDAMtpc 0607 | Laboratory resources
EDAMtpc 0608 | Cell culture resources

ID      CellMINT
Name    CellMINT database of protein localization and interactions
Desc    A database tool to integrate protein localization and interaction information.
URL     http://mint.bio.uniroma2.it/CellMINT/welcome.do
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0140 | Protein targeting and localization

ID      Centrosome:db
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.
URL     http://centrosome.dacya.ucm.es/
Taxon   9606 | Homo sapiens
EDAMtpc 0635 | Specific protein resources

ID      CEPHdb
Name    CEPH genotype database (CEPHdb)
Desc    A database of genotypes for genetic markers that have been typed on the CEPH reference family resource for linkage mapping.
URL     http://www.cephb.fr/fr/cephdb/
Taxon   9606 | Homo sapiens
EDAMtpc 0796 | Genetic mapping and linkage
EDAMtpc 0625 | Genotype and phenotype resources

ID      CG
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.
URL     http://www2.unil.ch/comparativegenometrics/
Taxon   1 | all
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0624 | Chromosomes
EDAMtpc 0097 | Nucleic acid structure analysis
EDAMdat 2086 | Nucleic acid structure report
EDAMid  2787 | NCBI genome accession
EDAMfmt 2331 | HTML
Query   Nucleic acid structure report {Nucleotide skews page} | HTML | NCBI genome accession | http://www2.unil.ch/comparativegenometrics/%s.htm
Query   Nucleic acid structure report {Nucleotide skews data} | Text | NCBI genome accession | http://www2.unil.ch/comparativegenometrics/docs/%s.txt
Example NCBI genome accession | NC_000913

ID      CDD
Name    Conserved domain database (CDD)
Desc    A collection of multiple sequence alignments for ancient domains and full-length proteins.
URL     http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Cat     Not available
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0736 | Protein domains and folds
EDAMdat 0901 | Protein features (domains)
EDAMdat 1384 | Sequence alignment (protein)
EDAMdat 0907 | Protein family annotation
EDAMid  2714 | CDD PSSM-ID
EDAMid  2666 | CDD ID
EDAMid  2327 | GI number (protein)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_FT | None
Query   Sequence alignment (protein) {Conserved Domain Summary} | HTML | CDD ID | http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s
Query   Sequence alignment (protein) {Conserved Domain Summary} | HTML | CDD PSSM-ID | http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s
Query   Protein family annotation {Conserved Domain Document Summary} | HTML | CDD ID | http://www.ncbi.nlm.nih.gov/sites/cdd?term=%s[Accn]
Query   Protein family annotation {Conserved Domain Document Summary} | HTML | CDD PSSM-ID | http://www.ncbi.nlm.nih.gov/cdd/%s
Query   Protein family annotation {Conserved Domain description} | XML | CDD PSSM-ID | http://www.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=cdd&id=%s&retmode=xml
Query   Protein features (domains) {Conserved Protein structure report (domain)} | HTML | Sequence accession (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s
Query   Protein features (domains) {Conserved Protein structure report (domain)} | HTML | GI number (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s
Query   Protein features (domains) {Conserved Protein structure report (domain)} | XML | Sequence accession (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s&output=xml
Query   Protein features (domains) {Conserved Protein structure report (domain)} | XML | GI number (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s&output=xml
Example CDD PSSM-ID | 153083
Example CDD ID | cd00576
Example Sequence accession (protein) | P26675
Example GI number (protein) | 76800652

ID      CGD
Acc     DB-0126
Name    Candida genome database (CGD)
Desc    A resource for genomic sequence data and gene and protein information for Candida albicans.
URL     http://www.candidagenome.org/
Cat     Organism-specific databases
Taxon   5476 | Candida albicans
EDAMtpc 2817 | Yeast
EDAMdat 0916 | Gene annotation
EDAMid  1898 | Locus ID (CGD)
EDAMid  2794 | ORF ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | Locus ID (CGD)
Query   Gene annotation | HTML | ORF ID | http://www.candidagenome.org/cgi-bin/locus.pl?locus=%s
Query   Gene annotation | HTML | Locus ID (CGD) | http://www.candidagenome.org/cgi-bin/locus.pl?locus=%s
Example ORF ID | orf19.3127
Example Locus ID (CGD) | CAL0002268

ID      ChEBI
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.
URL     http://www.ebi.ac.uk/chebi/
Taxon   None
EDAMtpc 0154 | Small molecules
EDAMdat 0962 | Small molecule report
EDAMid  1174 | ChEBI ID
EDAMfmt 2331 | HTML
Query   Small molecule report | HTML | ChEBI ID | http://www.ebi.ac.uk/chebi/searchId.do;?chebiId=CHEBI:%s
Example ChEBI ID | 15356

ID      ChEMBL
Name    ChEMBL
Desc    A database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).
URL     https://www.ebi.ac.uk/chembl/
Taxon   1 | all
EDAMtpc 0620 | Drugs and targets

ID      ChemIDplus
Name    ChemIDplus
Desc    Structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases, including the TOXNET® system. ChemIDplus also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.
URL     http://www.nlm.nih.gov/pubs/factsheets/chemidplusfs.html
Taxon   1 | all
EDAMtpc 0154 | Small molecules
EDAMtpc 2811 | Nomenclature

ID      CiteXplore
Name    CiteXplore literature database
Desc    CiteXplore combines literature search with text mining tools for biology.
URL     http://www.ebi.ac.uk/citexplore
Taxon   None
EDAMtpc 0606 | Literature data resources
EDAMdat 0970 | Bibliographic reference
EDAMid  1187 | PubMed ID
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Query   Bibliographic reference {PubMedView} | HTML | PubMed ID | http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=%s&dataSource=MED
Query   Bibliographic reference {PubMedXML} | XML | PubMed ID | http://www.ebi.ac.uk/citexplore/viewXML.do?externalId=%s&dataSource=MED
Example PubMed ID | 7729218

ID      CleanEx
Acc     DB-0008
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.
URL     http://www.cleanex.isb-sib.ch/
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMdat 0931 | Experiment annotation (microarray)
EDAMdat 0928 | Gene expression profile
EDAMid  2709 | CleanEx entry name
EDAMid  2710 | CleanEx dataset code
EDAMfmt 2331 | HTML
Xref    SP_explicit | CleanEx entry name
Query   Gene expression profile {CleanEx entry} | HTML | CleanEx entry name | http://www.cleanex.isb-sib.ch/cgi-bin/get_doc?db=cleanex&format=nice&entry=%s
Query   Experiment annotation (microarray) {CleanEx dataset} | HTML | CleanEx dataset code | http://www.cleanex.isb-sib.ch/cgi-bin/get_doc?db=cleanex_ref&format=nice&entry=%s
Example CleanEx entry name | HS_BMP5
Example CleanEx dataset code | GSE2109_DOC

ID      CLIMA
Name    Database for cell line integrated molecular authentication (CLIMA)
Desc    Cell line integrated molecular authentication.
URL     http://bioinformatics.istge.it/clima/
Taxon   1 | all
EDAMtpc 0608 | Cell culture resources
EDAMdat 0963 | Cell line annotation
EDAMid  2317 | Cell line name (exact)
EDAMid  2318 | Cell line name (truncated)
EDAMid  2319 | Cell line name (no punctuation)
EDAMid  2320 | Cell line name (assonant)
EDAMfmt 2331 | HTML
Query   Cell line annotation {CLIMA entrys} | HTML | Cell line name (exact) | http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=exact
Query   Cell line annotation {CLIMA entry} | HTML | Cell line name (truncated) | http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=truncated
Query   Cell line annotation {CLIMA entry} | HTML | Cell line name (no punctuation) | http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=nopunct
Query   Cell line annotation {CLIMA entry} | HTML | Cell line name (assonant) | http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=soundex
Example Cell line name (exact) | SaOS2

ID      CluSTr
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.
URL     http://www.ebi.ac.uk/clustr/
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 3052 | Sequence clusters and classification

ID      CMR
Acc     DB-0009
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.
URL     http://cmr.tigr.org/
Cat     Genome annotation databases
Taxon   2 | Bacteria
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0622 | Genomics
EDAMdat 0916 | Gene annotation
EDAMdat 2711 | Genome metadata
EDAMid  3021 | UniProt accession
EDAMid  1179 | NCBI taxonomy ID
EDAMid  2292 | GenBank identifier
EDAMid  2774 | Gene ID (JCVI)
EDAMid  2786 | NCBI Genome Project ID
EDAMfmt 2331 | HTML
Xref    SP_implicit | UniProt accession
Query   Gene annotation | HTML | Gene ID (JCVI) | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=%s
Query   Gene annotation | HTML | GenBank identifier | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=SP&acc=%s
Query   Gene annotation | HTML | UniProt accession | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=protein_id&acc=%s
Query   Genome metadata {CMR genome page} | HTML | NCBI taxonomy ID | http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?taxon_id=%s
Query   Genome metadata {CMR genome page} | HTML | NCBI Genome Project ID | http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?ncbi_project_id=%s
Example Gene ID (JCVI) | BA_0001
Example GenBank identifier | AAP24059.1
Example UniProt accession | Q81W35
Example NCBI taxonomy ID | 198094
Example NCBI Genome Project ID | 309

ID      COG
Name    Clusters of Orthologous Groups of proteins (COG)
Desc    Phylogenetic classification of proteins encoded in complete genomes. A COG is a cluster of orthologous group of proteins (COG); proteins that are inferred to be orthologs (direct evolutionary counterparts). 
URL     http://www.ncbi.nlm.nih.gov/COG
NARid   7
NARCat  /nar/database/cat/3 | Protein sequence databases
NARSub  /nar/database/subcat/3/9 | Protein domain databases; protein classification
NARCat  /nar/database/cat/5 | Genomics Databases (non-vertebrate)
NARSub  /nar/database/subcat/5/17 | General genomics databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/29/1/22


ID      COGEME
Name    Phytopathogenic fungi and oomycete EST database (COGEME)
Desc    Phytopathogenic fungi and oomycete EST database.
URL     http://cogeme.ex.ac.uk/
Taxon   4751 | Fungi
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0783 | Pathogens
EDAMtpc 0782 | Fungi
EDAMdat 0849 | Sequence record
EDAMid  2729 | COGEME EST ID
EDAMid  2730 | COGEME unisequence ID
EDAMfmt 2331 | HTML
Query   Sequence record {Unisequence} | HTML | COGEME unisequence ID | http://cogeme.ex.ac.uk/cgi-bin/uni.pl?uni=x
Query   Sequence record {EST} | HTML | COGEME EST ID | http://cogeme.ex.ac.uk/cgi-bin/est.pl?est=x
Example COGEME EST ID | Bg13901527
Example COGEME unisequence ID | BgCon[0123]

ID      ColiBase
Name    ColiBase Enterobactericaiae genome database
Desc    A database for comparative genome analysis of Enterobactericaiae, e.g. Escherichia, Shigella etc..
URL     http://xbase.bham.ac.uk/colibase/
Taxon   543 | Enterobactericaiae
EDAMtpc 0797 | Comparative genomics
EDAMtpc 1811 | Prokaryotes and archae


ID      CMD
Name    Collagen Mutation Database (CMD)
Desc    Database of osteogenesis imperfecta and type III collagen variants.
URL     https://eds.gene.le.ac.uk
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 0634 | Disease resources
EDAMdat 0918 | Sequence variation annotation
EDAMid  2747 | Database name (CMD)
EDAMfmt 2331 | HTML
Query   Sequence variation annotation {Sequence variants} | HTML | Database name (CMD) | https://eds.gene.le.ac.uk/home.php?select_db=%s
Example Database name (CMD) | COL3A1
Example Database name (CMD) | COL5A1
Example Database name (CMD) | COL5A2

ID      Columba
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.
URL     http://www.columba-db.de
Taxon   1 | all
EDAMtpc 3040 | Protein structure
EDAMtpc 0694 | Protein secondary structure

ID      COMPLUYEAST-2DPAGE
Acc     DB-0010
Name    COMPLUYEAST-2DPAGE database
Desc    A two-dimensional polyacrilamide gel electrophoresis federated database.
URL     http://compluyeast2dpage.dacya.ucm.es/
Cat     2D gel databases
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s
Query   Experiment annotation (2D PAGE) | HTML | Protein identifier | http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s
Example UniProt accession | P83784
Example Protein identifier | CAP6_CANAL

ID      ConoServer
Acc     DB-0156
Name    Cone snail toxin database (ConoServer)
Desc    Conotoxin peptide sequences and structures.
URL     http://www.conoserver.org/
Cat     Organism-specific databases
Taxon   6490 | Conus
EDAMtpc 2661 | Toxins and targets
EDAMdat 0896 | Protein report
EDAMid  2804 | Protein ID (ConoServer)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein ID (ConoServer)
Query   Protein report | HTML | Protein ID (ConoServer) | http://www.conoserver.org/?page=card&table=protein&id=%s
Example Protein ID (ConoServer) | 3271

ID      ConsensusPathDB
Name    ConsensusPathDB database of human functional interaction networks
Desc    Information on physical molecular interactions, biochemical pathways, and gene regulatory networks in human.
URL     http://cPDB.molgen.mpg.de/
Taxon   9606 | Homo sapiens
EDAMtpc 2846 | Gene regulatory networks
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0602 | Pathways, networks and models
EDAMdat 2984 | Pathway or network report
EDAMdat 2767 | Identifier with metadata
EDAMdat 0906 | Protein report (interaction)
EDAMid  2342 | Pathway or network name
EDAMid  2345 | Pathway ID (ConsensusPathDB)
EDAMid  2776 | ConsensusPathDB entity ID
EDAMid  2777 | ConsensusPathDB entity name
EDAMid  2091 | Accession
EDAMfmt 2331 | HTML
Query   Pathway or network report | HTML | Pathway or network name | http://cPDB.molgen.mpg.de/CPDB/search?nameacc=name&keywords=%s&searchspace=Pathway
Query   Identifier with metadata {Physical entities} | HTML | ConsensusPathDB entity name | http://cPDB.molgen.mpg.de/CPDB/search?nameacc=name&keywords=%s&searchspace=PhysicalEntity
Query   Identifier with metadata {Physical entities} | HTML | Accession {Physical entity external accession number} | http://cPDB.molgen.mpg.de/CPDB/search?nameacc=acc&keywords=PFKL&searchspace=PhysicalEntity
Query   Protein report (interaction) {Interactions of pathway} | HTML | Pathway ID (ConsensusPathDB) | http://cPDB.molgen.mpg.de/CPDB/getInteractionsOfObjs?objs:list=%s&objtype=p
Query   Protein report (interaction) {Interactions of physical entity} | HTML | ConsensusPathDB entity ID | http://cPDB.molgen.mpg.de/CPDB/getInteractionsOfObjs?objs:list=%s&objtype=e
Query   Protein report (interaction) {Shortest interaction path between two physical entities} | HTML | ConsensusPathDB entity ID;ConsensusPathDB entity ID | http://cPDB.molgen.mpg.de/CPDB/shortestPath?objs1:list=%s1&objs2:list=%s2
Example Pathway name | glycolysis
Example ConsensusPathDB entity name | puma
Example Accession | PFKL
Example Pathway ID (ConsensusPathDB) | 9494
Example ConsensusPathDB entity ID | 9304
Example ConsensusPathDB entity ID | 31812

ID      CORG
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.
URL     http://corg.molgen.mpg.de
Taxon   7711 | Chordata
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0204 | Gene regulation resources

ID      CORUM
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.
URL     http://mips.gsf.de/genre/proj/corum
Taxon   40674 | Mammalia
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0140 | Protein targeting and localization
EDAMdat 2712 | Protein structure report (protein complex)
EDAMid  2713 | Protein ID (CORUM)
EDAMfmt 2331 | HTML
Query   Protein structure report (protein complex) | HTML | Protein ID (CORUM) | http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=%s
Example Protein ID (CORUM) | 178

ID      CoryneRegNet4
Name    CoryneRegNet 4.0 cornyebacterial gene regulation database
Desc    Reference database for cornyebacterial transcription factors and gene regulatory networks.
URL     http://www.coryneregnet.de/
Taxon   1716 | Corynebacterium
EDAMtpc 2846 | Gene regulatory networks
EDAMtpc 0749 | Transcription factors and regulatory sites

ID      COSMIC
Name    Catalogue of somatic mutations in cancer (COSMIC)
Desc    Somatic mutation information and related details and information relating to human cancers.
URL     http://www.sanger.ac.uk/genetics/CGP/cosmic/
Taxon   9606 | Homo sapiens
EDAMtpc 2640 | Cancer resources

ID      Cornea-2DPAGE
Acc     DB-0011
Name    Human cornea 2-DE database (Cornea-2DPAGE)
Desc    Two-dimensional polyacrylamide gel electrophoresis federated database.
URL     http://www.cornea-proteomics.com/
Cat     2D gel databases
Taxon   9606 | Homo sapiens
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.daimi.au.dk/cgi-jje/2d/2d.cgi#%s
Query   Experiment annotation (2D PAGE) | Text | UniProt accession | http://www.daimi.au.dk/cgi-jje/2d/2d.cgi?ac=%s&format=text&database=cornea
Example UniProt accession | P02647

ID      cPath
Name    Pathway Commons database
Desc    A collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.
URL     http://www.pathwaycommons.org/pc/home.do
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models

ID      CREST
Name    Crop ESTs database (CREST)
Desc    Sequence, classification, clustering, and annotation data of crop EST projects.
URL     http://pgrc.ipk-gatersleben.de/cr-est/
Taxon   35493 | Streptophyta
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0722 | Nucleic acid classification

ID      CRISPRdb
Name    Database of clustered regularly interspaced short palindromic repeats (CRISPRdb)
Desc    Clustered regularly interspaced short palindromic repeats.
URL     http://crispr.u-psud.fr/
Taxon   1 | all
EDAMtpc 0641 | Repeat sequences
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0722 | Nucleic acid classification

ID      CSA
Name    Catalytic site atlas (CSA)
Desc    Catalytic sites in proteins.
URL     http://www.ebi.ac.uk/thornton-srv/databases/CSA/
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0821 | Enzymes and reactions

ID      CSDBase
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.
URL     http://www.chemie.uni-marburg.de/~csdbase/
Taxon   2 | Bacteria
EDAMtpc 0635 | Specific protein resources

ID      CTD
Acc     DB-0140
Name    Comparative Toxicogenomics Database (CTD)
Desc    CTD includes manually curated data describing cross-species chemical–gene/protein interactions and chemical– and gene–disease relationships to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. 
URL     http://ctd.mdibl.org/
Taxon   1 | all
EDAMtpc 2661 | Toxins and targets
EDAMtpc 0625 | Genotype and phenotype resources
EDAMdat 0916 | Gene annotation
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {CTD}
Query   Gene annotation | HTML | Identifier {CTD} | http://ctd.mdibl.org/detail.go?type=gene&db=GENE&acc=%s
Example Identifier {CTD} | 36288

ID      CUTG
Name    Codon Usage Tabulated from GenBank (CUTG)
Desc    Codon usage tables
URL     http://www.kazusa.or.jp/codon/
NARid   30
EDAMtpc 0107 | Codon usage analysis
NARCat  /nar/database/cat/1 | Nucleotide Sequence Databases
NARSub  /nar/database/subcat/1/2 | Coding and non-coding DNA
Abstrct http://nar.oupjournals.org/cgi/content/abstract/28/1/292

ID      CuticleDB
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.
URL     http://biophysics.biol.uoa.gr/cuticleDB/
Taxon   6656 | Arthropoda
EDAMtpc 0635 | Specific protein resources
EDAMdat 0896 | Protein report
EDAMid  2715 | Protein ID (CuticleDB)
EDAMfmt 2331 | HTML
Query   Protein report | HTML | Protein ID (CuticleDB) | http://bioinformatics.biol.uoa.gr/cuticleDB/protview.jsp?id=%s
Example Protein ID (CuticleDB) | 639

ID      CycleBase
Name    CycleBase cell cycle database
Desc    A standardized resource for researchers to inspect and download cell-cycle datasets.
URL     http://cyclebase.org/
Taxon   1 | all
EDAMtpc 2229 | Cell biology resources

ID      CYGD
Acc     DB-0012
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.
URL     http://mips.gsf.de/genre/proj/yeast
Cat     Organism-specific databases
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0782 | Fungi
EDAMtpc 0797 | Comparative genomics
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene symbol
Query   Gene annotation | HTML | Gene symbol | http://mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=%s
Example Gene symbol | YAL001c

ID      CyMoBase
Name    Database for cytoskeletal and motor proteins (CyMoBase)
Desc    Structure, function and phylogeny of cytoskeletal and motor proteins.
URL     http://www.cymobase.org
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0084 | Phylogenetics

ID      Cytokine
Name    Cytokine gene polymorphism database
Desc    Cytokine gene polymorphism in human disease.
URL     http://www.nanea.dk/cytokinesnps/
Taxon   9606 | Homo sapiens
EDAMtpc 0199 | Genetic variation
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      Dali
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.
URL     http://ekhidna.biocenter.helsinki.fi/dali/start
Taxon   1 | all
EDAMtpc 2826 | Protein structure alignment

ID      DBAli
Name    DBAli structure alignment database
Desc    Database of protein structure alignments.
URL     http://salilab.org/DBAli/
Taxon   1 | all
EDAMtpc 2826 | Protein structure alignment

ID      DBD
Name    Transcription factor prediction database (DBD)
Desc    Predicted transcription factors in completely sequenced genomes.
URL     http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Home
Taxon   1 | all
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMdat 2147 | Protein report (transcription factor)
EDAMid  2716 | DBD ID
EDAMfmt 2331 | HTML
Query   Protein report (transcription factor) {DBD entry} | HTML | DBD ID | http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Search/Domain+domain:%s+cat:DBD
Example DBD ID | PF02928

ID      dbEST
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.
URL     http://www.ncbi.nlm.nih.gov/dbEST/
Cat     Not available
Taxon   1 | all
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMdat 0849 | Sequence record
EDAMid  2314 | GI number
EDAMid  1105 | dbEST accession
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2532 | GenBank-HTML
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query   Sequence record | HTML {est} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query   Sequence record | HTML {docsum} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query   Sequence record | FASTA-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query   Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query   Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query   Sequence record | HTML {est} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query   Sequence record | HTML {docsum} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query   Sequence record | FASTA-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query   Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Example dbEST accession | f12345
Example GI number | 706694

ID      dbProbe
IDalt   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.
URL     http://www.ncbi.nlm.nih.gov/probe
Cat     Not available
Taxon   1 | all
EDAMtpc 0607 | Laboratory resources
EDAMtpc 0632 | Probes and primers
EDAMdat 2717 | Oligonucleotide probe annotation
EDAMid  2719 | dbProbe ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Oligonucleotide probe annotation {dbProbe report} | HTML | dbProbe ID | http://www.ncbi.nlm.nih.gov/genome/probe/reports/probereport.cgi?uid=%s
Example dbProbe ID | 12019

ID      dbSNP
Acc     DB-0013
Name    Database of single nucleotide polymorphism (dbSNP)
Desc    Single nucleotide polymorphisms.
URL     http://www.ncbi.nlm.nih.gov/SNP/
Cat     Polymorphism databases
Taxon   1 | all
EDAMtpc 2277 | SNPs
EDAMdat 2092 | SNP annotation
EDAMid  1106 | dbSNP ID
EDAMfmt 2331 | HTML
Xref    SP_FT | dbSNP ID
Query   SNP annotation {dbSNP entry} | HTML | dbSNP ID | http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s
Example dbSNP ID | rs11542705

ID      DDBJ
Acc     DB-0014
Name    DNA Data Bank of Japan (DDBJ)
Desc    The DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database".DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.
URL     http://www.ddbj.nig.ac.jp/
NARid   1
NARCat  /nar/database/cat/1 | Nucleotide Sequence Databases
NARSub  /nar/database/subcat/1/1 | International Nucleotide Sequence Database Collaboration
Abstrct http://nar.oupjournals.org/cgi/content/abstract/39/suppl_1/D22
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 0640 | Nucleic acid sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 1936 | GenBank format
EDAMfmt 2532 | GenBank-HTML
Xref    SP_implicit | Sequence accession (nucleic acid)
Query   Sequence record full | GenBank-HTML | Sequence accession (nucleic acid) | http://getentry.ddbj.nig.ac.jp/search/get_entry?accnumber=%s
Query   Sequence record full | GenBank format | Sequence accession (nucleic acid) | http://xml.nig.ac.jp/rest/Invoke?service=GetEntry&method=getDDBJEntry&accession=%s
Example Sequence accession (nucleic acid) | AB000100

ID      Degradome
Name    Degradome database of mammalian proteases and diseases
Desc    Mammalian proteases and diseases.
URL     http://degradome.uniovi.es/
Taxon   40674 | Mammalia
EDAMtpc 0634 | Disease resources

ID      Diamond
Name    Blackfan Anemia mutation database (Diamond)
Desc    Blackfan Anemia mutation database.
URL     http://www.dbagenes.unito.it
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 0634 | Disease resources
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Query   Gene annotation | HTML | Gene symbol | http://www.dbagenes.unito.it/home.php?select_db=%s
Example Gene symbol | RPS19
Example Gene symbol | RPS24
Example Gene symbol | RPS17
Example Gene symbol | RPS7
Example Gene symbol | RPL5
Example Gene symbol | RPL11
Example Gene symbol | RPS10
Example Gene symbol | RPS26
Example Gene symbol | RPL35A

ID      diArk
Name    diArk eukaryotic genome research database
Desc    Database for eukaryotic sequencing projects.
URL     http://www.diark.org/diark/
Taxon   2759 | Eukaryota
EDAMtpc 2818 | Eukaryotes

ID      Diatom
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.
URL     http://avesthagen.sznbowler.com/
Taxon   2836 | Bacillariophyta
EDAMtpc 0655 | mRNA, EST or cDNA

ID      dictyBase
IDalt   DICB
Acc     DB-0015
Name    Dictyostelium discoideum online informatics resource (dictyBase)
Desc    Database for the biology and genomics of the social amoeba Dictyostelium discoideum.
URL     http://dictybase.org/
Cat     Organism-specific databases
Taxon   44689 | Dictyostelium discoideum
EDAMtpc 2821 | Unicellular eukaryotes
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene ID
Xref    EMBL_explicit | Gene ID
Query   Gene annotation | HTML | Gene ID | http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=%s
Example Gene ID | DDB_G0269138

ID      DIMA
Name    DIMA domain interaction map
Desc    Functional and physical interactions among conserved protein-domains, including experimental data and computational predictions.
URL     http://mips.gsf.de/genre/proj/dtest/index.html
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMdat 2359 | Domain-domain interaction
EDAMid  1138 | Pfam accession number
EDAMfmt 2331 | HTML
Query   Domain-domain interaction | HTML | Pfam accession number | http://webclu.bio.wzw.tum.de/dima/DomQuery?domain=%s
Example Pfam accession number | PF00419

ID      DIP
Acc     DB-0016
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.
URL     http://dip.doe-mbi.ucla.edu/
Cat     Protein-protein interaction databases
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 3044 | Protein interaction networks
EDAMdat 1565 | Protein-protein interaction
EDAMid  2616 | DIP ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | DIP ID
Query   Protein-protein interaction {DIP entry} | HTML | DIP ID | dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s
Example DIP ID | DIP-27044N

ID      DiProDB
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.
URL     http://diprodb.fli-leibniz.de/
Taxon   None
EDAMtpc 0097 | Nucleic acid structure analysis
EDAMdat 2720 | Dinucleotide property
EDAMdat 2086 | Nucleic acid structure report
EDAMid  2721 | DiProDB ID
EDAMfmt 2331 | HTML
Query   Nucleic acid structure report {DiProDB Table} | HTML | None | http://diprodb.fli-leibniz.de/GetEntries.php
Query   Dinucleotide property {Dinucleotide Property} | HTML | DiProDB ID | http://diprodb.fli-leibniz.de/GetEntries.php?ID=%s
Example DiProDB ID | 5

ID      DisProt
Acc     DB-0017
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.
URL     http://www.disprot.org/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure
EDAMdat 2722 | Protein structure report (disordered protein)
EDAMid  2723 | Protein ID (DisProt)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein ID (DisProt)
Query  Protein structure report (disordered protein) {DisProt entry} | HTML | Protein ID (DisProt) | http://www.disprot.org/protein.php?id=%s
Example Protein ID (DisProt) | DP00001

ID      DNAReplication
Name    DNA replication database
Desc    A Resource for eukaryotic DNA replication.
URL     http://www.dnareplication.net/
Taxon   1 | all
EDAMtpc 0654 | DNA

ID      Dockground
Name    Dockground database for molecular modelling of protein interactions
Desc    Benchmarks, decoys, templates and other knowledge resources for docking.
URL     http://dockground.bioinformatics.ku.edu/
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions

ID      DOMINO
Name    DOMINO domain peptide interactions database
Desc    Database of annotated experiments describing interactions mediated by protein-interaction domains.
URL     http://mint.bio.uniroma2.it/domino/search/searchWelcome.do
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions

ID      DoOP
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.
URL     http://doop.abc.hu/
Taxon   1 | all
! EDAMtpc 0111 | Promoters
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0204 | Gene regulation resources

ID      DOSAC-COBS-2DPAGE
Acc     DB-0018
Name    DOSAC-COBS 2D-PAGE database
Desc    Two-dimensional polyacrylamide gel electrophoresis federated database.
URL     http://www.dosac.unipa.it/2d/
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=O43818
Example UniProt accession | O43818

ID      DPDB
Name    Drosophila polymorphism database (DPDB)
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.
URL     http://bioinf3.uab.cat/dPDB/dPDB.asp
Taxon   7215 | Drosophila
EDAMtpc 0199 | Genetic variation
EDAMtpc 0211 | Flies

ID      DPVweb
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.
URL     http://www.dpvweb.net/
Taxon   10239 | Viruses
EDAMtpc 0781 | Viruses
EDAMtpc 0780 | Plants
EDAMdat 2307 | Virus annotation
EDAMdat 2308 | Virus annotation (taxonomy)
EDAMid  2733 | Genus name (virus)
EDAMid  2734 | Family name (virus)
EDAMid  2836 | DPVweb ID
EDAMfmt 2331 | HTML
Query   Virus annotation | HTML | DPVweb ID | http://www.dpvweb.net/dpv/showdpv.php?dpvno=%s
Query   Virus annotation (taxonomy) | HTML | Family name (virus) | http://www.dpvweb.net/notes/showfamily.php?family=%s
Query   Virus annotation (taxonomy) | HTML | Genus name (virus) | http://www.dpvweb.net/notes/showgenus.php?genus=%s
Example DPVweb ID | 1
Example Family name (virus) | Alphaflexiviridae
Example Genus name (virus) | Alfamovirus

ID      DQCS
Name    The Database of Quantitative Cellular Signaling
Desc    A repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models.
URL     http://doqcs.ncbs.res.in/
Taxon   1 | all
EDAMtpc 0754 | Signaling pathways



ID      DRC
Name    Database of ribosomal crosslinks (DRC)
Desc    Biochemical data about structure of the ribosome from ribosomal cross-linking.
URL     http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/
Taxon   1 | all
EDAMtpc 0617 | Ribosomal genes and proteins

ID      DrugBank
Acc     DB-0019
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.
URL     http://www.drugbank.ca/
Cat     Other
Taxon   9606 | Homo sapiens
EDAMtpc 0620 | Drugs and targets
EDAMtpc 0202 | Pharmacoinformatics
EDAMdat 1696 | Drug annotation
EDAMid  2326 | DrugBank ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | DrugBank ID
Query   Drug annotation | HTML | DrugBank ID | http://www.drugbank.ca/drugs/%s
Example DrugBank ID | None

ID      DSD
Name    Database of dehydrogenase stereospecificities (DSD)
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).
URL     http://www.darrenflower.info/DSD/
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions

ID      DSMM
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.
URL     http://atlas.villa-bosch.de/dbase/dsmm/
Taxon   None
EDAMtpc 0176 | Molecular dynamics

ID      DSSP
Name    DSSP secondary structure database
Desc    Secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
URL     http://swift.cmbi.ru.nl/gv/dssp/
Taxon   1 | all
EDAMtpc 3040 | Protein structure
EDAMtpc 0694 | Protein secondary structure
EDAMdat 0876 | Protein features (secondary structure)
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Query   Protein features (secondary structure) {DSSP report} | HTML | PDB ID | http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=dssp&id=%s
Example PDB ID | 2hva

ID      DynaProt
Name    DynaProt 2D proteome database of Lactococcus lactis
Desc    2D reference maps and summarized protein information for Lactococcus lactis.
URL     http://www.wzw.tum.de/proteomik/lactis/
Taxon   1358 | Lactococcus lactis
EDAMtpc 0767 | Protein and peptide identification

ID      EASED
Name    EASED database
Desc    Extended Alternatively Spliced EST Database
URL     http://eased.bioinf.mdc-berlin.de/
Taxon   1 | all
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0114 | Gene structure and RNA splicing

ID      EcID
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.
URL     http://www.pdg.cnb.uam.es/i2h/info.html
Taxon   562 | Escherichia coli
EDAMtpc 0147 | Protein-protein interactions
EDAMid  1026 | Gene symbol
EDAMdat 0896 | Protein report
EDAMdat 1565 | Protein-protein interaction
EDAMdat 2093 | Data reference
EDAMid  0989 | Protein identifier
EDAMid  2802 | Protein ID (EcID)
EDAMfmt 2331 | HTML
Query   Data reference {Protein sequence ID table} | HTML | Protein identifier | http://ecid.bioinfo.cnio.es/Php/PreQuery.php?busca=%s
Query   Protein-protein interaction {Predictions Mode} | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/Summary.php?view=pred&ID=%s1&seq=%s2&gn=%s3
Query   Protein-protein interaction {Experimental Mode} | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/Summary.php?ID=%s1&seq=%s2&gn=%s3&view=exp
Query   Protein report | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/ProtInfo.php?busca=%s1seq=%s2&gn=%s3
Example Protein identifier | NRDD_ECOLI
Example Protein identifier;Protein ID (EcID);Gene symbol | NRDD_ECOLI;1639;nrdD

ID      ECO2DBASE
IDalt   2DBase-Ecoli
IDalt   EC-2D-GEL
Acc     DB-0115
Name    2D-PAGE database of Escherichia coli
Desc    2D-PAGE database of Escherichia coli
URL     None
Cat     2D gel databases
Taxon   562 | Escherichia coli
EDAMtpc 0767 | Protein and peptide identification
EDAMid  0842 | Identifier
Xref    SP_explicit | Identifier {ECO2DBASE}
Example Identifier | H021.1

ID      2DBase-Ecoli
IDalt   EC-2D-GEL
Acc     DB-0122
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 various functional categories enabling quick and subsequent analysis.
URL     http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi
Cat     2D gel databases
Taxon   562 | Escherichia coli
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) {ECO2DBASE entry} | HTML | UniProt accession | http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?%s
Example UniProt accession | P02930
Example UniProt accession | P52697

ID      EcoGene
Acc     DB-0021
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.
URL     http://ecogene.org/
Cat     Organism-specific databases
Taxon   562 | Escherichia coli
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 0916 | Gene annotation
EDAMid  1795 | Gene ID (EcoGene)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene ID (EcoGene)
Xref    SP_FT | Gene ID (EcoGene)
Query   Gene annotation | HTML | Gene ID (EcoGene) | http://www.ecogene.org/geneInfo.php?eg_id=%s
Example Gene ID (EcoGene) | EG11277

ID      EchoBASE
Acc     DB-0020
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.
URL     http://www.york.ac.uk/res/thomas/
Cat     Organism-specific databases
Taxon   562 | Escherichia coli
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 0916 | Gene annotation
EDAMid  1026 | Gene symbol
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene symbol
Query   Gene annotation {EchoBASE entry} | HTML | Gene symbol | http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=%s
Example Gene symbol | EB1017

ID      EDS
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.
URL     http://eds.bmc.uu.se/eds/
Taxon   1 | all
EDAMtpc 0081 | Structure analysis
EDAMdat 0896 | Protein report
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Query   Protein report | HTML | PDB ID | http://eds.bmc.uu.se/cgi-bin/eds/uusfs?PDBCode=%s
Example PDB ID | 2hha

ID      EGA
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.
URL     http://www.ebi.ac.uk/ega/
Taxon   9606 | Homo sapiens
EDAMtpc 0625 | Genotype and phenotype resources
EDAMdat 2381 | Experiment annotation (genotype)
EDAMid  2383 | EGA accession
EDAMfmt 2331 | HTML
Query   Experiment annotation (genotype) | HTML | EGA accession | http://www.ebi.ac.uk/ega/page.php?page=study&study=%s&cat=www.ovcare.studies.xml&subcat=OVCARE
Example EGA accession | EGAS00000000040

ID      eggNOG
Acc     DB-0152
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.
URL     http://eggnog.embl.de/
Taxon   1 | all
EDAMtpc 0722 | Nucleic acid classification
EDAMtpc 0623 | Genes, gene family or system

ID      ELM
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.
URL     http://elm.eu.org/
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMdat 1298 | Sequence features (motifs)
EDAMid  2705 | GO term ID (cellular compartment)
EDAMid  2291 | UniProt ID
EDAMid  0842 | Identifier
EDAMid  1868 | Taxon
EDAMfmt 2331 | HTML
Query   Sequence features (motifs) {ELM report} | HTML | UniProt ID | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s
Query   Sequence features (motifs) {ELM report} | HTML | UniProt ID;Taxon;GO term ID (cellular compartment) | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s1&userSpecies=%s2&userCC=%s3
Query   Sequence features (motifs) {ELM report} | HTML | Identifier {Protein sequence} | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&sequence=%s
Example UniProt ID;Taxon;GO term ID (cellular compartment) | src_human;10116;GO:0005634
Example UniProt ID | src_human
Example Identifier {Protein sequence} | MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL

ID      EMAP
Name    Edinburgh Mouse Atlas (EMAP)
Desc    A digital Atlas of mouse embryonic development consisting of a database of anatomical terms that includes the names of anatomical structures that are found at different stages of mouse embryo development, and a set of 3D volumetric digital embryo models at different stages of mouse 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.
URL     http://www.emouseatlas.org/Atlas/intro.html
NARid   20
NARCat  /nar/database/cat/7 | Human and other Vertebrate Genomes
NARSub  /nar/database/subcat/7/28 | Model organisms, comparative genomics
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct  http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/2/259
Taxon   10088 | Mus
EDAMtpc 0213 | Mice or rats
EDAMtpc 3067 | Anatomy resources
EDAMdat 2724 | Embryo annotation
EDAMid  1149 | EMAGE ID
EDAMfmt 2331 | HTML
Query   Embryo annotation {Emage entry} | HTML | EMAGE ID | http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s
Example EMAGE ID | 1000

ID      EMBL
IDalt   EMBL-Bank
Acc     DB-0022
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.
URL     http://www.ebi.ac.uk/embl/
Cat     Sequence databases
Taxon   1 | all
EDAMdat 2201 | Sequence record full
EDAMtpc 0640 | Nucleic acid sequence analysis
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 1927 | EMBL format
EDAMfmt 2311 | EMBL-HTML
Xref    SP_explicit | Sequence accession (nucleic acid)
Xref    SP_FT | Sequence accession (nucleic acid)
Query   Sequence record full | EMBL-HTML | Sequence accession (nucleic acid) | http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&id=%s&Submit=Go
Query   Sequence record full | EMBL format | Sequence accession (nucleic acid) | http://www.ebi.ac.uk/cgi-bin/emblfetch?style=raw&id=%s&Submit=Go
Example Sequence accession (nucleic acid) | AE014292

ID      EMDB
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.
URL     http://www.emdatabank.org
Taxon   1 | all
EDAMtpc 2226 | Structure determination

ID      EMGlib
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.
URL     http://pbil.univ-lyon1.fr/emglib/emglib.html
Taxon   1 | all
EDAMtpc 2817 | Yeast
EDAMtpc 1811 | Prokaryotes and archae

ID      ENA
Desc    A comprehensive repository for public nucleotide sequence data.  Includes sequencing information including raw data, assembly and mapping information (relating fragmented raw sequence reads into contigs and higher order structures) and functional annotation of nucleic acid molecules.
Desc    European nucleotide short read and trace archive (ENA).
URL     http://www.ebi.ac.uk/ena
NARid   2
NARCat  /nar/database/cat/1 | Nucleotide Sequence Databases
NARSub  /nar/database/subcat/1/1 | International Nucleotide Sequence Database Collaboration
Abstrct http://nar.oupjournals.org/cgi/content/abstract/39/suppl_1/D28
DOI     http://dx.doi.org/10.1093/nar/gkq967
Taxon   1 | all
EDAMtpc 0640 | Nucleic acid sequence analysis

ID      EndoNet
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
URL     http://endonet.bioinf.med.uni-goettingen.de/index.jsp
Taxon   9606 | Homo sapiens
EDAMtpc 0754 | Signaling pathways

ID      Ensembl
Acc     DB-0023
Name    Ensembl eukaryotic genome annotation project
Desc    Genome databases for vertebrates and other eukaryotic species.
URL     http://www.ensembl.org/
Cat     Genome annotation databases
Taxon   33208 | Metazoa
EDAMtpc 2818 | Eukaryotes
EDAMdat 0849 | Sequence record
EDAMdat 0916 | Gene annotation
EDAMid  1033 | Gene ID (Ensembl)
EDAMid  2725 | Transcript ID (Ensembl)
EDAMfmt 1929 | FASTA format
EDAMfmt 2331 | HTML
Xref    SP_explicit | Transcript ID (Ensembl);Protein ID (Ensembl);Gene ID (Ensembl)
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s
Query   Sequence record | FASTA format | Gene ID (Ensembl);Transcript ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=%s1;output=fasta;r=13:31787617-31871809;strand=feature;t=%s2;time=1244110856.85314;st=cdna;st=coding;st=peptide;st=utr5;st=utr3;st=exons;st=introns;genomic=unmasked;_format=Text
Example Gene ID (Ensembl);Transcript ID (Ensembl) | ENSG00000139618;ENST00000380152

ID      Ensembl-Genome
Name    Ensembl-Genome
Desc    A system for the annotation, analysis and display of vertebrate genomes and for bacteria, protists, fungi, plants and invertebrate metazoa. 
URL     http://www.ensemblgenomes.org/
Taxon   1 | all
EDAMtpc 2818 | Eukaryotes

ID      EnsemblBacteria
Acc     DB-0147
Name    Ensembl bacterial genome annotation project
Desc    Genome databases for bacterial species.
URL     http://bacteria.ensembl.org/
Cat     Genome annotation databases
Taxon   2 | Bacteria
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 0916 | Gene annotation
EDAMid  2725 | Transcript ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Transcript ID (Ensembl)
Query   Gene annotation | HTML | Transcript ID (Ensembl) | www.ensemblgenomes.org/id/%s
Example Transcript ID (Ensembl) | EBMYCT00000015323


ID      EnsemblFungi
Acc     DB-0148
Name    Ensembl gungial genome annotation project
Desc    Genome databases for fungal species.
URL     http://fungi.ensembl.org/
Cat     Genome annotation databases
Taxon   4751 | Fungi
EDAMtpc 0782 | Fungi
EDAMdat 0916 | Gene annotation
EDAMid  2725 | Transcript ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Transcript ID (Ensembl)
Query   Gene annotation | HTML | Transcript ID (Ensembl) | www.ensemblgenomes.org/id/%s
Example Transcript ID (Ensembl) | SPAC922.03-1


ID      EnsemblMetazoa
Acc     DB-0149
Name    Ensembl invertebrate metazoan genome annotation project
Desc    Genome databases for invertebrate metazoan species.
URL     http://metazoa.ensembl.org/
Cat     Genome annotation databases
Taxon   33208 | Metazoa
EDAMtpc 2819 | Invertebrates
EDAMdat 0916 | Gene annotation
EDAMid  2725 | Transcript ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Transcript ID (Ensembl)
Query   Gene annotation | HTML | Transcript ID (Ensembl) | www.ensemblgenomes.org/id/%s
Example Transcript ID (Ensembl) | FBtr0087976


ID      EnsemblPlants
Acc     DB-0150
Name    Ensembl plant genome annotation project
Desc    Genome databases for plant species.
URL     http://plants.ensembl.org/
Cat     Genome annotation databases
Taxon   58024 | Spermatophyta
EDAMtpc 0780 | Plants
EDAMdat 0916 | Gene annotation
EDAMid  2725 | Transcript ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Transcript ID (Ensembl)
Query   Gene annotation | HTML | Transcript ID (Ensembl) | www.ensemblgenomes.org/id/%s
Example Transcript ID (Ensembl) | AT1G22300.1


ID      EnsemblProtists
Acc     DB-0151
Name    Ensembl protist genome annotation project
Desc    Genome databases for protist species.
URL     http://protists.ensembl.org/
Cat     Genome annotation databases
Taxon   2759 | Eukaryota
EDAMtpc 2818 | Eukaryotes
EDAMdat 0916 | Gene annotation
EDAMid  2725 | Transcript ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Transcript ID (Ensembl)
Query   Gene annotation | HTML | Transcript ID (Ensembl) | www.ensemblgenomes.org/id/%s
Example Transcript ID (Ensembl) | AT1G22300.1


ID      ENZYME
IDalt   EC_number
Acc     DB-0024
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.
URL     http://www.expasy.org/enzyme/
Cat     Enzyme and pathway databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 2811 | Nomenclature
EDAMdat 1509 | Protein report (enzyme)
EDAMid  1011 | EC number
EDAMfmt 2331 | HTML
Xref    Other | EC number
Query   Protein report (enzyme) | Text | EC number | http://www.expasy.ch/enzyme/%s.txt
Query   Protein report (enzyme) | HTML | EC number | http://www.expasy.ch/enzyme/%s
Example EC number | 1.5.99.11

ID      EPConDB
Name    EPConDB
Desc    Information about genes expressed in cells of the pancreas and their transcriptional regulation. EPConDB includes expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. 
URL     http://www.cbil.upenn.edu/EPConDB
NARid   13
NARCat  /nar/database/cat/8 | Human Genes and Diseases
NARSub  /nar/database/subcat/8/34 | Gene-, system- or disease-specific databases
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/35/suppl_1/D751
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics

ID      EPD
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.
URL     http://www.epd.isb-sib.ch/
Taxon   2759 | Eukaryota
! EDAMtpc 0111 | Promoters
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMdat 1312 | Gene features (promoter)
EDAMid  2386 | EPD ID
EDAMfmt 2331 | HTML
Xref    EMBL_explicit | EPD ID
Query   Gene features (promoter) {EPD entry} | Text | EPD ID | http://www.epd.isb-sib.ch/cgi-bin/query_result.pl?out_format=text&from=-499&to=100&Entry_0=%s
Query   Gene features (promoter) {EPD entry} | HTML | EPD ID | http://www.epd.isb-sib.ch/cgi-bin/query_result.pl?out_format=HTML&from=-499&to=100&Entry_0=%s
Query   Gene features (promoter) {EPD entry} | HTML {nice view} | EPD ID | http://www.epd.isb-sib.ch/cgi-bin/get_doc?db=epd&format=nice&entry=%s
Example EPD ID | MSV_105_1

ID      ERIC
Name    Enteropathogen resource integration center (ERIC)
Desc    Annotated enterobacterial genome and associated information.
URL     http://www.ericbrc.org/portal/eric/
Cat     Not available
Taxon   543 | Enterobacteriaceae
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0783 | Pathogens
Xref    SP_FT | None

ID      eSLDB
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.
URL     http://gpcr.biocomp.unibo.it/esldb/
Taxon   2759 | Eukaryota
EDAMtpc 0820 | Membrane proteins
EDAMtpc 0140 | Protein targeting and localization

ID      ESP-SOLDB
Name    Genomic generic database applied to tomato fruit quality (ESP-SOLDB)
Desc    Genomic generic database applied to tomato fruit quality (ESP-SOLDB).
URL     http://www.bitlab-es.com/espsol
Taxon   4081 | Solanum lycopersicum
EDAMtpc 0780 | Plants

ID      ESTHER
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.
URL     http://bioweb.ensam.inra.fr/ESTHER/general?what=index
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources

ID      euHCVdb
Acc     DB-0025
Name    European Hepatitis C virus database (euHCVdb)
Desc    European Hepatitis C virus database.
URL     http://euhcvdb.ibcp.fr/euHCVdb/
Cat     Organism-specific databases
Taxon   11103 | Hepatitis C virus
EDAMtpc 0781 | Viruses
EDAMdat 0849 | Sequence record
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Sequence accession (nucleic acid)
Query   Sequence record {euHCVdb entry} | HTML | Sequence accession (nucleic acid) | http://euhcvdb.ibcp.fr/euHCVdb/jsp/HCVResultTextForm.jsp?AC=%s
Example Sequence accession (nucleic acid) | AF009606


ID      EuroPhenome
Name    EuroPhenome mouse phenotype resource
Desc    Software system for capturing, storing and analysing raw phenotyping data from SOPs contained in EMPReSS.
URL     http://www.europhenome.org
Taxon   10088 | Mus
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0213 | Mice or rats

ID      EVEREST
Name    Evolutionary ensembles of recurrent segments (EVEREST)
Desc    An automatic identification and classification of protein domains.
URL     http://www.everest.cs.huji.ac.il
Taxon   1 | all
EDAMtpc 0736 | Protein domains and folds

ID      ExplorEnz
Name    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.
URL     http://www.enzyme-database.org/
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 2811 | Nomenclature

ID      EXProt
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.
URL     http://www.cmbi.kun.nl/EXProt/
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0639 | Protein sequence analysis
EDAMtpc 1775 | Protein function analysis

ID      ExTopoDB
Name    Experimentally derived topological models of transmembrane proteins (ExTopoDB)
Desc    Experimentally derived topological models of transmembrane proteins.
URL     http://bioinformatics.biol.uoa.gr/ExTopoDB
Taxon   1 | all
EDAMtpc 0820 | Membrane proteins

ID      EyeSite
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.
URL     http://eyesite.cryst.bbk.ac.uk/
Taxon   2759 | Eukaryota
EDAMtpc 0635 | Specific protein resources
EDAMtpc 3052 | Sequence clusters and classification

ID      FaCD
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.
URL     http://www.facd.info
Taxon   9606 | Homo sapiens
EDAMtpc 2640 | Cancer resources

ID      FANTOM_DB
Name    Database of functional annotation of mammalian Genome (FANTOM_DB)
Desc    Functional annotation of mammalian genome.
URL     http://fantom.gsc.riken.jp/4/
Cat     Not available
Taxon   40674 | Mammalia
EDAMtpc 3048 | Mammals
Xref    SP_FT | None
Example Identifier | 0610005A07

ID      FASTDB
Name    Friendly alternative splicing and transcripts database (FASTDB)
Desc    Alternative splicing and transcripts database.
URL     http://www.fast-db.com
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing

ID      FCP
Name    Functional coverage of the proteome (FCP)
Desc    Functional coverage of the proteome.
URL     http://cgl.imim.es/fcp/
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms


ID      FGDB
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).
URL     http://mips.gsf.de/genre/proj/FGDB/
Taxon   5126 | Gibberella 
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0782 | Fungi

ID      FINDBase
Name    FINDBase
Desc    Information about the frequency of different mutations leading to inherited disorders in various populations around the globe.
URL     http://www.findbase.org/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 0634 | Disease resources

ID      FireDB
Name    Database of functionally important residues from protein structures (FireDB)
Desc    A database of Protein Data Bank structures, ligands and annotated functional site residues.
URL     http://firedb.bioinfo.cnio.es/index.php
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0148 | Protein-ligand interactions
EDAMtpc 0166 | Protein structural motifs and surfaces

ID      FLAGdb++
Name    FLAGdb++ a database for the functional analysis of the Arabidopsis genome
Desc    Integrative database around plant genomes.
URL     http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/index.shtml
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0780 | Plants

ID      FLIGHT
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.
URL     http://flight.licr.org/
Taxon   7215 | Drosophila
EDAMtpc 0211 | Flies
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0625 | Genotype and phenotype resources

ID      FlyBase
Acc     DB-0026
Name    FlyBase database of genetic and molecular data of Drosophila
Desc    A Database of Drosophila genes and genomes.
URL     http://flybase.bio.indiana.edu/
Cat     Organism-specific databases
Taxon   7215 | Drosophila
EDAMtpc 0211 | Flies
EDAMdat 0916 | Gene annotation
EDAMid  1796 | Gene ID (FlyBase)
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | Gene ID (FlyBase)
Xref    SP_FT | None
Query   Gene annotation {FlyBase entry} | HTML | Gene ID (FlyBase) | http://flybase.org/cgi-bin/gbrowse/dmel/?dontadjust=1&name=%s
Query   Gene annotation {FlyBase entry} | XML | Gene ID (FlyBase) | http://flybase.org/chadoxml/id/%s
Example Gene ID (FlyBase) | FBgn0000165
Example Gene ID (FlyBase) | FBgn0000024
Example Gene ID (FlyBase) | FBgn0000490

ID      FlyMine
Name    FlyMine Drosophila genome database
Desc    An integrated database for Drosophila and Anopheles genomics.
URL     http://www.flymine.org
Taxon   7215 | Drosophila
EDAMtpc 0211 | Flies

ID      FLYSNP
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.
URL     http://flysnp.imp.ac.at/
Taxon   7215 | Drosophila
EDAMtpc 2277 | SNPs
EDAMtpc 0211 | Flies

ID      FlyTF
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
URL     http://www.flytf.org
Taxon   7215 | Drosophila
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0211 | Flies

ID      FlyView
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.
URL     http://flyview.uni-muenster.de/
NARid   14
NARCat  /nar/database/cat/5 | Genomics Databases (non-vertebrate)
NARSub  /nar/database/subcat/5/23 | Invertebrate genome databases
Taxon   7215 | Drosophila
EDAMtpc 2229 | Cell biology resources
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0211 | Flies

ID      FPSPD
Name    Functional protein sequence pattern database (FPSPD)
Desc    Accumulates functional protein sequence patterns derived from the structurally-aligned homologous families in the HOMSTRAD database.
URL     http://torsa.bioc.cam.ac.uk/~fpspd/home_d.html
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features

ID      FunCoup
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.
URL     http://funcoup.sbc.su.se/
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0140 | Protein targeting and localization

ID      FungalGenomeSize
Name    Fungal genome size database
Desc    Fungal genome size database
URL     http://www.zbi.ee/fungal-genomesize/
Taxon   4751 | Fungi
EDAMtpc 0622 | Genomics
EDAMtpc 0782 | Fungi

ID      FUNPEP
Name    FUNPEP information system for "low complexity sequence regions"
Desc    Information system for "low complexity sequence regions".
URL     http://swift.cmbi.kun.nl/swift/FUNPEP/info/
Taxon   1 | all
EDAMtpc 0642 | Low complexity sequences

ID      FunShift
Name    FunShift database
Desc    A compilation of function shift analysis performed between subfamilies in protein families.
URL     http://FunShift.cgb.ki.se
Taxon   1 | all
EDAMtpc 1775 | Protein function analysis
EDAMtpc 0724 | Protein families

ID      FunSimMat
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.
URL     http://funsimmat.bioinf.mpi-inf.mpg.de/
Taxon   1 | all
EDAMtpc 1775 | Protein function analysis




ID      FUNYBASE
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.
URL     http://genome.jouy.inra.fr/funybase/funybase_start.cgi
Taxon   4751 | Fungi
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0724 | Protein families
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0782 | Fungi
EDAMtpc 0194 | Phylogenomics

ID      FusionDB
Name    FusionDB database of bacterial and archaeal gene fusion events
Desc    A database of bacterial and archaeal gene fusion events.
URL     http://www.igs.cnrs-mrs.fr/FusionDB/
Taxon   2 | Bacteria
Taxon   2157 | Archaea
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMtpc 1811 | Prokaryotes and archae

ID      G2Cdb
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.
URL     http://www.genes2cognition.org
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 0634 | Disease resources

ID      GabiPD
Name    GabiPD: primary database of plant integrative biology
Desc    Primary database of plant integrative biology.
URL     http://www.gabipd.org/
Taxon   58024 | Spermatophyta
EDAMtpc 0780 | Plants
Xref    SP_FT | None
Example Identifier | HA05J18

ID      GABI-Kat
Name    GABI-Kat tags mutagenised A. thaliana
Desc    Generation of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants.
URL     http://www.gabi-kat.de/
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0796 | Genetic mapping and linkage

ID      GBIFFI
Name    Global biodiversity information facility, Finland (GBIFFI)
Desc    Global biodiversity data.
URL     http://www.gbif.fi
Taxon   1 | all
EDAMtpc 0610 | Ecoinformatics
EDAMtpc 3050 | Biodiversity

ID      GDB
Name    Human Genome Database (GDB)
Desc    Community curated collection of human genomic data - now obsolete.
Taxon   9606 | Homo sapiens
EDAMtpc 2815 | Humans
Xref    EMBL_explicit | Identifier {GDB}
Example Identifier {GDB} | 4466301

ID      GenAtlas
Acc     DB-0027
Name    GenAtlas human gene database
Desc    Information on gene mapping and genetic diseases.
URL     http://www.dsi.univ-paris5.fr/genatlas/
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 2815 | Humans
EDAMdat 0916 | Gene annotation
EDAMid  1026 | Gene symbol
EDAMfmt 2331 | HTML
Xref    SP_implicit | Gene symbol
Query   Gene annotation {GenAtlas entry} | HTML | Gene symbol | http://www.dsi.univ-paris5.fr/genatlas/fiche.php?symbol=%s
Example Gene symbol | RPL35A

ID      GenBank
Acc     DB-0028
Name    GenBank nucleotide sequence database
Desc    A comprehensive database of public nucleotide sequences for more than 300 000 organisms named, from small and large-scale sequencing projects. Data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage.
URL     http://www.ncbi.nlm.nih.gov/
NARid   3
NARCat  /nar/database/cat/1 | Nucleotide Sequence Databases
NARSub  /nar/database/subcat/1/1 | International Nucleotide Sequence Database Collaboration
Abstrct http://nar.oupjournals.org/cgi/content/abstract/39/suppl_1/D32
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 0640 | Nucleic acid sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2532 | GenBank-HTML
Xref    SP_implicit | Sequence accession (nucleic acid)
Query   Sequence record full | GenBank-HTML | Sequence accession (nucleic acid) | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=%s
Example Sequence accession (nucleic acid) | AE014292

ID      GenBank-dbSTS
IDalt   dbSTS
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.
URL     http://www.ncbi.nlm.nih.gov/dbSTS/
Cat     Not available
Taxon   1 | all
EDAMtpc 0796 | Genetic mapping and linkage
EDAMdat 2201 | Sequence record full
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2532 | GenBank-HTML
Xref    SP_FT | None
Query   Sequence record full | GenBank-HTML | Sequence accession (nucleic acid) | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=%s
Example Sequence accession (nucleic acid) | G06709

ID      Gene3D
Acc     DB-0029
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.
URL     http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
URLlink http://gene3d.biochem.ucl.ac.uk/Gene3D/linking
URLsoap http://funcnet.eu/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 1775 | Protein function analysis
EDAMdat 0907 | Protein family annotation
EDAMid  1040 | CATH domain ID
EDAMid  2701 | CATH node ID (family)
EDAMfmt 2331 | HTML
Xref    SP_explicit | CATH node ID (family)
Query   Protein family annotation {Gene3D entry} | HTML | CATH node ID (family) | http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?family=%s
Query   Protein family annotation {Gene3D entry} | HTML | CATH domain ID | http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?domain_id=%s
Query   Protein family annotation {Gene3D entry} | HTML | CATH node ID (family) | http://www.cathdb.info/cgi-bin/GotoCath.pl?cath=%s
Example CATH node ID (family) | 2.10.10.10
Example CATH domain ID | 1cukA00
Example CATH node ID (family) | G3DSA:3.40.30.10

ID      GeneAnnot
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.
URL     http://bioinfo2.weizmann.ac.il/geneannot/
Taxon   9606 | Homo sapiens
EDAMtpc 0632 | Probes and primers

ID      GeneCards
Acc     DB-0030
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.
URL     http://www.genecards.org/
Cat     Human genes and diseases database
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 3078 | Gene and protein resources
EDAMtpc 0078 | Protein analysis
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0199 | Genetic variation
EDAMtpc 2815 | Humans
EDAMid  3021 | UniProt accession
EDAMid  1026 | Gene symbol
EDAMid  2298 | Gene ID (HGNC)
EDAMid  1025 | Gene identifier
EDAMid  1904 | Locus ID (EntrezGene)
EDAMid  2610 | Ensembl ID
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | Gene identifier {GeneCards}
Query   Gene annotation | HTML | Gene symbol | http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s
Query   Gene annotation | HTML | UniProt accession | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | HTML | Locus ID (EntrezGene) | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | HTML | Ensembl ID | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | HTML | Gene ID (HGNC) | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | XML | Gene symbol | http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s&format=xmlByFunction
Query   Gene annotation | HTML | Gene identifier {GeneCards} | http://www.genecards.org/cgi-bin/carddisp.pl?gc_id=%s
Example Gene symbol | CASP3
Example Locus ID (EntrezGene) | 1956
Example Ensembl ID | ENSG00000146648
Example Gene ID (HGNC) | 2041
Example Gene identifier {GeneCards} | GC20P040256

ID      GeneDB
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).
URL     http://www.genedb.org/
Taxon   1 | all
EDAMtpc 0783 | Pathogens
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene symbol | http://www.genedb.org/gene/%s
Example Gene symbol | ECA4014

ID      GeneDB_Spombe
Acc     DB-0031
Name    Schizosaccharomyces pombe genome database (GeneDB_Spombe)
Desc    Sequence data and annotation/curation for Schizosaccharomyces pombe (fission yeast), including known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs.
URL     http://www.genedb.org/genedb/pombe/
Cat     Organism-specific databases
Taxon   4896 | Schizosaccharomyces pombe
EDAMtpc 2817 | Yeast
EDAMtpc 0659 | Functional RNA
EDAMtpc 0798 | Mobile genetic elements
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Xref    EMBL_explicit | Gene symbol
Xref    SP_explicit | Gene symbol
Query   Gene annotation | HTML | Gene symbol | http://www.genedb.org/genedb/Search?submit=Search+for&name=%s&organism=pombe&desc=yes
Example Gene symbol | SPAC922.03


ID      GeneExpressionTooth
Name    Gene expression in tooth database
Desc    Gene expression in tooth database
URL     http://bite-it.helsinki.fi/
Taxon   9347 | Eutheria
EDAMtpc 0197 | Gene expression resources

ID      GeneFarm
Acc     DB-0032
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.
URL     http://urgi.versailles.inra.fr/Genefarm/index.htpl
Cat     Organism-specific databases
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 3078 | Gene and protein resources
EDAMtpc 0780 | Plants
EDAMdat 0916 | Gene annotation
EDAMdat 0907 | Protein family annotation
EDAMid  2295 | Gene ID
EDAMid  2731 | Protein family ID (GeneFarm)
EDAMfmt 2331 | HTML
Xref    SP_explicit |  Protein family ID (GeneFarm)
Query   Gene annotation | HTML | Gene ID | http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s
Query   Protein family annotation | HTML | Protein family ID (GeneFarm) | http://urgi.versailles.inra.fr/Genefarm/Family/display_family.htpl?FAM_ID=%s
Example Protein family ID (GeneFarm) | 59
Example Gene ID | 907

ID      GeneID
Acc     DB-0118
Name    GeneID database of genes from NCBI RefSeq genomes
Desc    Database of genes from NCBI RefSeq genomes
URL     http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
Cat     Genome annotation databases
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMdat 0916 | Gene annotation
EDAMid  2339 | Ontology term name
EDAMid  1176 | GO term ID
EDAMid  1026 | Gene symbol
EDAMid  1045 | Species name
EDAMid  1011 | EC number
EDAMid  0987 | Chromosome name
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMid  0842 | Identifier
EDAMid  1187 | PubMed ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {Unique ID}
Query   Gene annotation {GeneID gene list} | HTML | Identifier {Keyword} | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=%s
Query   Gene annotation {GeneID gene list} | HTML | Sequence accession (nucleic acid) | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[accn]
Query   Gene annotation {GeneID gene list} | HTML | Gene symbol | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[sym]
Query   Gene annotation {GeneID gene list} | HTML | PubMed ID | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[PMID]
Query   Gene annotation {GeneID gene list} | HTML | Ontology term name {GO} | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="%s"[GO]
Query   Gene annotation {GeneID gene list} | HTML | GO term ID | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="%s"[GO]
Query   Gene annotation {GeneID gene list} | HTML | Chromosome name;Species name | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s1[CHR]+AND+%s2[ORGN]
Query   Gene annotation {GeneID gene list} | HTML | EC number | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[EC]
Query   Gene annotation {GeneID gene list} | HTML | Identifier {Unique ID} | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[uid]
Example Identifier {Keyword} | haem
Example Sequence accession (nucleic acid) | M11313
Example Gene symbol | BRCA1
Example PubMed ID | 11331580
Example Ontology term name {GO} | cell+adhesion
Example Chromosome name | Y
Example Species name | human
Example EC number | 1.9.3.1
Example Identifier {Unique ID} | 4156251

ID      GeneLoc
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.
URL     http://genecards.weizmann.ac.il/geneloc/index.shtml
Taxon   9606 | Homo sapiens
EDAMtpc 2815 | Humans
EDAMtpc 0624 | Chromosomes

ID      GeneNest
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.
URL     http://genenest.molgen.mpg.de/
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMtpc 0722 | Nucleic acid classification
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0655 | mRNA, EST or cDNA

ID      GeneNote
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.
URL     http://genecards.weizmann.ac.il/genenote/
Taxon   9606 | Homo sapiens
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      GeneSapiens
Name    GeneSapiens human transcriptome database
Desc    Human transcriptome database.
URL     http://www.genesapiens.org/
Taxon   9606 | Homo sapiens
EDAMtpc 0197 | Gene expression resources

ID      GeneSNPs
IDalt   NIEHS-SNPs
Name    SNPs Program at the University of Washington (GeneSNPs)
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.
URL     http://egp.gs.washington.edu/
Cat     Polymorphism databases
Taxon   9606 | Homo sapiens
EDAMtpc 2277 | SNPs
EDAMtpc 2815 | Humans
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMdat 2092 | SNP annotation
EDAMid  2805 | GeneSNP ID
EDAMfmt 2331 | HTML
Query   SNP annotation {GeneSNPs entry} | HTML | GeneSNP ID | http://egp.gs.washington.edu/data/%s/


ID      GeneTide
Name    GeneTide database
Desc    An automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes.
URL     http://genecards.weizmann.ac.il/genetide/
Taxon   9606 | Homo sapiens
EDAMtpc 0655 | mRNA, EST or cDNA


ID      GeneTree
Acc     DB-0162
Name    GeneTree
Desc    GeneTree
URL     http://www.ensemblgenomes.org
Cat     Phylogenomic databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0194 | Phylogenomics
EDAMdat 0916 | Gene annotation
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {GeneTree}
Query   Gene annotation | HTML | Identifier {GeneTree} | http://www.ensemblgenomes.org/id-genetree/%s
Example Identifier {GeneTree} | EMGT00050000006238


ID      Genevestigator
Acc     DB-0142
Name    Genevestigator
Desc    Genevestigator
URL     http://www.genevestigator.com/
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMdat 0916 | Gene annotation
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Gene annotation | HTML | UniProt accession | http://www.genevestigator.com/gv/directlink.jsp?geneIDs=%s&geneIDType=SwissPro
Example UniProt accession | P48347

ID      Genolevures
Name    Genolevures 18 yeast genomes
Desc    Annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes.
URL     http://www.genolevures.org/
Taxon   4892 | Saccharomycetales
EDAMtpc 2817 | Yeast
EDAMtpc 0722 | Nucleic acid classification

ID      GenoList
Acc     DB-0157
Name    GenoList comparative analysis of microbial genomes
Desc    An integrated environment for the analysis of microbial genomes.
URL     http://genolist.pasteur.fr/GenoList
Taxon   2 | Bacteria
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0797 | Comparative genomics
EDAMdat 3028 | Taxonomic data
EDAMdat 0916 | Gene annotation
EDAMid  1868 | Taxon
EDAMid  1026 | Gene symbol
EDAMid  2739 | Gene ID (Genolist)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene ID (Genolist)
Query   Gene annotation | HTML | Gene ID (Genolist) | http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/goToGene?accNum=%s
Query   Gene annotation | HTML | Gene symbol | http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/goToGene?geneName=%s
Query   Taxonomic data {GenoList organism(s)} | HTML | Taxon {GenoList organism} | http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/goToTaxoRank?level=%s
Example Gene ID (Genolist) | BSU00010
Example Gene symbol | abrB
Example Taxon | Bacillus

ID      GenomeReviews
IDalt   GR
Acc     DB-0034
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.
URL     http://www.ebi.ac.uk/GenomeReviews/
Cat     Genome annotation databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMdat 2711 | Genome metadata
EDAMid  2751 | GenomeReviews ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | GenomeReviews ID
Xref    EMBL_explicit | GenomeReviews ID
Query   Genome metadata {GenomeReviews entry} | HTML | GenomeReviews ID | http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[GENOMEREVIEWS:%s]+-e
Example GenomeReviews ID | ab000109_gr

ID      GenomicThreadingDatabase
Name    Genomic threading database
Desc    Structural annotations of proteomes, translated from the genomes of key organisms.
URL     http://bioinf.cs.ucl.ac.uk/GTD/
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms


ID      GenomeRNAi
Name    GenomeRNAi database
Desc    Phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells.
URL     http://www.dkfz.de/signaling2/rnai/ernai.html
Taxon   7215 | Drosophila
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0211 | Flies

ID      Germlinep53Mutations
Name    Germline p53 Mutations database
Desc    Germline p53 mutations
URL     http://www.lf2.cuni.cz/projects/germline_mut_p53.htm
Taxon   9606 | Homo sapiens
EDAMtpc 2640 | Cancer resources

ID      GermOnline
Acc     DB-0035
Name    Gametogenesis and reproductive tissue expression
Desc    High-throughput expression data relevant for germline development and fertility across species.
URL     http://www.germonline.org/
Cat     Gene expression databases
Taxon   2759 | Eukaryota
EDAMtpc 0197 | Gene expression resources
EDAMdat 0916 | Gene annotation
EDAMid  1026 | Gene symbol
EDAMid  1045 | Species name
EDAMid  1033 | Gene ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene symbol
Query   Gene annotation | HTML | Species name;Gene symbol | http://www.germonline.org/%s1/geneview?gene=%s2
Query   Gene annotation | HTML | Species name;Gene ID (Ensembl) | http://www.germonline.org/%s1/geneview?db=core|gene=%s2
Example Species name | Saccharomyces_cerevisiae
Example Gene symbol | YHL022C
Example Gene ID (Ensembl) | ENSG00000054796

ID      GETDB
Name    Gene Expression in Tooth Database
Desc    Gene expression in dental tissue
URL     http://bite-it.helsinki.fi/
NARid   24
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases


ID      GlycateBase
Name    GlycateBase glycation prediction
Desc    Glycation of amino groups of lysines in mammalian proteins.
URL     http://www.cbs.dtu.dk/databases/GlycateBase-1.0/
Taxon   40674 | Mammalia
EDAMtpc 0748 | Protein sites and features

ID      GlycomeDB
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).
URL     http://www.glycome-db.org/About.action
Taxon   1 | all
EDAMtpc 0152 | Carbohydrates

ID      GlycoSuiteDB
Acc     DB-0036
Name    GlycoSuiteDB glycan database
Desc    An annotated and curated relational database of glycan structures.
URL     http://glycosuitedb.expasy.org/
Cat     PTM databases
Taxon   1 | all
EDAMtpc 0152 | Carbohydrates
EDAMdat 2313 | Carbohydrate structure report
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Carbohydrate structure report {GlycoSuiteDB entry} | HTML | UniProt accession | http://glycosuitedb.expasy.org/glycosuite/results?prot_swissprot=%s;results_index=protein;ig_hist=1
Example UniProt accession | P02763

ID      GO
Acc     DB-0037
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.
URL     http://www.geneontology.org/
Cat     Ontologies
Taxon   None
EDAMtpc 0089 | Ontologies
EDAMdat 0966 | Ontology term
EDAMid  1176 | GO term ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | GO term ID
Xref    SP_FT | GO term 
Query   Ontology term | HTML | GO term ID | http://www.ebi.ac.uk/ego/QuickGO?mode=display&entry=%s
Example GO term ID | GO:0006915

ID      GOA
IDalt   GOA-UniProt
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).
URL     http://www.ebi.ac.uk/goa
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0089 | Ontologies
EDAMdat 0966 | Ontology term
EDAMdat 2093 | Data reference
EDAMid  1009 | Protein name
EDAMid  3021 | UniProt accession
EDAMid  1176 | GO term ID
EDAMid  2339 | Ontology term name
EDAMfmt 2331 | HTML
Xref    SP_implicit | UniProt accession
Xref    EMBL_explicit | UniProt accession
Query   Data reference {GOA-UniProt protein entry} | HTML | UniProt accession | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein
Query   Data reference {GOA-UniProt protein entry} | HTML | Protein name | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein
Query   Ontology term | HTML | GO term ID | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO
Query   Ontology term | HTML | Ontology term name {GO biological process} | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO
Example Ontology term name {GO biological process} | apoptosis
Example GO term ID | GO:0006915
Example Protein name | tropomyosin
Example UniProt accession | P06727


ID      GOLD
Name    Genomes database
Desc    Information on complete and ongoing genome projects, as well as metagenomes and metadata.
URL     http://www.genomesonline.org/
Taxon   1 | all
EDAMtpc 0622 | Genomics

ID      GOLDDB
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.
URL     https://gold.tugraz.at/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 0635 | Specific protein resources


ID      GoPubMed
Name    GoPubMed ontology-based literature search
Desc    Ontology-based literature search.
URL     http://www.gopubmed.org
Taxon   None
EDAMtpc 0606 | Literature data resources
EDAMtpc 0089 | Ontologies


ID      GPCRDB
Acc     DB-0038
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.
URL     http://www.gpcr.org/7tm/
Cat     Protein family/group databases
Taxon   2759 | Eukaryota
EDAMtpc 0820 | Membrane proteins
EDAMtpc 0148 | Protein-ligand interactions
EDAMdat 1456 | Protein report (membrane protein)
EDAMid  1131 | Protein family name
EDAMfmt 2331 | HTML
Xref    SP_implicit | Protein family name
Query   Protein report (membrane protein) {GPCRDB entry} | HTML | Protein family name | http://www.gpcr.org/7tm/proteins/%s
Example Protein family name | a1kyp5_petma

ID      GPCR_NaVa
Name    GPCR natural variants database
Desc    Sequence variants within the family of human G Protein-Coupled Receptors (GPCRs).
URL     http://nava.liacs.nl/index.html
Taxon   9606 | Homo sapiens
EDAMtpc 0820 | Membrane proteins

ID      GlycosciencesDB
IDalt   DBGLYCOSCIENCES.de
Name    Glycosciences database
Desc    Carbohydrate structure database.
URL     http://www.glycosciences.de/sweetdb/index.php
Taxon   None
EDAMtpc 0152 | Carbohydrates
EDAMdat 2753 | Carbohydrate conformational map
EDAMdat 2313 | Carbohydrate structure report
EDAMid  1127 | PDB ID
EDAMid  2752 | GlycoMap ID
EDAMid  2796 | Linucs ID
EDAMfmt 2331 | HTML
Query   Carbohydrate structure report {GLYCOSCIENCES.DB entry} | HTML | Linucs ID | http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=%s
Query   Carbohydrate structure report {GLYCOSCIENCES.de PDB entry} | HTML | PDB ID | http://www.glycosciences.de/database/start.php?action=explore_PDBcode&PDB_code=%s
Query   Carbohydrate conformational map {GlycoMapsDB entry} | HTML | GlycoMap ID | http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=%s
Example Linucs ID | 288
Example PDB ID | 1tl0
Example GlycoMap ID | 7147

ID      gPDB
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.
URL     http://bioinformatics.biol.uoa.gr/gPDB/
Taxon   2759 | Eukaryota
EDAMtpc 0820 | Membrane proteins

ID      Gramene
Acc     DB-0039
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.
URL     http://www.gramene.org/
Cat     Organism-specific databases
Taxon   4479 | Poaceae
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0780 | Plants
EDAMtpc 0602 | Pathways, networks and models
EDAMdat 0896 | Protein report
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Protein report {Gramene entry} | HTML | UniProt accession | http://www.gramene.org//db/protein/protein_search?acc=%s
Example UniProt accession | P93436


ID      GreenPhylDB
Name    A phylogenomic database for plant comparative genomics
Desc    Database for comparative genomic analyses of Arabidopsis thaliana and Oryza sativa full genomes.
URL     http://greenphyl.cirad.fr/cgi-bin/greenphyl.cgi
Taxon   58024 | Spermatophyta
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0084 | Phylogenetics
EDAMtpc 0194 | Phylogenomics
EDAMtpc 0780 | Plants

ID      GRIN
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.
URL     http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl
Cat     Not available
Taxon   58024 | Spermatophyta
EDAMtpc 0780 | Plants
EDAMtpc 2811 | Nomenclature
EDAMtpc 0637 | Taxonomy
Xref    SP_FT | None
Example Identifier | 1005973

ID      GXD
Name    Mouse Gene Expression Database (GXD)
Desc    Gene expression information for the mouse, including expression profiles of transcripts and proteins in different mouse strains and mutants. Data are taken from the literature and via submission. 
URL     http://www.informatics.jax.org/menus/expression_menu.shtml
NARid   15
NARCat  /nar/database/cat/7 | Human and other Vertebrate Genomes
NARSub  /nar/database/subcat/7/28 | Model organisms, comparative genomics
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/39/suppl_1/D835
DOI: http://dx.doi.org/10.1093/nar/gkq1132
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics


ID      GyDB
Name    Gypsy database of mobile genetic elements
Desc    Molecular diversity and evolutionary relationships of mobile genetic elements, viruses and related host genes.
URL     http://gydb.uv.es/index.php/Main_Page
Taxon   1 | all
EDAMtpc 0781 | Viruses
EDAMtpc 0798 | Mobile genetic elements

ID      H-InvDB
Acc     DB-0040
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.
URL     http://www.h-invitational.jp/
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0203 | Transcriptomics
EDAMtpc 0199 | Genetic variation
EDAMtpc 0753 | Metabolic pathways
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 2815 | Humans
EDAMtpc 0659 | Functional RNA
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0140 | Protein targeting and localization
EDAMdat 2399 | Gene annotation (transcript)
EDAMdat 0916 | Gene annotation
EDAMid  2770 | HIT ID
EDAMid  2771 | HIX ID
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | HIX ID
Xref    EMBL_explicit | HIT ID
Query   Gene annotation (transcript) | HTML | HIT ID | http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=%s
Query   Gene annotation | HTML | HIX ID | http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=%s
Query   Gene annotation (transcript) | Text | HIT ID | http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=%s&status=flat
Query   Gene annotation | Text | HIX ID | http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0005064&status=flat
Query   Gene annotation (transcript) | XML | HIT ID | http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=HIT000053961&status=xml
Query   Gene annotation | XML | HIX ID | http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0005064&status=xml
Example HIT ID | HIT000053961
Example HIX ID | HIX0005064

ID      HaemB
Name    Haemophilia B Mutation Database
Desc    Point mutations and short additions and deletions in the factor IX gene
URL     http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      HAMAP
Acc     DB-0041
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.
URL     http://www.expasy.org/sprot/hamap/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0724 | Protein families
EDAMdat 0896 | Protein report
EDAMdat 0849 | Sequence record
EDAMdat 2872 | ID list
EDAMid  2766 | HAMAP ID
EDAMfmt 2331 | HTML
EDAMfmt 2188 | uniprot
Xref    SP_explicit | HAMAP ID
Query   ID list {HAMAP family members} | Text | HAMAP ID | http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=tab&columns=id
Query   Sequence record {HAMAP family sequences} | uniprot | HAMAP ID | http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=txt
Query   Protein report {HAMAP family rules} | HTML | HAMAP ID | http://www.expasy.org/unirule/MF_%s
Query   Protein report {HAMAP family rules} | Text | HAMAP ID | http://www.expasy.org/unirule/MF_%s.txt
Example HAMAP ID | 00314

ID      HAMASTERS
Name    Haemophilia A FVIII mutation database (HAMASTERS)
Desc    Resources for Haemophilia A / factor VIII (FVIII) genetic variation at the DNA and protein level.
URL     http://europium.csc.mrc.ac.uk/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      HCAD
Name    Human chromosome aberration database (HCAD)
Desc    Human chromosome aberration database.
URL     http://www.pdg.cnb.uam.es/UniPub/HCAD/
Taxon   9606 | Homo sapiens
EDAMtpc 0624 | Chromosomes

ID      HepSeq
Name    HepSeq international repository for Hepatitis B virus strain data
Desc    Molecular, clinical and epidemiological database for hepatitis B infection.
URL     http://www.hpa-bioinfodatabases.org.uk/hepatitis_open/main.php
Taxon   10407 | Hepatitis B virus
EDAMtpc 0781 | Viruses

ID      HERVd
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.
URL     http://herv.img.cas.cz/
Taxon   9606 | Homo sapiens
EDAMtpc 0781 | Viruses
EDAMtpc 0640 | Nucleic acid sequence analysis

ID      HGDP-CEPH
Name    HGDP-CEPH diversity panel database (HGDP-CEPH)
Desc    Polymorphic marker genotypes generated by users of the DNAs of the HGDP-CEPH Diversity Panel.
URL     http://www.cephb.fr/fr/hgdp/
Taxon   9606 | Homo sapiens
EDAMtpc 0796 | Genetic mapping and linkage

ID      HGMD
Name    Human gene mutation database (HGMD)
Desc    Known (published) gene lesions responsible for human inherited disease.
URL     http://www.hgmd.org
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      HGNC
IDalt   Genew
Acc     DB-0042
Name    Human gene nomenclature database (HGNC)
Desc    Database of unique and meaningful names for all human genes.
URL     http://www.genenames.org/
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
EDAMtpc 2815 | Humans
EDAMtpc 0622 | Genomics
EDAMtpc 2811 | Nomenclature
EDAMdat 0916 | Gene annotation
EDAMid  2298 | Gene ID (HGNC)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene ID (HGNC)
Xref    EMBL_explicit | Gene ID (HGNC)
Query   Gene annotation {HGNC entry} | HTML | Gene ID (HGNC) | http://www.genenames.org/data/hgnc_data.php?hgnc_id=%s
Example Gene ID (HGNC) | 2041
Example Gene ID (HGNC) | HGNC:12849


ID      HGT-DB
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.
URL     http://genomes.urv.es/HGT-DB/
Taxon   1 | all
EDAMtpc 0084 | Phylogenetics
EDAMtpc 1811 | Prokaryotes and archae

ID      HGVbaseG2P
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.
URL     http://www.hgvbaseg2p.org
Taxon   9606 | Homo sapiens
EDAMtpc 0625 | Genotype and phenotype resources

ID      HIC-Up
Name    Hetero-compound information (HIC-Up)
Desc    Structural biology of hetero-compounds ("small molecules").
URL     http://xray.bmc.uu.se/hicup/
Taxon   None
EDAMtpc 0154 | Small molecules

ID      HmtDB
Name    Human mitochondrial genomic database (HmtDB)
Desc    Human mitochondrial genomic database based on variability studies supporting population genetics and biomedical research.
URL     http://www.hmtdb.uniba.it/
Taxon   9606 | Homo sapiens
EDAMtpc 0779 | Mitochondrial genes and proteins
EDAMtpc 2815 | Humans

ID      HOGENOM
Acc     DB-0044
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.
URL     http://pbil.univ-lyon1.fr/databases/hogenom3.html
Cat     Phylogenomic databases
Taxon   1 | all
EDAMtpc 0740 | Nucleic acid sequence alignment
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0084 | Phylogenetics
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0194 | Phylogenomics
EDAMdat 0872 | Phylogenetic tree
EDAMdat 2925 | Sequence data
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Phylogenetic tree {Trees and families} | HTML | UniProt accession | http://pbil.univ-lyon1.fr/cgi-bin/acnuc-ac2tree?query=%s&db=HOGENOM
Query   Sequence data {HOGENOM  entry} | HTML | UniProt accession | http://pbil.univ-lyon1.fr/cgi-bin/acnuc-search-ac?query=%s&db=HOGENOM
Query   Sequence data {HOGENOM  family} | HTML | UniProt accession | http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?query=%s&db=HOGENOM
Example UniProt accession | Q5ZJV9


ID      HOINVGEN
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.
URL     http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html
Taxon   33208 | Metazoa
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0740 | Nucleic acid sequence alignment
EDAMtpc 0084 | Phylogenetics
EDAMtpc 0797 | Comparative genomics

ID      HOVERGEN
Acc     DB-0045
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.
URL     http://pbil.univ-lyon1.fr/databases/hovergen.html
Cat     Phylogenomic databases
Taxon   7711 | Chordata
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0740 | Nucleic acid sequence alignment
EDAMtpc 0084 | Phylogenetics
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0194 | Phylogenomics
EDAMdat 2201 | Sequence record full
EDAMdat 0916 | Gene annotation
EDAMdat 0872 | Phylogenetic tree
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Phylogenetic tree {Trees and families} | HTML | UniProt accession | http://pbil.univ-lyon1.fr/cgi-bin/acnuc-ac2tree?query=%s&db=HOVERGEN
Query   Sequence record full {HOVERGEN entry} | HTML | UniProt accession | http://pbil.univ-lyon1.fr/cgi-bin/acnuc-search-ac?query=%s&db=HOVERGEN
Query   Gene annotation {HOVERGEN family} | HTML | UniProt accession | http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?query=%s&db=HOVERGEN
Example UniProt accession | Q5ZJV9
Q5ZJV9
HBG051044

ID      HomeoboxPage
Name    HomeoboxPage homeobox gene page
Desc    Information relevant to homeobox genes, in particular about classification/evolution.
URL     http://www.biosci.ki.se/groups/tbu/homeo.html
Taxon   33208 | Metazoa
EDAMtpc 0623 | Genes, gene family or system

ID      HomoMINT
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.
URL     http://mint.bio.uniroma2.it/HomoMINT
Taxon   9606 | Homo sapiens
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 3044 | Protein interaction networks

ID      Homophila
Name    Homophila
Desc    Homophila links the human and fly genomes to assist the planning of functional genomic investigations in Drosophila that address questions about human genetic disease. Searches over human disease descriptions, fly phenotypes, human or fly gene names and sequence similarity are allowed. Homophila links disease genes compiled in Online Mendelian Inheritance in Man and the complete Drosophila genomic sequence. 
URL     http://superfly.ucsd.edu/homophila/
NARid   8
NARCat  /nar/database/cat/5 | Genomics Databases (non-vertebrate)
NARSub  /nar/database/subcat/5/23 | Invertebrate genome databases
NARCat  /nar/database/cat/7 | Human and other Vertebrate Genomes
NARSub  /nar/database/subcat/7/28 | Model organisms, comparative genomics
Abstrct http://nar.oupjournals.org/cgi/content/abstract/30/1/149

ID      HOMSTRAD
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.
URL     http://tardis.nibio.go.jp/homstrad/
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment
EDAMtpc 0724 | Protein families

ID      Hoppsigen
Name    Homologous processed pseudogenes database (Hoppsigen)
Desc    Nucleic database of homologous processed pseudogenes.
URL     http://pbil.univ-lyon1.fr/databases/hoppsigen.html
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system

ID      HORDE
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.
URL     http://bioportal.weizmann.ac.il/HORDE/
Taxon   9606 | Homo sapiens
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0623 | Genes, gene family or system


ID      HotSprint
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.
URL     http://prism.ccbb.ku.edu.tr/hotsprint/
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions

ID      HPA
Acc     DB-0046
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.
URL     http://www.proteinatlas.org/
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
EDAMtpc 0197 | Gene expression resources
EDAMtpc 2640 | Cancer resources
EDAMtpc 2226 | Structure determination
EDAMtpc 0140 | Protein targeting and localization
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 2815 | Humans
EDAMdat 2394 | Gene annotation (functional)
EDAMid  1791 | Gene name (HGNC)
EDAMid  1033 | Gene ID (Ensembl)
EDAMid  2772 | HPA antibody id
EDAMfmt 2331 | HTML
Xref    SP_explicit | HPA antibody id
Query  Gene annotation (functional) | HTML | Gene ID (Ensembl) | http://www.proteinatlas.org/gene_info.php?ensembl_gene_id=%s
Query   Gene annotation (functional) | HTML | Gene name (HGNC) | http://www.proteinatlas.org/gene_info.php?hugo_id=%s
Query   Gene annotation (functional) | HTML | HPA antibody id | http://www.proteinatlas.org/gene_info.php?antibody_id=%s
Example Gene ID (Ensembl) | ENSG00000196371
Example Gene name (HGNC) | FUT4
Example HPA antibody id | CAB000014

ID      HS3D
Name    Homo sapiens splice sites dataset (HS3D)
Desc    Homo Sapiens Exon, Intron and Splice regions extracted from GenBank.
URL     http://www.sci.unisannio.it/docenti/rampone/
Taxon   9606 | Homo sapiens
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0114 | Gene structure and RNA splicing


ID      HSSP
Acc     DB-0048
Name    Homology-derived secondary structure of proteins database (HSSP)
Desc    Homology-derived secondary structure of proteins database.
URL     http://swift.cmbi.kun.nl/swift/hssp/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0694 | Protein secondary structure
EDAMdat 0876 | Protein features (secondary structure)
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | PDB ID
Xref    EMBL_explicit | PDB ID
Query   Protein features (secondary structure) {HSSP report} | HTML | PDB ID | http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=dssp&id=%s
Example PDB ID | 2hva

ID      HTPSELEX
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.
URL     http://www.isrec.isb-sib.ch/htpselex/
Taxon   1 | all
EDAMtpc 0749 | Transcription factors and regulatory sites

ID      HUGE
Acc     DB-0049
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.
URL     http://www.kazusa.or.jp/huge/
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 2815 | Humans
EDAMdat 0896 | Protein report
EDAMid  2393 | mFLJ/mKIAA number
EDAMfmt 2331 | HTML
Xref    SP_implicit | mFLJ/mKIAA number
Query   Protein report {HUGE entry} | HTML | mFLJ/mKIAA number | http://www.kazusa.or.jp/tech-cgi/view_direct.cgi?id=%s
Example mFLJ/mKIAA number | KIAA0001

ID      HugeIndex
Name    HugeIndex - Human Gene Expression Index
Desc    Gene expression data on normal human tissues from high-density oligonucleotide arrays. 
URL     http://www.hugeindex.org
NARid   23
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/30/1/214


ID      HumanPAX6
Name    Human PAX6 allelic variant database (HumanPAX6)
Desc    Human PAX6 allelic variant database.
URL     http://pax6.hgu.mrc.ac.uk/
Taxon   9606 | Homo sapiens
EDAMtpc 0625 | Genotype and phenotype resources

ID      HMDB
Name    Human Metabolome Database (HMDB)
Desc    Information about small molecule metabolites found in the human body.  It contains or links three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data.
URL     http://www.genpat.uu.se/mtDB
Taxon   9606 | Homo sapiens
EDAMtpc 0154 | Small molecules
EDAMtpc 0079 | Metabolites

ID      HumanMtDB
Name    Human mitochondrial genome database (HumanMtDB)
Desc    Human mitochondrial genome database.
URL     http://www.genpat.uu.se/mtDB
Taxon   9606 | Homo sapiens
EDAMtpc 0779 | Mitochondrial genes and proteins
EDAMtpc 2815 | Humans

ID      HuSiDa
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.
URL     http://itb.biologie.hu-berlin.de/~nebulus/sirna/index.htm
Taxon   9606 | Homo sapiens
! EDAMtpc 0662 | siRNA
EDAMtpc 3060 | Regulatory RNA


ID      HvrBase++
Name    HvrBase++ phylogenetic database for primate species
Desc    Hypervariable regions database.
URL     http://www.hvrbase.org
Taxon   9443 | Primates
EDAMtpc 0084 | Phylogenetics

ID      HyperCAT
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.
URL     http://mlstoslo.uio.no/
Taxon   1396 | Bacillus cereus
EDAMtpc 0199 | Genetic variation
EDAMtpc 0625 | Genotype and phenotype resources

ID      HyperCLDB
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.
Taxon   9606 | Homo sapiens
URL     http://bioinformatics.istge.it/cldb/indexes.html
EDAMtpc 0608 | Cell culture resources

ID      IARCTP53
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.
URL     http://www-p53.iarc.fr/
Taxon   9606 | Homo sapiens
EDAMtpc 2640 | Cancer resources

ID      IDbases
Name    IDbases immunodeficiency mutation databases
Desc    Locus-specific databases for immunodeficiency-causing mutations.
URL     http://bioinf.uta.fi/base_root/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMdat 0918 | Sequence variation annotation
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMid  1025 | Gene identifier
Query   Sequence variation annotation {IDbase patient entry} | Text | Gene identifier;Sequence accession (nucleic acid) | http://bioinf.uta.fi/cgi-bin/fetch_idbase.cgi?gene=%s1&ac=%s2&view=full
Example Gene identifier;Sequence accession (nucleic acid) | BTK;A0625

ID      IDbases-BTKbase
IDalt   BTKbase
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.
URL     http://bioinf.uta.fi/BTKbase/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMdat 0918 | Sequence variation annotation
EDAMid  1097 | Sequence accession (nucleic acid)
Query   Sequence variation annotation {BTKbase patient entry} | Text | Sequence accession (nucleic acid) | http://bioinf.uta.fi/cgi-bin/fetch_idbase.cgi?gene=BTK&ac=%s&view=full
Example Sequence accession (nucleic acid) | A0625

ID      IMGT
Acc     DB-0050
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.
URL     http://imgt.cines.fr/
Cat     Protein family/group databases
Taxon   7711 | Chordata
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMdat 0849 | Sequence record
EDAMid   0002773 | IMGT/HLA ID
EDAMfmt 1927 | EMBL format
Xref    SP_implicit | IMGT/HLA ID
Xref    EMBL_explicit | IMGT/HLA ID
Query   Sequence record {IMGT/LIGM-DB flat-file} | EMBL format | IMGT/HLA ID | http://www.imgt.org/services/get?id=%s
Example IMGT/HLA ID | AABR03048499

ID      IMGT_HLA
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.
URL     http://www.ebi.ac.uk/imgt/hla/
Taxon   9606 | Homo sapiens
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMtpc 2811 | Nomenclature
EDAMdat 0896 | Protein report
EDAMid  2773 | IMGT/HLA ID
EDAMfmt 2331 | HTML
Xref    EMBL_explicit | IMGT/HLA ID
Query   Protein report {IMGT/HLA entry} | HTML | IMGT/HLA ID | http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fItl1b_a0N+-e+[IMGTHLA:%27%s%27]+-qnum+1+-enum+1
Example IMGT/HLA ID | HLA00236

ID      IMGT_3Dstructure-DB
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.
URL     http://www.imgt.org/3Dstructure-DB/
Taxon   9711 | Chordata
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMtpc 0698 | Protein tertiary structure

ID      IMGT_GENE-DB
Name    IMGT gene database for immunoglobulins (IG) and T cell recetors (TR)
Desc    IMGT gene database for immunoglobulins (IG) and T cell recetors (TR).
URL     http://www.imgt.org/IMGT_GENE-DB/GENElect?livret=0
Taxon   9711 | Chordata
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
Example Identifier | IGKC

ID      IMGT_LIGM
IDalt   LIGM-DB
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).
URL     http://www.imgt.org/IMGTPrimerDB/
Taxon   9711 | Chordata
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMtpc 0639 | Protein sequence analysis
EDAMid  1097 | Sequence accession (nucleic acid)
Xref    EMBL_explicit | Sequence accession (nucleic acid)
Example Sequence accession (nucleic acid) | U03895

ID      IMGT_PRIMER-DB
Name    IMGT primer database for immunoglobulins (IG) and T cell recetors (TR)
Desc    IMGT primer database for immunoglobulins (IG) and T cell recetors (TR).
URL     http://www.imgt.org/cgi-bin/IMGTlect.jv?livret=0
Taxon   9711 | Chordata
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMtpc 0632 | Probes and primers

ID      INFEVERS
Name    Familial mediterranean fever (FMF) mutations database (INFEVERS)
Desc    The registry of familial mediterranean fever (FMF) and hereditary auto-inflammatory disorders mutations.
URL     http://fmf.igh.cnrs.fr/infevers
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      InParanoid
Acc     DB-0146
Name    Inparanoid orthologs database
Desc    Eukaryotic orthholog groups.
URL     http://InParanoid.sbc.su.se
Taxon   1 | all
EDAMtpc 0722 | Nucleic acid classification

ID      IntAct
Acc     DB-0051
Name    IntAct protein interaction database and analysis system
Desc    Protein interaction database and analysis system.
URL     http://www.ebi.ac.uk/intact/
Cat     Protein-protein interaction databases
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMdat 0906 | Protein report (interaction)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | IntAct accession number
Query   Protein report (interaction) {IntAct entry} | HTML | UniProt accession | http://www.ebi.ac.uk/intact/binary-search/faces/search.xhtml?query=%s
Example UniProt accession | P32234


ID      Integr8
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.
URL     http://www.ebi.ac.uk/integr8/
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms

ID      INTEGRALL
Name    INTEGRALL integron integrases and gene cassettes
Desc    Database of DNA sequences and genetic arrangements.
URL     http://integrall.bio.ua.pt/
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing

ID      IntEnz
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.
URL     http://www.ebi.ac.uk/intenz
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 2811 | Nomenclature

ID      InterPro
Acc     DB-0052
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.
URL     http://www.ebi.ac.uk/interpro/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0641 | Repeat sequences
EDAMdat 1355 | Protein signature
EDAMid  1133 | InterPro accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | InterPro accession
Xref    SP_FT | InterPro accession
Xref    EMBL_explicit | InterPro accession
Query   Protein signature | HTML | InterPro accession | http://www.ebi.ac.uk/interpro/IEntry?ac=%s
Example InterPro accession | IPR000059

ID      ICD
Name    International Classification of Diseases
Desc    The ICD is the international standard diagnostic classification of diseases for all general epidemiological, many health management purposes and clinical use. It is used to classify diseases and other health problems recorded on many types of health and vital records including death certificates and health records.
URL     http://www.who.int/classifications/icd/en/
Taxon   1 | all
EDAMtpc 0634 | Disease resources

ID      ICDS
Name    Interrupted coding sequences (ICDS)
Desc    Interrupted coding sequences.
URL     http://www-bio3d-igbmc.u-strasbg.fr/ICDS/
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing

ID      IPD
Name    Immuno polymorphism database (IPD)
Desc    Database for the study of polymorphism in genes of the immune system.
URL     http://www.ebi.ac.uk/ipd/
Taxon   9711 | Chordata
EDAMtpc 0199 | Genetic variation
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens

ID      IPD-ESTDAB
Name    Immuno polymorphism EST database (IPD-ESTDAB)
Desc    Searchable database of tumour cell lines.
URL     http://www.ebi.ac.uk/ipd/estdab/index.html
Taxon   9711 | Chordata
EDAMtpc 2640 | Cancer resources
EDAMtpc 0199 | Genetic variation
EDAMtpc 0655 | mRNA, EST or cDNA

ID      IPD-HPA
Name    Immuno polymorphism human platelet antigens database (IPD-HPA)
Desc    Information on human platelet antigens (HPA).
URL     http://www.ebi.ac.uk/ipd/hpa/index.html
Taxon   9606 | Homo sapiens
EDAMtpc 0199 | Genetic variation
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens

ID      IPD-KIR
Name    Immuno polymorphism killer-cell Immunoglobulin-like receptor database (IPD-KIR)
Desc    Sequences of human Killer-cell Immunoglobulin-like Receptors (KIR).
URL     http://www.ebi.ac.uk/ipd/kir/index.html
Taxon   9606 | Homo sapiens
EDAMtpc 0199 | Genetic variation
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMtpc 0639 | Protein sequence analysis

ID      IPD-MHC
Name    Immuno polymorphism  major histocompatibility complex database (IPD-MHC)
Desc    Sequences of the the major histocompatibility complex in a number of species.
URL     http://www.ebi.ac.uk/ipd/mhc
Taxon   9711 | Chordata
EDAMtpc 0199 | Genetic variation

ID      IPI
Acc     DB-0132
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.
URL     http://www.ebi.ac.uk/IPI
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMdat 0849 | Sequence record
EDAMid  2384 | IPI protein ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | IPI protein ID
Query   Sequence record {IPI entry} | HTML | IPI protein ID | http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=%s
Example IPI protein ID | IPI00177866

ID      iRefIndex
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.
URL     http://irefindex.uio.no/wiki/iRefIndex
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions

ID      IRESdb
Name    Internal ribosome entry site database (IRESdb)
Desc    Internal ribosome entry sites.
URL     http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
Taxon   1 | all
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0617 | Ribosomal genes and proteins

ID      IRESite
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.
URL     http://www.iresite.org
Taxon   1 | all
EDAMtpc 0617 | Ribosomal genes and proteins
EDAMtpc 0747 | Nucleic acid sites and features

ID      ISfinder
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.
URL     http://www-is.biotoul.fr
Taxon   1 | all
EDAMtpc 0798 | Mobile genetic elements
Xref    SP_FT | None
Example Identifier | ISA1083-2

ID      ISGDB
Name    Interferon Stimulated Gene Database
Desc    Interferon stimulated genes (ISGs) assigned into functional categories with links to sequence and Unigene information.  Interferons (IFN) are a family of multifunctional cytokines that activate transcription of a subset of genes responsible for antiviral, antiproliferative and immunomodulatory properties.
URL     http://www.lerner.ccf.org/labs/williams/xchip-html.cgi
NARid   16
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
NARCat  /nar/database/cat/14 | Immunological databases


ID      ISOLA
Name    Italian Solanaceae genome resource (ISOLA)
Desc    Solanaceae genome resource.
URL     http://biosrv.cab.unina.it/isola
Taxon   4070 | Solanaceae
EDAMtpc 0780 | Plants


ID      ITS2
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.
URL     http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?about
Taxon   1 | all
EDAMtpc 0740 | Nucleic acid sequence alignment
EDAMtpc 0697 | RNA structure and alignment

ID      ITTACA
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.
URL     http://bioinfo-out.curie.fr/ittaca/
Taxon   9606 | Homo sapiens
EDAMtpc 0197 | Gene expression resources
EDAMtpc 2640 | Cancer resources

ID      IUPAC
Name    IUPAC nomenclature database
Desc    Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc.
URL     http://www.chem.qmul.ac.uk/iupac/
Taxon   None
EDAMtpc 2811 | Nomenclature

ID      IUPHAR-DB
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.
URL     http://www.iuphar-db.org
Taxon   None
EDAMtpc 0620 | Drugs and targets
EDAMtpc 2811 | Nomenclature

ID      IXDB
Name    Integrated X chromosome database (IXDB)
Desc    Integrated X chromosome database.
URL     http://ixdb.mpimg-berlin-dahlem.mpg.de
Taxon   9606 | Homo sapiens
EDAMtpc 0624 | Chromosomes

ID      JAIL
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.
URL     http://bioinformatics.charite.de/jail/
Taxon   1 | all
EDAMtpc 0128 | Protein interactions
EDAMtpc 0081 | Structure analysis

ID      JASPAR
Name    JASPAR eukaryotic transcription factor binding profiles
Desc    High-quality transcription factor binding profile database.
URL     http://jaspar.cgb.ki.se/
Taxon   2759 | Eukaryota
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0188 | Sequence profiles and HMMs

ID      JCM
Name    Japan collection of microorganisms
Desc    Japan collection of microorganisms.
URL     http://www.jcm.riken.go.jp/JCM/catalogue.shtml
Cat     Not available
Taxon   2 | Bacteria
EDAMtpc 0637 | Taxonomy
Xref    SP_FT | None
Example Identifier | 1339

ID      JenaLib
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.
URL     http://www.fli-leibniz.de/IMAGE.html
Taxon   1 | all
EDAMtpc 0081 | Structure analysis

ID      JPGV
Name    Jena prokaryotic genome viewer (JPGV)
Desc    Visualization and analysis of prokaryotic genomes.
URL     http://jpgv.fli-leibniz.de
Taxon   2 | Bacteria
EDAMtpc 1811 | Prokaryotes and archae

ID      JWS
Name    JWS Online
Desc    JWS Online aims to provide a service to the Systems Biology community by 1) giving access to a database of curated models of biological systems, and 2) allowing the users to run these models in a web browser via an easy to use interface, and 3) helping in reviewing of manuscripts containing kinetic models. 
URL     http://jjj.biochem.sun.ac.za/index.html
Taxon   1 | all
EDAMtpc 2259 | Systems biology

ID      KaryotypeDB
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.
URL     http://www.nenno.it/karyotypedb/
Taxon   2759 | Eukaryota
EDAMtpc 0624 | Chromosomes

ID      KEGG
Acc     DB-0053
Name    Kyoto encyclopedia of genes and genomes (KEGG)
Desc    Encyclopedia of genes and genomes.
URL     http://www.genome.jp/kegg/
Cat     Genome annotation databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0622 | Genomics
EDAMdat 2984 | Pathway or network report
EDAMdat 2589 | Hierarchy annotation
EDAMdat 2018 | Annotation
EDAMid  2891 | Biological model accession
EDAMid  1154 | KEGG object identifier
EDAMid  2343 | Pathway ID (KEGG)
EDAMfmt 2331 | HTML
Xref    SP_explicit | KEGG object identifier
Query   Pathway or network report | HTML | Pathway ID (KEGG) | http://www.kegg.jp/pathway/%s
Query   Hierarchy annotation {Brite hierarchy} | HTML | Biological model accession {Brite hierarchy ID} | http://www.kegg.jp/brite/%s
Query   Annotation {KEGG entry} | HTML | KEGG object identifier | http://www.kegg.jp/dbget-bin/www_bget?%s
Example KEGG object identifier | tpv:TP04_0437 
Example Pathway ID (KEGG) | map00010
Example Biological model accession {Brite hierarchy ID} | ko00001

ID      KDD
Name    Kidney development database
Desc    Data from a large number of developmental studies that have a bearing on the study of kidney development.
URL     http://golgi.ana.ed.ac.uk/kidhome.html
NARid   17
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Taxon   9711 | Chordata
EDAMtpc 2229 | Cell biology resources

ID      KinMutBase
Name    KinMutBase registry of disease-causing mutations in protein kinase domains database
Desc    Disease-causing mutations in protein kinase domains.
URL     http://www.uta.fi/imt/bioinfo/KinMutBase/
Taxon   9606 | Homo sapiens
EDAMtpc 2640 | Cancer resources

ID      Kinomer
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.
URL     http://www.compbio.dundee.ac.uk/kinomer
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMtpc 0188 | Sequence profiles and HMMs
EDAMtpc 0635 | Specific protein resources

ID      KNOTTIN
Name    KNOTTIN database
Desc    Database of knottins; intriguing miniproteins with strong potential in drug design.
URL     http://knottin.cbs.cnrs.fr
Taxon   9606 | Homo sapiens
EDAMtpc 0202 | Pharmacoinformatics
EDAMtpc 0698 | Protein tertiary structure
EDAMtpc 0635 | Specific protein resources

ID      L1Base
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.
URL     http://line1.molgen.mpg.de
Taxon   9347 | Eutheria
EDAMtpc 0798 | Mobile genetic elements
EDAMtpc 0213 | Mice or rats
EDAMtpc 2815 | Humans

ID      LEGER
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.
URL     http://leger2.gbf.de/cgi-bin/expLeger.pl
Taxon   1637 | Listeria
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0140 | Protein targeting and localization

ID      LegioList
Acc     DB-0054
Name    Legionella pneumophila genome database
Desc    Legionella pneumophila genome database.
URL     http://genolist.pasteur.fr/LegioList/
Cat     Organism-specific databases
Taxon   445 | Legionella
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 0916 | Gene annotation
EDAMid  1026 | Gene symbol
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Sequence accession (nucleic acid)
Query   Gene annotation | HTML | Sequence accession (nucleic acid) | http://genolist.pasteur.fr/LegioList/genome.cgi?external_query+%s
Query   Gene annotation | HTML | Gene symbol | http://genolist.pasteur.fr/LegioList/genome.cgi?external_query+%s
Example Sequence accession (nucleic acid) | LPC_2308
Example Gene symbol | aacA4


ID      Leproma
Acc     DB-0055
Name    Mycobacterium leprae genome database
Desc    Mycobacterium leprae genome database.
URL     http://genolist.pasteur.fr/Leproma/
Cat     Organism-specific databases
Taxon   1769 | Mycobacterium leprae
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 0916 | Gene annotation
EDAMid  1026 | Gene symbol
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Sequence accession (nucleic acid)
Query   Gene annotation | HTML | Sequence accession (nucleic acid) | http://genolist.pasteur.fr/Leproma/genome.cgi?external_query+%s
Query   Gene annotation | HTML | Gene symbol | http://genolist.pasteur.fr/Leproma/genome.cgi?external_query+%s
Example Sequence accession (nucleic acid) | ML0981
Example Gene symbol | 35kd_ag

ID      LGICdb
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.
URL     http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment
EDAMtpc 0166 | Protein structural motifs and surfaces
EDAMtpc 0084 | Phylogenetics
EDAMdat 1456 | Protein report (membrane protein)
EDAMid  2797 | Protein ID (LGICdb)
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Query   Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} | HTML | Protein ID (LGICdb) | http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/%s.php
Query   Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} | XML | Protein ID (LGICdb) | http://www.ebi.ac.uk/compneur-srv/LGICdb/XML/%s.xml
Example Protein ID (LGICdb) | 5HT3Arano

ID      LigAsite
Name    Ligand attachment site database (LigAsite)
Desc    A gold-standard dataset of biologically relevant binding sites in protein structures.
URL     http://www.scmbb.ulb.ac.be/Users/benoit/LigASite
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0148 | Protein-ligand interactions
EDAMtpc 0166 | Protein structural motifs and surfaces

ID      LipidBank
Name    LipidBank
Desc    A database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.
URL     http://lipidbank.jp/index.html
Taxon   1 | all
EDAMtpc 0153 | Lipids

ID      LMSD
Name    LIPID MAPS Structure Database (LMSD)
Desc    Structures and annotations of biologically relevant lipids.
URL     http://www.lipidmaps.org/data/structure/index.html
Taxon   1 | all
EDAMtpc 0153 | Lipids

ID      LipaseEngineering
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.
URL     http://www.led.uni-stuttgart.de/
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources


ID      LumbriBASE
Name    Lumbricus rubellus genome project database
Desc    Genome database for the earthworm, Lumbricus rubellus.
URL     http://xyala.cap.ed.ac.uk/Lumbribase/index.shtml
Taxon   35632 | Lumbricus rubellus
EDAMtpc 2819 | Invertebrates

ID      MAGEST
Name    MAGEST
Desc    A database of maternal gene expression information for Halocynthia roretzi. Data includes sequences from the fertilized egg cDNA library, the result of similarity search against the GenBank, the expression data from whole mount in situ hybridization and the amino acid fragment sequences predicted from the EST data set. 
URL     http://magest.hgc.jp/
NARid   18
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/31/1/119


ID      MaizeGDB
IDalt   MaizeDB
Acc     DB-0058
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.
URL     http://www.maizegdb.org/
Cat     Organism-specific databases
Taxon   4577 | Zea mays
EDAMtpc 0780 | Plants
EDAMdat 2703 | Gene annotation (clone or EST)
EDAMid  2798 | MaizeDB ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | MaizeDB ID
Xref    SP_FT | None
Query   Gene annotation (clone or EST) {MaizeGDB entry} | HTML | MaizeDB ID | http://www.maizegdb.org/cgi-bin/id_search.cgi?id=%s
Example MaizeDB ID | 635633

ID      MAMEP
Name    Molecular anatomy of mouse embryo project (MAMEP)
Desc    Functional analysis of pattern formation, tissue development and organogenesis in mouse.
URL     http://mamep.molgen.mpg.de/
Taxon   10088 | Mus
EDAMtpc 0213 | Mice or rats
EDAMtpc 3067 | Anatomy resources
EDAMtpc 3065 | Embryology resources

ID      MamPol
Name    Mammalia polymorphism database (MamPol)
Desc    A collection of all the existing polymorphic sequences in the Mammalia group.
URL     http://mampol.uab.es
Taxon   40674 | Mammalia
EDAMtpc 0199 | Genetic variation

ID      MAPU
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.
URL     http://www.mapuproteome.com/
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms

ID      MAtDB
Name    Arabadopsis genome database (MAtDB)
Desc    A repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project.
URL     http://mips.gsf.de/proj/thal/db
Taxon   3701 | Arabidopsis
EDAMtpc 0780 | Plants


ID      MatrixDB
Name    MatrixDB
Desc    A database of interactions established by extracellular proteins and polysaccharides.
URL     http://matrixdb.ibcp.fr/
Taxon   1 | all
EDAMtpc 0128 | Protein interactions

ID      MACiE
Name    Mechanism, annotation and classification in enzymes (MACiE) database
Desc    A database of enzyme reaction mechanisms, detailing the chemical compounds involved, individual reaction stages, mechanisms, alternative mechanisms, amino acids involved as well as the species name in which the reaction occurs.
URL     http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions

ID      MedOBIS
Name    Mediterranean ocean biogeographic information system (MedOBIS)
Desc    Regional repository of marine biodiversity data.
URL     http://www.medobis.org
Taxon   1 | all
EDAMtpc 0610 | Ecoinformatics
EDAMtpc 3050 | Biodiversity

ID      MeGX
IDalt   MegDB
Name    MeGX marine microbial ecological genomics database
Desc    Specialized database for genome-wide analysis of marine bacteria and metagenomics, integrating genomic, metagenomic and ribosomal RNA data with primary environmental data and curated metadata.
Taxon   1 | all
URL     http://www.megx.net
EDAMtpc 0610 | Ecoinformatics

ID      MMMP
Name    Melanoma Molecular Map Project (MMMP) i
Desc    A multidatabase dedicated to research on melanoma biology and therapy.  It collects and integrates published data including melanoma-related molecular (or cellular) pathways of interest (Biomaps), structured and standardized information on single melanoma-related molecules of interest (Biocards), molecular derangements demonstrated in human melanoma (Melanoma Molecular Profile), preclinical and clinical information regarding drugs tested for melanoma treatment (Drug Development Database), Results form clinical trials (with therapeutic and/or, prognostic/predictive purposes), epidemiological studies, and meta-analyses (clinical Trial Database), key terms (or expressions, concepts) used in the MMMP site (Glossary).
Taxon   1 | all
URL     http://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp
EDAMtpc 2640 | Cancer resources

ID      MEPD
Name    Medaka expression pattern database (MEPD)
Desc    Medaka gene expression data examined through whole mount in situ hybridization.
URL     http://ani.embl.de:8080/mepd/
Taxon   8090 | Oryzias latipes
EDAMtpc 0197 | Gene expression resources

ID      MEROPS
Acc     DB-0059
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.
URL     http://merops.sanger.ac.uk/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 2811 | Nomenclature
EDAMdat 0896 | Protein report
EDAMid  2629 | Enzyme ID (MEROPS)
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Enzyme ID (MEROPS)
Query   Protein report {MEROPS page} | HTML | Identifier {Clan} | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Query   Protein report {MEROPS page} | HTML | Identifier {Family} | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Query   Protein report {MEROPS page} | HTML | Enzyme ID (MEROPS) | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Example Enzyme ID (MEROPS) | A01.001

ID      MetaCrop
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.
URL     http://metacrop.ipk-gatersleben.de
Taxon   58024 | Spermatophyta
EDAMtpc 0753 | Metabolic pathways
EDAMtpc 0780 | Plants

ID      MetaGrowth
Name    MetaGrowth database of culture conditions of obligate parasitic bacteria
Desc    Evidence and hypotheses for the study of culture conditions of obligate parasitic bacteria.
URL     http://www.igs.cnrs-mrs.fr/axenic/
Taxon   2 | Bacteria
EDAMtpc 0608 | Cell culture resources

ID      Metal-MACiE
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.
URL     http://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions

ID      MethDB
Name    MethDB DNA methylation database
Desc    Data on DNA methylation and environmental epigenetic effects including methylation patterns, profiles and total methylation content data for different species, tissues and phenotypes.
URL     http://www.methdb.de
NARid   19
NARCat  /nar/database/cat/1 | Nucleotide Sequence Databases
NARSub  /nar/database/subcat/1/2 | Coding and non-coding DNA
Abstrct http://nar.oupjournals.org/cgi/content/abstract/29/1/270
Taxon   1 | all
EDAMtpc 0654 | DNA

ID      MfunGD
Name    MIPS mouse functional genome database (MfunGD)
Desc    Mouse genome database including DNA and protein sequences, annotation, gene models and mapping etc.
URL     http://mips.gsf.de/genre/proj/mfungd/
Taxon   10088 | Mus
EDAMtpc 0213 | Mice or rats
EDAMdat 0916 | Gene annotation
EDAMid  2799 | Gene ID (MfunGD)
EDAMfmt 2331 | HTML
Query   Gene annotation {Mfungd Entry} | HTML | Gene ID (MfunGD) | http://mips.helmholtz-muenchen.de/genre/proj/mfungd/singleGeneReport.html?entry=%s
Example Gene ID (MfunGD) | mc1000056

ID      MGI
IDalt   MGD
Acc     DB-0060
Name    Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
Desc    Integrated genetic, genomic, and biological data for mouse.
URL     http://www.informatics.jax.org/
URLlink http://www.informatics.jax.org/mgihome/other/link_instructions.shtml
Cat     Organism-specific databases
Taxon   10088 | Mus
EDAMtpc 0213 | Mice or rats
EDAMdat 2093 | Data reference
EDAMid  1792 | Gene name (MGD)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene name (MGD)
Xref    SP_FT | None
Query   Data reference {MGI entry} | HTML | Gene name (MGD) | http://www.informatics.jax.org/searches/accession_report.cgi?id=%s
Example Gene name (MGD) | 1894891

ID      Micado
Acc     DB-0061
Name    Microbial advanced database organisation (Micado)
Desc    Microbial genome and functional analysis of Bacillus subtilis.
URL     http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi
Cat     Organism-specific databases
Taxon   1423 | Bacillus subtilis
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 2093 | Data reference
EDAMid  1026 | Gene symbol
EDAMfmt 2331 | HTML
Xref    SP_implicit | Gene symbol
Query   Data reference {Micado entry} | HTML | Gene symbol | http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi?species=Bacillus+subtilis&gene=%s
Example Gene symbol | ypuD

ID      ModelDB
Name    ModelDB
Desc    Computational neuroscience models. 
URL     http://senselab.med.yale.edu/ModelDB/
Taxon   1 | all
EDAMtpc 0771 | Biological models

ID      MMDB
IDalt   Entrez Structure
Name    Molecular Modeling DataBase (MMDB)
Desc    A database of experimentally determined structures obtained from the RCSB Protein Data Bank (PDB). Useful features are added that facilitate computation on the data and link them to many other data types in the Entrez system.
URL     http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure

ID      MTRDB
Name    Microorganisms tandem repeats database
Desc    Microorganisms tandem repeats database.
URL     http://minisatellites.u-psud.fr
Taxon   2 | Bacteria
EDAMtpc 0641 | Repeat sequences

ID      MIM
IDalt   OMIM
Acc     DB-0062
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.
URL     http://www.ncbi.nlm.nih.gov/omim/
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 2815 | Humans
EDAMtpc 0625 | Genotype and phenotype resources
EDAMdat 0920 | Genotype/phenotype annotation
EDAMid  1153 | OMIM ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | OMIM ID
Xref    SP_FT | None
Query   Genotype/phenotype annotation {OMIM entry} | HTML | OMIM ID | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=OMIM&dopt=Detailed&tmpl=dispomimTemplate&list_uids=%s
Example OMIM ID | 125700

ID      MINT
Acc     DB-0158
Name    Molecular interaction Database (MINT)
Desc    Experimentally verified protein-protein interactions mined from the scientific literature by expert curators.
URL     http://mint.bio.uniroma2.it/mint/
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMdat 1565 | Protein-protein interaction
EDAMid  2615 | MINT ID
EDAMfmt 2331 | HTML
Query   Protein-protein interaction {MINT interaction} | HTML | MINT ID | http://mint.bio.uniroma2.it/mint/search/interaction.do?ac=MINT-%s
Example MINT ID | 3979570

ID      MIPSPlantsDB
Name    MIPS plants database
Desc    Data for individual plant species and a platform for integrative and comparative plant genome research.
URL     http://mips.gsf.de/proj/plant/jsf/genomes.jsp
Taxon   58024 | Spermatophyta
EDAMtpc 0780 | Plants
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0780 | Plants

ID      miRBase
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.
URL     http://microrna.sanger.ac.uk/
Taxon   1 | all
! EDAMtpc 0661 | miRNA
EDAMtpc 3060 | Regulatory RNA
EDAMtpc 0623 | Genes, gene family or system

ID      miriam
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).
URL     http://www.ebi.ac.uk/miriam/
Taxon   None
EDAMtpc 3047 | Molecular biology reference

ID      miROrtho
Name    miROrtho animal microRNA database
Desc    Catalogue of animal microRNA genes.
URL     http://cegg.unige.ch/mirortho
Taxon   33208 | Metazoa
! EDAMtpc 0661 | miRNA
EDAMtpc 3060 | Regulatory RNA
EDAMtpc 0623 | Genes, gene family or system

ID      MonosaccharideDB
Name    Monosaccharide database
Desc    Information on the residues used in glycan databases.
URL     http://www.monosaccharidedb.org/
Taxon   None
EDAMtpc 0152 | Carbohydrates
EDAMdat 2313 | Carbohydrate structure report
EDAMid  2746 | MonosaccharideDB ID
EDAMfmt 2331 | HTML
Query   Carbohydrate structure report {MonosaccharideDB entry} | HTML | MonosaccharideDB ID | http://www.monosaccharidedb.org/display_monosaccharide.action?id=%s
Example MonosaccharideDB ID | 1

ID      MMRUV
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.
URL     http://www.mmrmissense.net/
Taxon   9606 | Homo sapiens
EDAMtpc 0199 | Genetic variation

ID      MitoDrome
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.
URL     http://www2.ba.itb.cnr.it/MitoDrome/
Taxon   7215 | Drosophila
EDAMtpc 0779 | Mitochondrial genes and proteins
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0211 | Flies

ID      MITOP2
Name    Mitochondrial proteome database
Desc    Mitochondria-related genes, proteins and diseases.
URL     http://www.mitop.de:8080/mitop2/
Taxon   2759 | Eukaryota
EDAMtpc 0779 | Mitochondrial genes and proteins
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 2813 | Disease genes and proteins

ID      MitoRes
Name    MitoRes resource for mitochondria-related genes, transcripts and proteins
Desc    Mitochondria-related genes, transcripts and proteins
URL     http://www2.ba.itb.cnr.it/MitoNuc/
Taxon   2759 | Eukaryota
EDAMtpc 0779 | Mitochondrial genes and proteins
EDAMtpc 0621 | Genome, proteome and model organisms

ID      MLVAbank
Name    Bacterial MLVA-genotyping service (MLVAbank)
Desc    Bacterial MLVA-genotyping service.
URL     http://mlva.u-psud.fr/
Taxon   2 | Bacteria
EDAMtpc 0625 | Genotype and phenotype resources

ID      MMsINC
Name    MMsINC chemoinformatics database
Desc    Chemoinformatics database.
URL     http://mms.dsfarm.unipd.it/MMsINC/search/
Taxon   None
EDAMtpc 0154 | Small molecules

ID      MNCDB
Name    MNCDB Neurospora crassa genome database
Desc    Molecular structure and functional network of the entirely sequenced, filamentous fungus Neurospora crassa.
URL     http://mips.gsf.de/genre/proj/ncrassa/
Taxon   5141 | Neurospora crassa
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0782 | Fungi

ID      ModBase
Acc     DB-0063
Name    ModBase database of comparative protein structure models
Desc    Three-dimensional protein models calculated by comparative modelling.
URL     http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure
EDAMdat 2092 | SNP annotation
EDAMdat 1537 | Protein structure report
EDAMid  3021 | UniProt accession
EDAMid  1106 | dbSNP ID
EDAMfmt 2331 | HTML
Xref    SP_implicit | UniProt accession
Query   Protein structure report | HTML | UniProt accession | http://salilab.org/modbase/searchbyid?databaseID=%s
Query   SNP annotation {all SNPs} | HTML | UniProt accession | http://salilab.org/modbase/searchbyid?databaseID=%s&displaymode=snpview
Query   SNP annotation {specific SNP} | HTML | UniProt accession;dbSNP ID | http://salilab.org/modbase/searchbyid?databaseID=%s1&dbsnpID=%s2
Example UniProt accession | P43632
Example UniProt accession;dbSNP ID | P43632;rs1143507

ID      MODOMICS
Name    Database of RNA modification pathways
Desc    Database of RNA modification pathways.
URL     http://www.genesilico.pl/modomics
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models

ID      MoKA
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.
URL     http://strubiol.icr.ac.uk/extra/mokca/
Taxon   9606 | Homo sapiens
EDAMtpc 2640 | Cancer resources
EDAMtpc 0625 | Genotype and phenotype resources

ID      MolliGen
Name    MolliGen Mollicutes database
Desc    Comparative genomics of Mollicutes.
URL     http://cbi.labri.fr/outils/molligen/
Taxon   31969 | Mollicutes
EDAMtpc 0797 | Comparative genomics

ID      MOSAIC
Name    MOSAIC bacterial genome comparison database
Desc    Comparison of closely related bacterial genomes.
URL     http://genome.jouy.inra.fr/mosaic/
Taxon   2 | Bacteria
EDAMtpc 0797 | Comparative genomics

ID      MOsDB
Name    MOsDB rice genome database
Desc    Publicly available sequences of the rice (Oryza sativa L.) genome.
URL     http://mips.gsf.de/proj/plant/jsf/rice/index.jsp
Taxon   4530 | Oryza sativa
EDAMtpc 0780 | Plants

ID      MouseSAGE
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.
URL     http://mouse.img.cas.cz/sage/
Taxon   10088 | Mus
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0213 | Mice or rats

ID      MouseBook
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.
URL     http://www.mousebook.org
Taxon   10088 | Mus
EDAMtpc 0213 | Mice or rats

ID      Mpact
Name    MPact: Representation of Interaction Data at MIP
Desc    Protein interaction resources from MIPS, designed to support the PSI-MI standard.
URL     http://mips.gsf.de/genre/proj/mpact
Taxon   1 | all
EDAMtpc 0128 | Protein interactions

ID      Mugen
Name    MUGEN mouse database
Desc    Database of murine models of immune processes and immunological diseases.
URL     http://www.mugen-noe.org/database
Taxon   10088 | Mus
EDAMtpc 0804 | Immunoinformatics
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 0213 | Mice or rats


ID      MUMDB
Name    MIPS Ustilago maydis Database (MUMDB)
Desc    Molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis.
URL     http://mips.gsf.de/genre/proj/ustilago/
Taxon   5270 | Ustilago maydis
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0782 | Fungi

ID      MyHits
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.
URL     http://myhits.isb-sib.ch/cgi-bin/index
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMtpc 0736 | Protein domains and folds
EDAMtpc 0188 | Sequence profiles and HMMs


ID      NAPROC-13
Name    NAPROC-13 natural products 13C NMR database
Desc    Natural products 13C NMR, for the dereplication of natural product mixtures in bioassay-guided protocols.
URL     http://c13.usal.es
Taxon   None
EDAMtpc 0154 | Small molecules
EDAMtpc 2226 | Structure determination

ID      Narcisse
Name    Narcisse mirror view of conserved synteny
Desc    Mirror view of conserved synteny.
URL     http://narcisse.toulouse.inra.fr
Taxon   1 | all
EDAMtpc 0796 | Genetic mapping and linkage

ID      NBRC
IDalt   NITE-BRC
Name    NITE biological resource center
Desc    Microbial culture catalogue.
URL     http://www.nbrc.nite.go.jp/e/index.html
Cat     Not available
Taxon   1 | all
EDAMtpc 0608 | Cell culture resources
Xref    SP_FT | None

ID      NCL
Name    NCL Mutation Database
Desc    Published mutations and polymorphisms in the NCL genes together with unpublished data included with permission.
URL     http://www.ucl.ac.uk/ncl/mutation.shtml
Taxon   9606 | Homo sapiens
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0199 | Genetic variation

ID      ncRNAs
Name    ncRNAs database
Desc    Sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell.
URL     http://biobases.ibch.poznan.pl/ncRNA/
Taxon   1 | all
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0659 | Functional RNA

ID      NEMBASE
Name    NEMBASE database for analysis of nematode ESTs
Desc    Nematode EST datasets.
URL     http://www.nematodes.org/nembase3/index.shtml
Taxon   6231 | Nematoda
EDAMtpc 0655 | mRNA, EST or cDNA

ID      NESbase
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.
URL     http://www.cbs.dtu.dk/databases/NESbase
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources

ID      NeuroMorpho
Name    NeuroMorpho
Desc    NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons and associated metadata from peer-reviewed publications. 
URL     http://neuromorpho.org/neuroMorpho/index.jsp
Taxon   1 | all
EDAMtpc 2229 | Cell biology resources

ID      NeuronDB
Name    NeuronDB
Desc    NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.
URL     http://senselab.med.yale.edu/NeuronDB/
Taxon   1 | all
EDAMtpc 2229 | Cell biology resources


ID      NextBio
Acc     DB-0128
Name    NextBio gene-centric data for human, mouse, rat, fly, worm and yeast
Desc    NextBio gene-centric data for human, mouse, rat, fly, worm and yeast
URL     http://www.nextbio.com/
Cat     Other
Taxon   9606 | Homo sapiens
Taxon   10088 | Mus
Taxon   10114 | Rattus
Taxon   6239 | Caenorhabditis elegans
Taxon   7215 | Drosophila
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 2818 | Eukaryotes
EDAMtpc 0797 | Comparative genomics
EDAMdat 0916 | Gene annotation
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {NextBio}
Query   Gene annotation | HTML | Identifier {NextBio} | http://www.nextbio.com/b/home/home.nb?id=%s&type=feature
Example Identifier {NextBio} | 797758


ID      NextDB
Name    Nematode expression pattern dataBase (NextDB)
Desc    Nematode expression pattern dataBase.
URL     http://nematode.lab.nig.ac.jp/
Cat     Not available
Taxon   6231 | Nematoda
EDAMtpc 0197 | Gene expression resources
Xref    SP_FT | None
Example Identifier | CELK01662

ID      neXtProt
Acc     DB-0161
Name    neXtProt; the human protein knowledge platform
Desc    neXtProt; the human protein knowledge platform
URL     http://www.nextprot.org/
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
EDAMtpc 2815 | Humans
EDAMdat 0916 | Gene annotation
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {neXtProt}
Query   Gene annotation | HTML | Identifier {neXtProt} | http://www.nextprot.org/entry/%s
Example Identifier {neXtProt} | NX_P31946

ID      niaEST
Name    NIA mouse cDNA project
Desc    NIA mouse cDNA project
URL     http://lgsun.grc.nia.nih.gov/cDNA/
Cat     Not available
Taxon   10088 | Mus
EDAMtpc 0213 | Mice or rats
EDAMtpc 0655 | mRNA, EST or cDNA
Xref    SP_FT | None
Example Identifier | L0304H12-3

ID      NMPDR
Acc     DB-0125
Name    National microbial pathogen
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.
URL     http://www.nmpdr.org
URLlink  http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/LinkingToTheGenomeViewer
Cat     Genome annotation databases
Taxon   2 | Bacteria
EDAMtpc 0783 | Pathogens
EDAMtpc 0797 | Comparative genomics
EDAMdat 0916 | Gene annotation
EDAMid  1179 | NCBI taxonomy ID
EDAMid  2737 | FIG ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | FIG ID
Query   Gene annotation | HTML | NCBI taxonomy ID | http://www.nmpdr.org/linkin.cgi?genome=%s
Query   Gene annotation {Protein encoding gene or other feature} | HTML | FIG ID | http://www.nmpdr.org/linkin.cgi?id=%s
Example NCBI taxonomy ID | 83333.1
Example FIG ID | 83333.1.peg.123
Example FIG ID | 83333.1.rna.1

ID      NMRShift
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.
URL     http://nmrshiftdb.ice.mpg.de/
Taxon   None
EDAMtpc 2226 | Structure determination

ID      NOPDB
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.
URL     http://www.lamondlab.com/NOPDB3.0/
Taxon   9606 | Homo sapiens
EDAMtpc 0767 | Protein and peptide identification
EDAMtpc 0616 | Organelle genes and proteins

ID      NORINE
Name    NORINE database of nonribosomal peptides
Desc    Database of nonribosomal peptides.
URL     http://bioinfo.lifl.fr/norine/
Taxon   1 | all
EDAMtpc 0613 | Peptides and amino acids

ID      NPC-db
Name    Niemann-Pick Type C mutations
Desc    Niemann-Pick type C disease gene variation database (NPC-db).
URL     http://npc.fzk.de/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      NPD
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.
URL     http://npd.hgu.mrc.ac.uk
Taxon   9711 | Chordata
EDAMtpc 0635 | Specific protein resources

ID      NRESTdb
Name    Natural rubber EST database (NRESTdb)
Desc    Natural rubber EST database.
URL     http://genome.ukm.my/nrestdb/
Cat     Not available
Taxon   3981 | Hevea brasiliensis
EDAMtpc 0655 | mRNA, EST or cDNA
Xref    SP_FT | None
Example Identifier | Y01A01

ID      NRSub
Name    Non-Redundant B.subtilis database (NRSub)
Desc    Complete genome of Bacillus subtilis, plus additional data on gene mapping and codon usage.
URL     http://pbil.univ-lyon1.fr/nrsub/nrsub.html
Taxon   1423 | Bacillus subtilis
EDAMtpc 0107 | Codon usage analysis
EDAMtpc 1811 | Prokaryotes and archae

ID      NUREBASE
Name    Nuclear receptor database (NUREBASE)
Desc    Nuclear receptor database
URL     http://www.ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html
Taxon   2759 | Eukaryota
EDAMtpc 0635 | Specific protein resources

ID      OGLYCBASE
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.
URL     http://www.cbs.dtu.dk/databases/OGLYCBASE/
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0635 | Specific protein resources

ID      OGP
Acc     DB-0067
Name    Oxford glycoProteomics 2-DE database (OGP)
Desc    Two-dimensional polyacrylamide gel electrophoresis database.
URL     http://proteomewww.bioch.ox.ac.uk/2d/2d.html
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) {OGP entry} | HTML | UniProt accession | http://proteomewww.glycob.ox.ac.uk/cgi-bin/2d-search-ac?%s
Example UniProt accession | P04406

ID      OMA
Acc     DB-0137
Name    Identification of orthologs from complete genome data (OMA database)
Desc    Identification of orthologs from complete genome data.
URL     http://www.omabrowser.org
Cat     Phylogenomic databases
Taxon   1 | all
EDAMtpc 0722 | Nucleic acid classification
EDAMtpc 0084 | Phylogenetics
EDAMtpc 0194 | Phylogenomics
EDAMdat 2093 | Data reference
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier {OMA}
Query   Data reference | HTML | Protein identifier {OMA} | http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=%s
Example Protein identifier {OMA} | FDVARTG


ID      OPTIC
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.
URL     http://genserv.anat.ox.ac.uk/
Taxon   2759 | Eukaryota
EDAMtpc 0722 | Nucleic acid classification

ID      ORENZA
Name    Database of orphan enzyme activities (ORENZA)
Desc    Enzyme Activities for which no sequences are available in the main sequence protein databases.
URL     http://www.orenza.u-psud.fr/
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions

ID      Orphanet
Acc     DB-0068
Name    Orphanet portal for rare diseases and orphan drugs
Desc    Information on rare diseases and orphan drugs.
URL     http://www.orpha.net/consor/cgi-bin/home.php?Lng=GB
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
EDAMtpc 0620 | Drugs and targets
EDAMtpc 0634 | Disease resources
EDAMid  2800 | Orpha number
EDAMfmt 2331 | HTML
EDAMdat 1622 | Disease annotation
Xref    SP_explicit | Orpha number
Query   Disease annotation {Orphanet entry} | HTML | Orpha number | http://www.orpha.net//consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=%s
Example Orpha number | 69739

ID      OrthoDB
Acc     DB-0143
Name    Orthologous groups database (OrthoDB)
Desc    Orthologous groups database.
URL     hhttp://cegg.unige.ch/orthodb2
Taxon   1 | all
EDAMtpc 0722 | Nucleic acid classification
EDAMtpc 0623 | Genes, gene family or system

ID      OryGenesDB
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).
URL     http://orygenesdb.cirad.fr/
Taxon   4530 | Oryza sativa
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0640 | Nucleic acid sequence analysis
EDAMtpc 0780 | Plants

ID      Oryza
Name    Oryza tag line
Desc    Database for the functional analyis of the rice genome. Phenotypic data from evaluation of the Genoplante rice insertion line library. Sequence information (Flanking Sequence Tags) from the molecular characterization of the mutagen insertion sites.
URL     http://urgi.versailles.inra.fr/OryzaTagLine/
Taxon   4530 | Oryza sativa
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0780 | Plants

ID      Osteogenesis
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.
URL     https://oi.gene.le.ac.uk
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMdat 0918 | Sequence variation annotation
EDAMid  2748 | Database name (Osteogenesis)
EDAMfmt 2331 | HTML
Query   Sequence variation annotation {Sequence variants} | HTML | Database name (Osteogenesis) | http://oi.gene.le.ac.uk/home.php?select_db=%s
Example Database name (Osteogenesis) | COL1A1
Example Database name (Osteogenesis) | COL1A2
Example Database name (Osteogenesis) | CRTAP
Example Database name (Osteogenesis) | FKBP10
Example Database name (Osteogenesis) | LEPRE1
Example Database name (Osteogenesis) | PPIB
Example Database name (Osteogenesis) | SERPINH1

ID      p53FamTaG
Name    p53FamTaG direct target genes
Desc    A resource of human p53, p63, p73 direct target genes combining in silico prediction and microarray analysis.
URL     http://www2.ba.itb.cnr.it/p53FamTaG/
Taxon   9606 | Homo sapiens
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0197 | Gene expression resources

ID      PairsDB
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.
URL     http://pairsdb.csc.fi
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment

ID      PANDIT
Name    Protein and associated nucleotide domains with inferred trees (PANDIT)
Desc    Protein and associated nucleotide domains with inferred trees.
URL     http://www.ebi.ac.uk/goldman-srv/pandit/
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features

ID      PANDORA
Name    PANDORA visualization and annotation for protein sets
Desc    Keyword-based analysis of protein sets by integration of annotation sources.
URL     http://www.pandora.cs.huji.ac.il
Taxon   1 | all
EDAMtpc 0078 | Protein analysis

ID      PANTHER
Acc     DB-0069
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".
URL     http://www.pantherdb.org/
Cat     Family and domain databases; Protein sequence classification database
Taxon   1 | all
EDAMtpc 2225 | Protein databases
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0724 | Protein families
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0084 | Phylogenetics
EDAMdat 2984 | Pathway or network report
EDAMdat 0907 | Protein family annotation
EDAMid  1161 | Pathway ID (Panther)
EDAMid  2783 | Protein family ID (PANTHER)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein family ID (PANTHER)
Query   Protein family annotation {PANTHER Family} | HTML | Protein family ID (PANTHER) | http://www.pantherdb.org/panther/family.do?clsAccession=%s
Query   Pathway or network report | HTML | Pathway ID (Panther) | http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=%s
Example Protein family ID (PANTHER) | PTHR12649:SF6
Example Pathway ID (Panther) | P00002

ID      ParameciumDB
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.
URL     http://paramecium.cgm.cnrs-gif.fr
Taxon   5884 | Paramecium
EDAMtpc 2821 | Unicellular eukaryotes

ID      Pathema
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.
URL     http://www.jcvi.org/cms/research/projects/pathema/overview/
Cat     Not available
Taxon   1 | all
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0783 | Pathogens
Xref    SP_FT | None

ID      PathoPlant
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.
URL     http://www.pathoplant.de
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0780 | Plants
EDAMtpc 0754 | Signaling pathways
EDAMtpc 0780 | Plants
EDAMtpc 0783 | Pathogens

ID      Pathway_Interaction_DB
Acc     DB-0134
Name    NCI-Nature pathway interaction database
Desc    Biomolecular interactions and cellular processes assembled into human signaling pathways.
URL     http://pid.nci.nih.gov/
Cat     Enzyme and pathway databases
Taxon   9606 | Homo sapiens
EDAMtpc 0754 | Signaling pathways
EDAMdat 2984 | Pathway or network report
EDAMid  2344 | Pathway ID (NCI-Nature)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Pathway ID (NCI-Nature)
Query   Pathway or network report | HTML | Pathway ID (NCI-Nature) | http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=%s&source=NATURE&what=graphic&jpg=on&ppage=1
Example Pathway ID (NCI-Nature) | 200034

ID      PDB
Acc     DB-0070
Name    The RCSB Protein Data Bank
Desc    A repository for 3D biological macromolecular structure data.
URL     http://www.rcsb.org/PDB/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0081 | Structure analysis
EDAMdat 0883 | Structure
EDAMdat 2085 | Structure report
EDAMid  1127 | PDB ID
EDAMfmt 1476 | PDB format
EDAMfmt 1478 | PDBML
EDAMfmt 1477 | mmCIF
EDAMfmt 2331 | HTML
Xref    SP_explicit | PDB ID
Xref    EMBL_explicit | PDB ID
Query   Structure report | HTML | PDB ID | http://www.PDB.org/PDB/explore/explore.do?structureId=%s
Query   Structure | PDB format | PDB ID | http://www.PDB.org/PDB/files/%s.PDB
Query   Structure | mmCIF | PDB ID | http://www.PDB.org/PDB/files/%s.cif
Query   Structure | PDBML | PDB ID | http://www.PDB.org/PDB/files/%s.xml
Example PDB ID | 1rbp

ID      PDBe
Name    PDBe protein structure database in Europe
Desc    PDBe protein structure database in Europe
URL     http://www.ebi.ac.uk/PDBe/
Taxon   1 | all
EDAMtpc 0081 | Structure analysis

ID      PDBFINDER
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.
URL     http://swift.cmbi.ru.nl/gv/PDBfinder/
URLrest http://mrs.cmbi.ru.nl/mrsws/search/rest/GetEntry/db/PDBfinder2/id/%s
URLsoap http://mrs.cmbi.ru.nl/mrsws/wsdl
Taxon   1 | all
EDAMtpc 3040 | Protein structure
EDAMdat 2085 | Structure report
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Query   Structure report {PDBFinder report} | HTML | PDB ID | http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=PDBfinder2&id=%s
Example PDB ID | 2hva

ID      PDBfun
Name    PDBfun annotated protein structures
Desc    Database of annotated residues in proteins from PDB.
URL     http://PDBfun.uniroma2.it
Taxon   1 | all
EDAMtpc 3040 | Protein structure

ID      PDB-redo
Name    PDB-redo database of re-refined PDB entries
Desc    Re-refined macromolecular X-ray diffraction structures.
URL     http://swift.cmbi.ru.nl/PDBredo/index.html
Taxon   1 | all
EDAMtpc 0081 | Structure analysis
EDAMdat 0883 | Structure
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Query   Structure {PDB-redo} | HTML | PDB ID | http://www.cmbi.ru.nl/PDB_redo/yg/%s/index.html
Query   Structure {PDB-redo} | HTML | PDB ID | http://www.cmbi.ru.nl/PDB_redo/yg/1ygb/index.html

ID      PDBREPORT
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.
URL     http://swift.cmbi.ru.nl/gv/PDBreport/
Taxon   1 | all
EDAMtpc 3040 | Protein structure

ID      PDBselect
Name    PDBselect database of representative PDB chains
Desc    Selection of a representative set of PDB chains.
URL     http://bioinfo.tg.fh-giessen.de/PDBselect/
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure

ID      PDBsum
Acc     DB-0119
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.
URL     http://www.ebi.ac.uk/PDBsum
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 3040 | Protein structure
EDAMdat 2085 | Structure report
EDAMid  1127 | PDB ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | PDB ID
Query   Structure report {PDBSum entry} | HTML | PDB ID | http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e
Example PDB ID | 1kfv

ID      PDBTM
Name    Transmembrane proteins from PDB (PDBTM)
Desc    Transmembrane protein selection of the Protein Data Bank (PDB).
URL     http://PDBtm.enzim.hu/
Taxon   1 | all
EDAMtpc 0820 | Membrane proteins

ID      PED
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.
URL     http://www.pancreasexpression.org
Taxon   9347 | Eutheria
EDAMtpc 2640 | Cancer resources
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0204 | Gene regulation resources

ID      PEDANT
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.
URL     http://pedant.gsf.de
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0078 | Protein analysis

ID      PepSeeker
Name    PepSeeker database of proteome peptide identifications for investigating fragmentation patterns
Desc    Proteome peptide identifications for investigating fragmentation patterns.
URL     http://www.ispider.manchester.ac.uk/pepseeker/
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification

ID      Peptaibol
Name    Peptaibol database of natural fungal peptides
Desc    Natural fungal peptides.
URL     http://peptaibol.cryst.bbk.ac.uk
Taxon   4751 | Fungi
EDAMtpc 0613 | Peptides and amino acids
EDAMtpc 0782 | Fungi

ID      PeptideAtlas
Acc     DB-0071
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.
URL     http://www.peptideatlas.org
Cat     Proteomic databases; Peptide identification database; Mass spectrometry database
Taxon   1 | all
EDAMtpc 0613 | Peptides and amino acids
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 0896 | Protein report
EDAMdat 0945 | Peptide identification
EDAMdat 2536 | Mass spectrometry data
EDAMid  2384 | IPI protein ID
EDAMid  2398 | Protein ID (Ensembl)
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | Protein identifier {PeptideAtlas}
Query   Peptide identification | HTML | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY
Query   Peptide identification | XML | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=xml
Query   Peptide identification | Text | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=tsv
Query   Mass spectrometry data {Recommended transitions for human protein} | HTML | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ViewMRMList?protein_name_constraint=%s&atlas_build_id=182&consensus_library_id=9&action=QUERY
Query   Protein report {PeptideAtlas entry} | HTML | IPI protein ID | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?atlas_build_id=242&protein_name=%s&action=QUERY
Query   Protein report {PeptideAtlas entry} | HTML | Protein identifier {PeptideAtlas} | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=%s
Example Protein ID (Ensembl) | ENSP00000374576
Example IPI protein ID | IPI00795032
Example Protein identifier {PeptideAtlas} | P62258


ID      PeptideDB
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.
URL     http://www.peptides.be/
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0613 | Peptides and amino acids

ID      PeroxiBase
Acc     DB-0072
Name    PeroxiBase peroxidase family database
Desc    Sequences from peroxidase superfamilies with annotation on putative functions and transcription regulation.
URL     http://peroxibase.isb-sib.ch/index.php
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources
EDAMdat 0896 | Protein report
EDAMid  2792 | Protein ID (PeroxiBase)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein ID (PeroxiBase)
Query   Protein report {PeroxiBase entry} | HTML | Protein ID (PeroxiBase) | http://peroxibase.isb-sib.ch/listing.php?action=view&id=%s
Example Protein ID (PeroxiBase) | 6846

ID      PeroxisomeDB
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).
URL     http://www.peroxisomeDB.org
Taxon   2759 | Eukaryota
EDAMtpc 0753 | Metabolic pathways
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0621 | Genome, proteome and model organisms

ID      PespotDB
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.
URL     http://mint.bio.uniroma2.it/PepspotDB
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification

ID      Pfam
Acc     DB-0073
Name    Pfam protein domain database
Desc    Large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
URL     http://pfam.sanger.ac.uk/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment
EDAMtpc 0188 | Sequence profiles and HMMs
EDAMtpc 0724 | Protein families
EDAMtpc 0736 | Protein domains and folds
EDAMdat 0907 | Protein family annotation
EDAMid  1096 | Sequence accession (protein)
EDAMid  1138 | Pfam accession number
EDAMid  1179 | NCBI taxonomy ID
EDAMid  2758 | Pfam clan ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | Pfam accession number
Xref    SP_FT | Pfam accession number
Query   Protein family annotation {Pfam entry} | HTML | Sequence accession (protein) | http://pfam.sanger.ac.uk/protein/acc=%s
Query   Protein family annotation {Pfam entry} | HTML | Pfam accession number | http://pfam.sanger.ac.uk/family?acc=%s
Query   Protein family annotation {Pfam entry} | HTML | Pfam clan ID | http://pfam.sanger.ac.uk/clan?acc=%s
Query   Protein family annotation {Pfam entry} | HTML | NCBI taxonomy ID | http://pfam.sanger.ac.uk/proteome?taxId=%s
Example Sequence accession (protein) | VAV_HUMAN
Example Pfam accession number | PF07388
Example Pfam clan ID | CL0247
Example NCBI taxonomy ID | 349163

ID      PGN
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.
URL     http://pgn.cornell.edu/
Cat     Not available
Taxon   58024 | Spermatophyta
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0780 | Plants
Xref    SP_FT | None

ID      PharmGKB
Acc     DB-0074
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.
URL     http://www.pharmgkb.org
Cat     Organism-specific databases
Taxon   9606 | Homo sapiens
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0202 | Pharmacoinformatics
EDAMtpc 0208 | Pharmacogenomics
EDAMtpc 2815 | Humans
EDAMdat 0916 | Gene annotation
EDAMid  2649 | PharmGKB ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | PharmGKB ID
Query   Gene annotation | HTML | PharmGKB ID | http://www.pharmgkb.org/do/serve?objId=%s&objCls=Gene
Example PharmGKB ID | PA356

ID      PhenomicDB
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 indexes (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously.
URL     http://www.phenomicdb.de
Taxon   2759 | Eukaryota
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0722 | Nucleic acid classification

ID      PHCI-2DPAGE
Acc     DB-0075
Name    Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE)
Desc    Two-dimensional polyacrylamide gel electrophoresis database.
URL     http://www.gram.au.dk/2d/2d.html
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.gram.au.dk/cgi-bin/get-2d-entry?%s
Example UniProt accession | P17821

ID      PHI-base
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.
URL     http://www.phibase.org
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0783 | Pathogens

ID      PhosPhAt
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.
URL     http://phosphat.mpimp-golm.mpg.de/app.html
Taxon   3701 | Arabidopsis
EDAMtpc 0751 | Phosphorylation sites
EDAMtpc 0780 | Plants
EDAMtpc 0767 | Protein and peptide identification

ID      PhosphoELM
Name    PhosphoELM database of S/T/Y phosphorylation sites
Desc    Experimentally verified phosphorylation sites in eukaryotic proteins.
URL     http://phospho.elm.eu.org/
Taxon   1 | all
EDAMtpc 0751 | Phosphorylation sites
EDAMdat 2071 | Sequence motif (protein)
EDAMid  1096 | Sequence accession (protein)
EDAMid  2775 | Kinase name
EDAMid  1009 | Protein name
EDAMfmt 2331 | HTML
Query   Sequence motif (protein) {Phospho-ELM report} | HTML | Protein name {Substrate} | http://phospho.elm.eu.org/cgimodel.py?fun=Search&substrate=%s
Query   Sequence motif (protein) {Phospho-ELM report} | HTML | Sequence accession (protein) | http://phospho.elm.eu.org/cgimodel.py?fun=Search&accession=%s
Query   Sequence motif (protein) {Phospho-ELM report} | HTML | Kinase name | http://phospho.elm.eu.org/cgimodel.py?fun=Search&kinase=%s
Example Kinase | Abl2
Example Sequence accession (protein) | Q9H0E9
Example Protein name {Substrate} | Src substrate cortactin

ID      PHOSPHO3D
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.
URL     http://bioinformatica.uniroma2.it/phospho3d
Taxon   1 | all
EDAMtpc 0751 | Phosphorylation sites
EDAMtpc 0166 | Protein structural motifs and surfaces


ID      PhosphoPep
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).
URL     http://www.phosphopep.org/
Taxon   1 | all
EDAMtpc 0751 | Phosphorylation sites

ID      PhosphoSite
Acc     DB-0123
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.
URL     http://www.phosphosite.org
Cat     PTM databases
Taxon   1 | all
EDAMtpc 0751 | Phosphorylation sites
EDAMdat 2071 | Sequence motif (protein)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Sequence motif (protein) {PhosphoSite entry} | HTML | UniProt accession | http://www.phosphosite.org/uniprotAccAction.do?id=%s
Example UniProt accession | Q92844

ID      PhosSite
Acc     DB-0076
Name    Phosphorylation site database for Archaea and Bacteria
Desc    Phosphorylation site database for Archaea and Bacteria
URL     http://www.phosphorylation.biochem.vt.edu/
Cat     PTM databases
Taxon   2 | Bacteria
Taxon   2157 | Archaea
EDAMtpc 0751 | Phosphorylation sites
EDAMdat 2071 | Sequence motif (protein)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Sequence motif (protein) {PhosSite entry} | HTML | UniProt accession | http://www.phosphorylation.biochem.vt.edu/xpd2.cfm?extf=uniprot&extref=%s
Example UniProt accession | P36683


ID      PhylomeDB
Acc     DB-0144
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.
URL     http://phylomedb.bioinfo.cipf.es
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment
EDAMtpc 0084 | Phylogenetics

ID      PhyloPat
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.
URL     http://www.cmbi.ru.nl/phylopat
Taxon   1 | all
EDAMtpc 0084 | Phylogenetics

ID      PhytoProt
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).
URL     http://urgi.versailles.inra.fr/phytoprot/
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 3052 | Sequence clusters and classification

ID      PIPs
Name    Human protein-protein interaction prediction (PIPs)
Desc    Predicted human protein interactions.
URL     http://www.compbio.dundee.ac.uk/www-pips
Taxon   9606 | Homo sapiens
EDAMtpc 0147 | Protein-protein interactions

ID      PIR
Acc     DB-0078
Name    Protein sequence database of the Protein Information Resource (PIR)
Desc    Integrated protein informatics resource for genomic, proteomic and systems biology research.
URL     http://pir.georgetown.edu/
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier {PIR accession}
Xref    SP_FT | None
Query   Sequence record full | HTML | Protein identifier {PIR accession} | http://pir.georgetown.edu/cgi-bin/nbrfget?uid=%s
Example Protein identifier {PIR accession} | S12345


ID      PIRSF
Acc     DB-0079
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.
URL     http://pir.georgetown.edu/pirsf/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0724 | Protein families
EDAMdat 0907 | Protein family annotation
EDAMid  1136 | PIRSF ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | PIRSF ID
Query   Protein family annotation {PIRSF entry} | HTML | PIRSF ID | http://pir.georgetown.edu/cgi-bin/ipcSF?id=%s
Example PIRSF ID | SF000186

ID      PlantDNAC-values
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.
URL     http://data.kew.org/cvalues/
Taxon   58024 | Spermatophyta
EDAMtpc 0780 | Plants

ID      PlantsnoRNA
Name    Plant snoRNA database
Desc    Plant snoRNA database.
URL     http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
Taxon   58024 | Spermatophyta
! EDAMtpc 0664 | snRNA
EDAMtpc 0659 | Functional RNA
EDAMtpc 0780 | Plants

ID      PlantCARE
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.
URL     http://bioinformatics.psb.ugent.be/webtools/plantcare/html/
Taxon   58024 | Spermatophyta
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0780 | Plants

ID      PlantMarkers
Name    PlantMarkers database of predicted molecular markers from plants
Desc    Predicted molecular markers from plants.
URL     http://markers.btk.fi
Taxon   58024 | Spermatophyta
EDAMtpc 0796 | Genetic mapping and linkage
EDAMtpc 0780 | Plants

ID      PLANT-Pis
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.
URL     http://bighost.area.ba.cnr.it/PLANT-Pis
Taxon   58024 | Spermatophyta
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0780 | Plants

ID      PlantProm
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.
URL     http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom
Taxon   58024 | Spermatophyta
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0780 | Plants

ID      PlasmoDraft
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 lack 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.
URL     http://www.atgc-montpellier.fr/PlasmoDraft/
Taxon   5820 | Plasmodium
EDAMtpc 0089 | Ontologies
EDAMtpc 2821 | Unicellular eukaryotes


ID      PLMItRNA
Name    PLMItRNA database of tRNAs in plant mitochondria
Desc    A database for tRNA molecules and genes in mitochondria of photosynthetic eukaryotes.
URL     http://www.ba.itb.cnr.it/PLMItRNA/
Taxon   58024 | Spermatophyta
EDAMtpc 0779 | Mitochondrial genes and proteins
EDAMtpc 0663 | tRNA
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0780 | Plants

ID      Plprot
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.
Taxon   2759 | Eukaryota
URL     http://www.plprot.ethz.ch/
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0616 | Organelle genes and proteins

ID      PMAP-CutDB
Acc     DB-0138
Name    PMAP-CutDB proteolytic event database
Desc    Curated proteolytic events and pathways from the literature.
URL     http://www.proteolysis.org/
Cat     Other
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
EDAMdat 2093 | Data reference
Xref    SP_explicit | UniProt accession
Query   Data reference | HTML | UniProt accession | http://substrate.burnham.org/lookup/uniprot/%s
Example UniProt accession | P05067

ID      PMDB
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.
URL     http://www.caspur.it/PMDB/
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure

ID      Polymorphix
Name    Polymorphix intraspecific sequence polymorphism database
Desc    Families of polymorphic sequences.
URL     http://pbil.univ-lyon1.fr/polymorphix/query.php
Taxon   1 | all
EDAMtpc 0199 | Genetic variation

ID      PoMaMo
Name    PoMaMo potato maps database
Desc    Potato sequences, mapping info, SNPs etc.
URL     https://gabi.rzpd.de/PoMaMo.html
Taxon   4113 | Solanum tuberosum
EDAMtpc 0780 | Plants

ID      PPD
Name    PPD protein pKa values database
Desc    Protein pKa values.
URL     http://www.darrenflower.info/PPD/pKahomepage.htm
Taxon   1 | all
EDAMtpc 3047 | Molecular biology reference

ID      PPNEMA
Name    rRNA genes from plant-parasitic nematodes (PPNEMA)
Desc    Plant-parasitic nematodes multialigned ribosomal cistrons.
URL     http://www.ppnema.uniba.it/
Taxon   6231 | Nematoda
EDAMtpc 0660 | rRNA
EDAMtpc 0623 | Genes, gene family or system

ID      PptaseDB
Acc     DB-0081
Name    Prokaryotic protein phosphatase database (PptaseDB)
Desc    Prokaryotic protein phosphatases.
URL     http://vigen.biochem.vt.edu/p3d/p3d.htm
Cat     Protein family/group databases
Taxon   2 | Bacteria
EDAMtpc 0635 | Specific protein resources
EDAMdat 0896 | Protein report
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier
Query   Protein report {PptaseDB entry} | HTML | Protein identifier | http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=accession&extref=%s
Example Protein identifier | P3D0409136


ID      preDiCT
Name    preDiCT database of drug effects on the heart
Desc    Drug effects on the heart.
URL     http://www.vph-predict.eu/
Taxon   9606 | Homo sapiens
EDAMtpc 0202 | Pharmacoinformatics

ID      PRIDE
Acc     DB-0130
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.
URL     http://www.ebi.ac.uk/pride
URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do
Cat     Proteomic databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMtpc 0121 | Proteomics
EDAMdat 2536 | Mass spectrometry data
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Mass spectrometry data {PRIDE entry} | HTML | UniProt accession | http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=%s
Example UniProt accession | P29375


ID      PRINTS
Acc     DB-0082
Name    PRINTS protein motif fingerprint database
Desc    A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family.
URL     http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMdat 1355 | Protein signature
EDAMid  1137 | PRINTS code
EDAMfmt 2331 | HTML
Xref    SP_explicit | PRINTS code
Query   Protein signature {PRINTS entry} | HTML | PRINTS code | http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=pr00018
Example PRINTS code | pr00018

ID      Prism
Name    Prism protein interaction by structural matching
Desc    Database to explore protein interfaces and predict protein-protein interactions.
URL     http://prism.ccbb.ku.edu.tr/prism
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions

ID      probeBase
Name    probeBase database of rRNA-targeted oligonucleotide probes
Desc    rRNA-targeted oligonucleotide probes.
URL     http://www.microbial-ecology.net/probebase
Taxon   1 | all
EDAMtpc 0632 | Probes and primers
EDAMtpc 0660 | rRNA

ID      ProCMD
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.
URL     http://www.itb.cnr.it/procmd/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 0625 | Genotype and phenotype resources

ID      PROCOGNATE
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.
URL     http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 0148 | Protein-ligand interactions
EDAMtpc 0154 | Small molecules

ID      ProDom
Acc     DB-0083
Name    ProDom protein domain database
Desc    A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.
URL     http://prodom.prabi.fr/prodom/current/html/home.php
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0736 | Protein domains and folds
EDAMdat 0872 | Phylogenetic tree
EDAMdat 1298 | Sequence features (motifs)
EDAMdat 0907 | Protein family annotation
EDAMdat 1384 | Sequence alignment (protein)
EDAMid  1142 | ProDom accession number
EDAMfmt 2331 | HTML
Xref    SP_explicit | ProDom accession number
Query   Protein family annotation {ProDom entry} | HTML | ProDom accession number | http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=%s
Query   Sequence alignment (protein) {ProDom family alignment} | HTML | ProDom accession number | http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent1=%s&wanted=align
Query   Phylogenetic tree | HTML | ProDom accession number | http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent1=%s&wanted=tree
Query   Sequence features (motifs) {ProDom domain image} | HTML | ProDom accession number | http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?CG=0&question=DBLI&query=%s
Query   Sequence alignment (protein) {ProDom family alignment} | Text | ProDom accession number | http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent0=%s
Example ProDom accession number | PD000023

ID      PRODORIC
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.
URL     http://www.prodoric.de
Taxon   2 | Bacteria
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0749 | Transcription factors and regulatory sites

ID      PromEC
Name    PromEC verified E. coli promoters
Desc    E. coli mRNA promoters with experimentally identified transcriptional start sites.
URL     http://margalit.huji.ac.il/promec/
Taxon   562 | Escherichia coli
! EDAMtpc 0111 | Promoters
EDAMtpc 0749 | Transcription factors and regulatory sites


ID      ProMEX
Acc     DB-0124
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.
URL     http://promex.mpimp-golm.mpg.de/
Cat     Proteomic databases
Taxon   3701 | Arabidopsis
Taxon   3880 | Medicago trunculata
EDAMtpc 0767 | Protein and peptide identification
EDAMtpc 0780 | Plants
EDAMdat 0943 | Mass spectrometry spectra
EDAMid  1895 | Locus ID (AGI)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Locus ID (AGI)
Query   Mass spectrometry spectra {ProMEX entry} | HTML | Locus ID (AGI) | http://promex.mpimp-golm.mpg.de/cgi-bin/peplib.pl?action=11&txt_query=%s
Example Locus ID (AGI) | At5g50600

ID      PROPHECY
Name    PROPHECY profiling of phenotypic characteristics in yeast
Desc    Quantitative information about phenotypes for the complete collection of deletion strains in yeast (Saccharomyces cerevisiae).
URL     http://prophecy.lundberg.gu.se
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0782 | Fungi

ID      ProRule
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.
URL     http://www.expasy.org/prosite/prorule.html
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMtpc 0188 | Sequence profiles and HMMs

ID      ProSAS
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.
URL     http://www.bio.ifi.lmu.de/ProSAS/
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMtpc 3040 | Protein structure

ID      PROSAT2
Name    PROSAT2 protein structure annotation tool
Desc    Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein.
URL     http://projects.villa-bosch.de/dbase/PDBa/
Taxon   1 | all
EDAMtpc 3040 | Protein structure
EDAMtpc 0748 | Protein sites and features

ID      PROSITE
Acc     DB-0084
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.
URL     http://www.expasy.org/prosite/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0736 | Protein domains and folds
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMtpc 0188 | Sequence profiles and HMMs
EDAMdat 2071 | Sequence motif (protein)
EDAMid  1117 | Prosite accession number
EDAMfmt 2331 | HTML
Xref    SP_explicit | Prosite accession number
Query   Sequence motif (protein) {PROSITE entry} | Text | Prosite accession number | http://www.expasy.org/cgi-bin/get-prosite-raw.pl?%s
Query   Sequence motif (protein) {PROSITE entry} | HTML | Prosite accession number | http://www.expasy.org/cgi-bin/prosite-search-ac?%s
Example Prosite accession number | PDOC00022

ID      ProtClustDB
Acc     DB-0154
Name    Entrez Protein Clusters
Desc    Entrez Protein Clusters
URL     http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters
Cat     Phylogenomic databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0194 | Phylogenomics
EDAMdat 0907 | Protein family annotation
EDAMid  1075 | Protein family identifier
Xref    SP_explicit | Protein family identifier {ProtClustDB}
Query   Protein family annotation | HTML | Protein family identifier {ProtClustDB} | http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=%u
Example Protein family identifier {ProtClustDB} | CLSP2511638

ID      ProteinModelPortal
Acc     DB-0159
Name    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase
Desc    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase
URL     http://www.proteinmodelportal.org/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0736 | Protein domains and folds
EDAMdat 0896 | Protein report
EDAMid  3021 | UniProt accession
Xref    SP_explicit | UniProt accession
Query   Protein report | HTML | UniProt accession | http://www.proteinmodelportal.org/query/uniprot/%s
Example UniProt accession | Q91G65

ID      ProtoNet
Acc     DB-0085
Name    ProtoNet automatic hierarchical classification of proteins
Desc    Automatic hierarchical classification of protein sequences.
URL     http://www.protonet.cs.huji.ac.il/
Cat     Other
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMdat 0907 | Protein family annotation
EDAMfmt 1978 | DASGFF
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_implicit | UniProt accession
Query   Protein family annotation {ProtoNet entry} | HTML | UniProt accession | http://www.protonet.cs.huji.ac.il/sp.php?prot=%s
Query   Protein family annotation {ProtoNet entry} | DASGFF | UniProt accession | http://www.protonet.cs.huji.ac.il/das/protonet/features?segment=%s
Example UniProt accession | P01011


ID      Protepedia
Name    Protepedia collaborative 3D protein encyclopedia
Desc    Free, collaborative 3D encyclopedia of proteins & other molecules.
URL     http://www.proteopedia.org/wiki/index.php/Main_Page
Taxon   1 | all
EDAMtpc 0078 | Protein analysis

ID      ProTeus
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.
URL     http://www.proteus.cs.huji.ac.il
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs

ID      PseudoBase
Name    PseudoBase RNA pseudoknots database
Desc    Collection of RNA pseudoknots.
URL     http://www.ekevanbatenburg.nl/PKBASE/PKB.HTML
Taxon   1 | all
EDAMtpc 0697 | RNA structure and alignment

ID      PseudoCAP
Acc     DB-0086
Name    PseudoCAP pseudomonas genome database
Desc    Pseudomonas genome database.
URL     http://www.pseudomonas.com/
Cat     Organism-specific databases
Taxon   286 | Pseudomonas
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 0916 | Gene annotation
EDAMid  2314 | GI number
EDAMid  2744 | Locus ID (PseudoCAP)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Locus ID (PseudoCAP)
Query   Gene annotation | HTML | Locus ID (PseudoCAP) | http://www.pseudomonas.com/getAnnotation.do?locusID=%s
Query   Gene annotation | HTML | GI number | http://www.pseudomonas.com/getAnnotation.do?gi=%s
Example Locus ID (PseudoCAP) | PA0006
Example GI number | 15596473

ID      pSTIING
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.
URL     http://pstiing.licr.org/
Taxon   33208 | Metazoa
EDAMtpc 2846 | Gene regulatory networks
EDAMtpc 0128 | Protein interactions
EDAMtpc 0602 | Pathways, networks and models

ID      PTCH
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.
URL     http://www.cybergene.se/cgi-bin/w3-msql/ptchbase/index.html
Taxon   9606 | Homo sapiens
EDAMtpc 0199 | Genetic variation
EDAMtpc 2640 | Cancer resources

ID      PubChem
Name    PubChem
Desc    Information on the biological activities of small molecules, including bioassay records, chemical structures and substances.
URL     http://pubchem.ncbi.nlm.nih.gov/
Taxon   1 | all
EDAMtpc 0154 | Small molecules

ID      PubMeth
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.
URL     http://www.pubmeth.org
Taxon   2759 | Eukaryota
EDAMtpc 2640 | Cancer resources
EDAMtpc 0654 | DNA
EDAMid  1026 | Gene symbol
EDAMid  0976 | Identifier (typed)
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Query   Gene annotation {PubMeth gene entry} | HTML | Gene symbol | http://matrix.ugent.be/temp/static/%s.html
Query   Gene annotation {PubMeth gene entry (cancer record)} | HTML | Gene symbol;Identifier (typed) {Cancer type} | http://matrix.ugent.be/temp/static/%s1_%s2.html
Example Gene symbol | CDKN2A
Example Gene symbol;Identifier (typed) {Cancer type} | CDKN2A;lung

ID      PMMA-2DPAGE
Acc     DB-0080
Name    Purkyne Military Medical Academy 2D-PAGE database
Desc    Purkyne Military Medical Academy 2D-PAGE database
URL     http://www.pmma.pmfhk.cz/2d/2d.html
Cat     2D gel databases
Taxon   9606 | Homo sapiens
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2372 | 2D PAGE spot annotation
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   2D PAGE spot annotation | HTML | UniProt accession | http://www.pmma.pmfhk.cz/cgi-bin/get-2d-entry?%s
Example UniProt accession | P63101

ID      Rat-heart-2DPAGE
Acc     DB-0087
Name    2-DE database of rat heart, at German Heart Institute Berlin, Germany
Desc    2-DE database of rat heart, at German Heart Institute Berlin, Germany
Cat     2D gel databases
URL     http://www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d/
Taxon   9606 | Homo sapiens
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2372 | 2D PAGE spot annotation
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   2D PAGE spot annotation | HTML | UniProt accession | http://www.mpiib-berlin.mpg.de/mpiib-cgi/RAT-HEART/get-2d-entry?%s
Example UniProt accession | P62738

ID      RATMAP
Name    RATMAP rat genome database
Desc    Rat genome database.
URL     http://ratmap.gen.gu.se/
Cat     Not available
Taxon   10114 | Rattus
EDAMtpc 2820 | Vertebrates
Xref    SP_FT | None
Example Identifier | 5

ID      RDG
Name    Rat genome database (RDG)
Desc    Rat genome database.
URL     http://rgd.mcw.edu/
Cat     Not available
Taxon   10114 | Rattus
EDAMtpc 2820 | Vertebrates
Xref    SP_FT | None

ID      RB1GeneMutation
Name    RB1 gene mutation database (RB1GeneMutation)
Desc    Retinoblastoma genetics database.
URL     http://www.verandi.de/joomla/
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      Reactome
Acc     DB-0088
Name    Reactome knowledgebase of biological pathways
Desc    Curated knowledgebase of biological pathways and processes.
URL     http://www.reactome.org/
URLlink http://www.reactome.org/referring2GK.html
URLsoap http://www.reactome.org/download/index.html
Cat     Enzyme and pathway databases
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models
EDAMdat 2984 | Pathway or network report
EDAMdat 0896 | Protein report
EDAMid  0989 | Protein identifier
EDAMid  3021 | UniProt accession
EDAMid  1027 | Gene ID (NCBI)
EDAMid  1011 | EC number
EDAMid  1174 | ChEBI ID
EDAMid  1056 | Database name
EDAMid  0990 | Compound name
EDAMid  1155 | Pathway ID (reactome)
EDAMid  1176 | GO term ID
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | Pathway ID (reactome)
Query   Pathway or network report | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%s&ZOOM=2
Query   Pathway or network report | XML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/sbml_export?DB=gk_current&ID=%s
Query   Protein report {Reactome entry} | HTML | Database name;Protein identifier | http://www.reactome.org/cgi-bin/link?SOURCE=%s1&ID=%s2
Query   Protein report {Reactome entry} | HTML | UniProt accession | http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=%s
Query   Protein report {Reactome entry} | HTML | ChEBI ID | http://www.reactome.org/cgi-bin/link?SOURCE=CHEBI&ID=%s
Query   Protein report {Reactome entry} | HTML | Compound name | http://www.reactome.org/cgi-bin/link?SOURCE=COMPOUND&ID=%s
Query   Protein report {Reactome entry} | HTML | GO term ID | http://www.reactome.org/cgi-bin/link?SOURCE=GO&ID=%s
Query   Protein report {Reactome entry} | HTML | EC number | http://www.reactome.org/cgi-bin/link?SOURCE=EC&ID=%s
Query   Protein report {Reactome entry} | HTML | Gene ID (NCBI) | http://www.reactome.org/cgi-bin/link?SOURCE=Entrez+Gene&ID=%s
Query   Protein report {Reactome entry} | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/link?SOURCE=Reactome&ID=%s
Example UniProt accession | P30304
Example ChEBI ID | 15422
Example Compound name | C00002
Example GO term ID | 0030060
Example EC number | 1.1.1.37
Example Gene ID (NCBI) | 4171
Example Pathway ID (reactome) | REACT_1

ID      REBASE
Acc     DB-0089
Name    REBASE restriction enzymes and methylases database
Desc    Restriction enzymes and methylases database.
URL     http://rebase.neb.com/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMdat 1509 | Protein report (enzyme)
EDAMid  1012 | Enzyme name
EDAMid  2325 | REBASE enzyme number
EDAMfmt 2331 | HTML
Xref    SP_explicit | REBASE enzyme number
Query   Protein report (enzyme) | HTML | Enzyme name | http://rebase.neb.com/rebase/enz/%s.html
Query   Protein report (enzyme) | HTML | REBASE enzyme number | http://rebase.neb.com/rebase/enz/%s.html
Example Enzyme name | EcoRI
Example REBASE enzyme number | 993

ID      RECODE
Name    RECODE
Desc    Information on 'programmed' translational recoding events taken from the literature and personal communications, including programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. RECODE entries include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, and factors such as cis-elements that influence recoding.
URL     http://recode.genetics.utah.edu
NARid   21
NARCat  /nar/database/cat/1 | Nucleotide Sequence Databases
NARSub  /nar/database/subcat/1/2 | Coding and non-coding DNA
EDAMtpc 0617 | Ribosomal genes and proteins
Abstrct http://nar.oupjournals.org/cgi/content/abstract/31/1/87

ID      REDIdb
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.
URL     http://biologia.unical.it/py_script/overview.html
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMdat 2043 | Sequence record lite
EDAMdat 1383 | Sequence alignment (nucleic acid)
EDAMid  2781 | REDIdb ID
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2331 | HTML
Query   Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s
Query   Sequence record lite {REDIdb fasta} | FASTA-HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s
Query   Sequence alignment (nucleic acid) {REDIdb overview} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s
Query   Sequence alignment (nucleic acid) {REDIdb alignment} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/align.py?query=%s
Example REDIdb ID  | EDI_000000002

ID      RefSeq
Acc     DB-0117
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.
URL     http://www.ncbi.nlm.nih.gov/RefSeq/
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 3041 | Sequence databases
EDAMtpc 0797 | Comparative genomics
EDAMdat 0849 | Sequence record
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier {Refseq}
Query   Sequence record {RefSeq entry} | HTML | Protein identifier {Refseq} | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=%s
Example Protein identifier {Refseq} | YP_654574.1


ID      REPAIRtoire
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.
URL     http://repairtoire.genesilico.pl/
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models

ID      REPRODUCTION-2DPAGE
IDalt   REPRODUCTION2DPAGE
Acc     DB-0090
Name    REPRODUCTION-2DPAGE database
Desc    REPRODUCTION-2DPAGE 2D gel protein database.
URL     http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMid  3021 | UniProt accession
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s&format=text
Query   Experiment annotation (2D PAGE) | Text | UniProt accession | http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s
Example UniProt accession | P00352


ID      RESID
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.
URL     http://www.ebi.ac.uk/RESID/
Taxon   1 | all
EDAMtpc 0601 | Protein modifications
EDAMtpc 0166 | Protein structural motifs and surfaces
EDAMdat 2191 | Protein modification annotation
EDAMid  2619 | RESID ID
EDAMfmt 2332 | XML
Query   Protein modification annotation {RESID entry} | XML | RESID ID | http://www.ebi.ac.uk/ontology-lookup/RESIDService?resid_id=%s
Example RESID ID | AA0002

ID      RetrOryza
Name    RetrOryza database of rice LTR retrotransposons
Desc    Information and resources related to LTR-retrotransposons in rice genome.
URL     http://www.retroryza.org
Taxon   4530 | Oryza sativa
EDAMtpc 0798 | Mobile genetic elements
EDAMtpc 0780 | Plants

ID      RFAM
IDalt   RFam
Name    RNA families database of alignments and CMs
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.
URL     http://rfam.sanger.ac.uk/
Cat     Not available
Taxon   1 | all
EDAMtpc 0740 | Nucleic acid sequence alignment
EDAMtpc 0697 | RNA structure and alignment
EDAMdat 2354 | RNA family annotation
EDAMid  2356 | RFAM accession
EDAMid  2606 | RFAM name
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    EMBL_explicit | RFAM accession
Query   RNA family annotation | HTML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s
Query   RNA family annotation | HTML | RFAM name | http://rfam.sanger.ac.uk/family?acc=%s
Query   RNA family annotation | XML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s&output=xml
Query   RNA family annotation | XML | RFAM name | http://rfam.sanger.ac.uk/family?acc=%s&output=xml
Example RFAM accession | RF00522
Example RFAM name | PreQ1

ID      RGD
Acc     DB-0091
Name    Rat genome database
Desc    Rat genome database (RGD) goal is to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.
URL     http://rgd.mcw.edu/
Cat     Organism-specific databases
Taxon   10114 | Rattus
EDAMtpc 2820 | Vertebrates
EDAMdat 0916 | Gene annotation
EDAMid  2620 | RGD ID
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | RGD ID
Query   Gene annotation {RGD report} | HTML | RGD ID | http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=[%s]
Query   Gene annotation {RGD report} | XML | RGD ID | http://rgd.mcw.edu/rgdweb/search/genes.html?term=%s&speciesType=3&fmt=6
Example RGD ID | 620528

ID      Rhea
Name    Rhea
Desc    A reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. 
URL     http://www.ebi.ac.uk/rhea/about.xhtml
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions

ID      Rouge
Acc     DB-0092
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).
URL     http://www.kazusa.or.jp/rouge/
Cat     Organism-specific databases
Taxon   10088 | Mus
EDAMtpc 0639 | Protein sequence analysis
EDAMtpc 0213 | Mice or rats
EDAMdat 2394 | Gene annotation (functional)
EDAMid  2393 | mFLJ/mKIAA number
EDAMfmt 2331 | HTML
Xref    SP_implicit | mFLJ/mKIAA number
Query   Gene annotation (functional) {Rouge entry} | HTML | mFLJ/mKIAA number | http://www.kazusa.or.jp/rouge/gfpage/%s
Example mFLJ/mKIAA number | mFLJ00002

ID      RISSC
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.
URL     http://egg.umh.es/rissc
Taxon   1 | all
EDAMtpc 0617 | Ribosomal genes and proteins

ID      RNA-FRABASE
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.
URL     http://rnafrabase.ibch.poznan.pl/
Taxon   1 | all
EDAMtpc 0697 | RNA structure and alignment

ID      RNAVirusDB
Name    RNA virus genome database (RNAVirusDB)
Desc    RNA virus genome database.
URL     http://tree.bio.ed.ac.uk/rnavirusdb
Taxon   10239 | Viruses
EDAMtpc 0781 | Viruses
EDAMdat 2307 | Virus annotation
EDAMid  2784 | RNAVirusDB ID
EDAMfmt 2331 | HTML
Query   Virus annotation | HTML | RNAVirusDB ID | http://tree.bio.ed.ac.uk/rnavirusdb/virus.php?id=%s
Example RNAVirusDB ID | 56486

ID      RNRdb
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.
URL     http://rnrdb.molbio.su.se/
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources
EDAMtpc 0698 | Protein tertiary structure

ID      RsiteDB
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.
URL     http://bioinfo3d.cs.tau.ac.il/RsiteDB/
Taxon   1 | all
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0149 | Protein-nucleic acid interactions

ID      RTKdb
Name    Receptor tyrosine kinase database (RTKdb)
Desc    Receptor tyrosine kinase database.
URL     http://pbil.univ-lyon1.fr/RTKdb/
Taxon   2759 | Eukaryota
EDAMtpc 0635 | Specific protein resources

ID      RTPrimerDB
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.
URL     http://medgen.ugent.be/rtprimerdb/
Taxon   1 | all
EDAMtpc 0632 | Probes and primers

ID      S_MARtDB
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.
URL     http://smartdb.bioinf.med.uni-goettingen.de/
Taxon   2759 | Eukaryota
EDAMtpc 0635 | Specific protein resources

ID      S4
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.
URL     http://compbio.mds.qmw.ac.uk/S4.html
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment

ID      SABIO-RK
Name    Database for biochemical reactions and their kinetics.
Desc    Biochemical pathways and reaction kinetics.
URL     http://sabio.villa-bosch.de/SABIORK
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models
EDAMdat 2093 | Data reference
EDAMdat 2024 | Enzyme kinetics data
EDAMdat 0908 | Reaction annotation
EDAMid  2309 | Reaction ID (SABIO-RK)
EDAMid  2648 | Reaction kinetics ID (SABIO-RK)
EDAMid  1011 | EC number
EDAMfmt 2331 | HTML
Query   Reaction annotation {SABIO-RK reaction} | HTML | Reaction ID (SABIO-RK) | http://sabio.h-its.org/index2.jsp?reac=%s
Query   Enzyme kinetics data {SABIO-RK Kinetic Record} | HTML | Reaction kinetics ID (SABIO-RK) | http://sabio.h-its.org/kineticLawEntry.jsp?kinlawid=%s
Query   Data reference {SABIO-RK EC code} | HTML | EC number | http://sabio.h-its.org/index2.jsp?EC=%s
Example Reaction ID (SABIO-RK) | 75
Example Reaction kinetics ID (SABIO-RK) | 5046
Example EC number | 2.1.1.45

ID      Saffron_Genes
Name    Saffron genes database
Desc    EST sequences from saffron (Crocus sativus) stigmas.
URL     http://www.saffrongenes.org
Taxon   82528 | Crocus sativus
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 0623 | Genes, gene family or system


ID      SCOP
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.
URL     http://scop.mrc-lmb.cam.ac.uk/scop
Taxon   1 | all
EDAMtpc 0736 | Protein domains and folds
EDAMdat 1554 | SCOP node
EDAMdat 2093 | Data reference
EDAMid  1042 | SCOP sunid
EDAMid  1127 | PDB ID
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Query   SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Query   Data reference {PDB Entry search} | HTML | PDB ID | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?PDB=%s
Query   Data reference | HTML | Identifier {Keyword} | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s
Example SCOP sunid | 47718
Example PDB ID | 1djh
Example Identifier {Keyword} | immunoglobulin

ID      SCOPPI
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.
URL     http://www.scoppi.org
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions

ID      SCOWL
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.
URL     http://www.scowlp.org
Taxon   1 | all
EDAMtpc 0128 | Protein interactions
EDAMdat 2359 | Domain-domain interaction
EDAMid  1127 | PDB ID
EDAMid  1042 | SCOP sunid
EDAMfmt 2331 | HTML
Query   Domain-domain interaction | HTML | PDB ID | http://www.scowlp.org/scowlp/PDB.action?show=&PDBId=%s
Query   Domain-domain interaction | HTML | SCOP sunid {SCOP family id} | http://www.scowlp.org/scowlp/Search.action?childs=&currentChoice=SCOP_FAMILY%s
Example PDB ID | 1fxk
Example SCOP sunid | 2381635

ID      SeattleSNPs
Name    SeattleSNPs variation discovery resource
Desc    Database for identifying, genotyping, and modelling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.
URL     http://pga.gs.washington.edu/
Cat     Polymorphism databases
Taxon   9606 | Homo sapiens
EDAMtpc 2277 | SNPs
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0625 | Genotype and phenotype resources
EDAMdat 0916 | Gene annotation
EDAMid  1791 | Gene name (HGNC)
EDAMfmt 2331 | HTML
Xref    SP_implicit | Gene name (HGNC)
Query   Gene annotation | HTML | Gene name (HGNC) | http://pga.gs.washington.edu/data/%s/
Example Gene name (HGNC) | a4galt

ID      Sebida
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.
URL     http://www.sebida.de
Taxon   7164 | Anophelea
Taxon   7215 | Drosophila
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0197 | Gene expression resources

ID      SEED
Name    The SEED genome comparison environment
Desc    Environment for comparative genome analysis.
URL     http://www.theseed.org/
Cat     Not available
Taxon   1 | all
EDAMtpc 0797 | Comparative genomics
EDAMdat 2711 | Genome metadata
EDAMdat 2394 | Gene annotation (functional)
EDAMdat 0916 | Gene annotation
EDAMid  2737 | FIG ID
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Genome metadata | HTML | FIG ID {Genome fig} | http://www.theseed.org/linkin.cgi?genome=fig|%s
Query   Gene annotation (functional) | HTML | FIG ID {PEG ID} | http://www.theseed.org/linkin.cgi?id=fig|%s
Query   Gene annotation {RNA feature} | HTML | FIG ID {RNA fig} | http://www.theseed.org/linkin.cgi?id=fig|%s
Example FIG ID {Genome fig} | 83333.1
Example FIG ID {PEG ID} | 83333.1.peg.123
Example FIG ID {RNA fig} | 83333.1.rna.1

ID      Selectome
Name    Selectome database of positive selection
Desc    Database of positive selection based on a rigorous branch-site specific likelihood test.
URL     http://bioinfo.unil.ch/selectome/
Taxon   1 | all
EDAMtpc 0084 | Phylogenetics
EDAMtpc 0623 | Genes, gene family or system
EDAMdat 0872 | Phylogenetic tree
EDAMdat 2093 | Data reference
EDAMdat 0916 | Gene annotation
EDAMid  1131 | Protein family name
EDAMid  0842 | Identifier
EDAMid  0989 | Protein identifier
EDAMid  1127 | PDB ID
EDAMid  1868 | Taxon
EDAMfmt 2331 | HTML
Query   Phylogenetic tree {Selectome entry} | HTML | Identifier {Selectome identifier};Protein family name;Taxon | http://bioinfo.unil.ch/cgi-bin/selectome/subfamily.cgi?ac=%s1&sub=%s2&taxon=%s3
Query   Gene annotation {Selectome family} | HTML | Identifier {Selectome identifier} | http://bioinfo.unil.ch/cgi-bin/selectome/getFamily.cgi?query=%s
Query   Data reference {Selectome Xref} | HTML | Protein identifier {Cross-reference} | http://bioinfo.unil.ch/cgi-bin/selectome/getXref.cgi?query=%s
Query   Data reference {Selectome Xref} | HTML | PDB ID {Cross-reference} | http://bioinfo.unil.ch/cgi-bin/selectome/getXref.cgi?query=%s
Query   Data reference {Selectome genes} | HTML | Identifier {Keyword} | http://bioinfo.unil.ch/cgi-bin/selectome/getGene.cgi?query=%s
Query   Data reference {Selectome gene family} | HTML | Identifier {Keyword} | http://bioinfo.unil.ch/cgi-bin/selectome/getGeneFamily.cgi?query=%s
Example Identifier {Selectome identifier} | TF105041
Example Identifier {Selectome identifier};Protein family name;Taxon | TF105041;1;v
Example PDB ID | 1HCL
Example Protein identifier | P24941
Example Identifier {Keyword} | kidney
Example Identifier {Keyword} | Ascc3_F2
Example Identifier {Keyword} | BRCA2

ID      SGD
Acc     DB-0095
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.
URL     http://www.yeastgenome.org/
Cat     Organism-specific databases
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 2817 | Yeast
EDAMtpc 0782 | Fungi
EDAMdat 0916 | Gene annotation
EDAMid  1026 | Gene symbol
EDAMid  1807 | ORF name
EDAMid  1901 | Locus ID (SGD)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Locus ID (SGD)
Query   Gene annotation {Locus Summary page (gene page)} | HTML | Locus ID (SGD) | http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=%s
Query   Gene annotation {Locus Summary page (gene page)} | HTML | ORF name | http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=%s
Query   Gene annotation {Locus Summary page (gene page)} | HTML | Gene symbol | http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=%s
Example Locus ID (SGD) | S000000981
Example ORF name | YER179W
Example Gene symbol | DMC1

ID      Siena-2DPAGE
Acc     DB-0096
Name    2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy
Desc    2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy
Cat     2D gel databases
URL     http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi
Taxon   9606 | Homo sapiens
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2372 | 2D PAGE spot annotation
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   2D PAGE spot annotation | HTML | UniProt accession | http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi?%s
Example UniProt accession | P31937


ID      SignalingGateway
Name    UCSD-Nature Signaling Gateway Molecule Pages
Desc    Information on over 4000 proteins involved in cellular signaling. Each 'molecule page' contains regularly updated information derived from public data sources as well as sequence analysis, references and links to other databases.
URL     http://www.signaling-gateway.org/molecule/
Taxon   1 | all
EDAMtpc 0754 | Signaling pathways

ID      SILVA-LSU
Name    SILVA ribosomal RNA sequence data (large subunit)
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).
URL     http://www.arb-silva.de
Taxon   1 | all
EDAMtpc 0660 | rRNA
EDAMtpc 0640 | Nucleic acid sequence analysis
EDAMdat 0855 | Sequence metadata
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2331 | HTML
Xref    EMBL_explicit | Sequence accession (nucleic acid)
Query   Sequence metadata {SILVA database entry 23S/28S} | HTML | Sequence accession (nucleic acid) | http://www.arb-silva.de/browser/lsu/%s
Example Sequence accession (nucleic acid) | AB426552

ID      SILVA-SSU
Name    SILVA ribosomal RNA sequence data (small subunit)
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).
URL     http://www.arb-silva.de
Taxon   1 | all
EDAMtpc 0660 | rRNA
EDAMtpc 0640 | Nucleic acid sequence analysis
EDAMdat 0855 | Sequence metadata
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2331 | HTML
Xref    EMBL_explicit | Sequence accession (nucleic acid)
Query   Sequence metadata {SILVA database entry} | HTML | Sequence accession (nucleic acid) | http://www.arb-silva.de/browser/ssu/%s
Example Sequence accession (nucleic acid) | AB426552

ID      SIMAP
Name    Similarity matrix of proteins (SIMAP)
Desc    Pre-calculated protein similarities. It contains published protein sequences and is continuously updated.
URL     http://boinc.bio.wzw.tum.de/boincsimap/
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMdat 0896 | Protein report
EDAMdat 0857 | Database hits (sequence)
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Query   Protein report | HTML | Identifier {md5 hash of sequence} | http://webclu.bio.wzw.tum.de/portal/web/simap/link?p_p_id=LinkPortlet_WAR_SIMAP&p_p_action=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-2&p_p_col_count=2&method=proteinReport&md5=%s
Query   Database hits (sequence) {SIMAP sequence similarities} | HTML | Identifier {md5 hash of sequence} | http://webclu.bio.wzw.tum.de/portal/web/simap/link?p_p_id=LinkPortlet_WAR_SIMAP&p_p_action=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-2&p_p_col_count=2&method=sequenceHomologs&md5=%s
Query   Protein report {SIMAP domain architecture similarities} | HTML | Identifier {md5 hash of sequence} | http://webclu.bio.wzw.tum.de/portal/web/simap/link?p_p_id=LinkPortlet_WAR_SIMAP&p_p_action=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-2&p_p_col_count=2&method=domainHomologs&md5=%s
Example Identifier {md5 hash of sequence} | 5bd410d0d1f3fa2c0607eb453835857f

ID      siRNAdb
Name    siRNAdb database
Desc    siRNAdb database
URL     http://sirna.sbc.su.se/sirnadb_050915.txt
Taxon   1 | all
! EDAMtpc 0662 | siRNA
EDAMtpc 3060 | Regulatory RNA

ID      SISYPHUS
Name    SISYPHUS database of protein structure alignments
Desc    Structural alignments for proteins with non-trivial relationships.
URL     http://sisyphus.mrc-cpe.cam.ac.uk
Taxon   1 | all
EDAMtpc 2826 | Protein structure alignment
EDAMdat 1481 | Structure alignment (protein)
EDAMid  2793 | SISYPHUS ID
EDAMfmt 2332 | XML
Query   Structure alignment (protein) {SISYPHUS alignment} | XML | SISYPHUS ID | http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query=%s
Example SISYPHUS ID | AL00050692

ID      SitesBase
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.
URL     http://www.modelling.leeds.ac.uk/sb/
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0148 | Protein-ligand interactions
EDAMtpc 0741 | Protein sequence alignment

ID      SMPDB
Name    Small Molecule Pathway Database (SMPDB)
Desc    Small molecule pathways found in humans. It provides detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. 
URL     http://www.smPDB.ca/
Taxon   9606 | Homo sapiens
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0079 | Metabolites

ID      SMART
Acc     DB-0097
Name    Simple modular architecture research tool (SMART)
Desc    SMART protein domain database.
URL     http://smart.embl.de/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0736 | Protein domains and folds
EDAMdat 2377 | Protein structure report (domain)
EDAMid  1139 | SMART accession number
EDAMid  2782 | SMART domain name
EDAMfmt 2331 | HTML
Xref    SP_explicit | SMART accession number
Query   Protein structure report (domain) {SMART entry} | HTML | SMART domain name | http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY
Query   Protein structure report (domain) {SMART entry} | HTML | SMART accession number | http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY
Example SMART domain name | KISc
Example SMART accession number | SM00129

ID      SMD
Name    Stanford Microarray Database
Desc    Data from microarray experiments, including information from the literature and diverse biological annotation.
URL     http://genome-www.stanford.edu/microarray
NARid   22
NARCat  /nar/database/cat/9 | Microarray Data and other Gene Expression Databases
Abstrct http://nar.oupjournals.org/cgi/content/abstract/35/suppl_1/D766

ID      SMR
Acc     DB-0098
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.
URL     http://swissmodel.expasy.org/repository/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure
EDAMdat 1460 | Protein structure
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Protein structure {SMR entry} | HTML | UniProt accession | http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s
Example UniProt accession | P01009

ID      SNAP
Name    SNAP database of human gene variations
Desc    Human gene variations.
URL     http://platform.humgen.au.dk/
Taxon   9606 | Homo sapiens
EDAMtpc 0199 | Genetic variation

ID      SNAPPI
Name    SNAPPI database of structures, interfaces and alignments for protein-protein interactions
Desc    Structures, interfaces and alignments for protein-protein interactions.
URL     http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0698 | Protein tertiary structure
EDAMtpc 0741 | Protein sequence alignment

ID      Sno_scaRNAbase
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.
URL     http://gene.fudan.sh.cn/snoRNAbase.nsf
Taxon   2759 | Eukaryota
! EDAMtpc 0664 | snRNA
EDAMtpc 0659 | Functional RNA

ID      snoRNABase
IDalt   snoRNA-LBME-db
Name    snoRNABase database of human H/ACA and C/D box snoRNAs
Desc    Human H/ACA and C/D box snoRNAs.
URL     http://www-snorna.biotoul.fr/
Taxon   9606 | Homo sapiens
! EDAMtpc 0664 | snRNA
EDAMtpc 0659 | Functional RNA

ID      SNPeffect
Name    SNPeffect database of molecular phenotyping of human SNPs and disease mutations
Desc    Molecular phenotyping of human SNPs and disease mutations.
URL     http://snpeffect.vib.be
Taxon   9606 | Homo sapiens
EDAMtpc 2277 | SNPs
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 0625 | Genotype and phenotype resources

ID      SNPnexus
Name    SNPnexus database for SNP selection
Desc    SNP selection database.
URL     http://www.snp-nexus.org
Taxon   9606 | Homo sapiens
EDAMtpc 2277 | SNPs

ID      SNPSTR
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.
URL     http://www.sbg.bio.ic.ac.uk/~ino/cgi-bin/SNPSTRdatabase.html
Taxon   9606 | Homo sapiens
EDAMtpc 0796 | Genetic mapping and linkage
EDAMtpc 2277 | SNPs

ID      SOURCE
Acc     DB-0099
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.
URL     http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch
Cat     Other
Taxon   9606 | Homo sapiens
Taxon   10088 | Mus
Taxon   10114 | Rattus
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMdat 2703 | Gene annotation (clone or EST)
EDAMid  1108 | GenBank accession
EDAMid  2704 | Clone ID (IMAGE)
EDAMfmt 2331 | HTML
Xref    SP_implicit | GenBank accession
Query   Gene annotation (clone or EST) | HTML | Clone ID (IMAGE) | http://smd.stanford.edu/cgi-bin/source/sourceResult?option=CloneID&criteria=%s&choice=cDNA
Query   Gene annotation (clone or EST) | HTML | GenBank accession | http://smd.stanford.edu/cgi-bin/source/sourceResult?option=Number&criteria=%s&choice=cDNA
Example Clone ID (IMAGE) | IMAGE:611245
Example GenBank accession | AA603779

ID      SoyBase
Name    SoyBase soybean genome database
Desc    Database of soybean genetics and molecular biology.
URL     http://soybase.agron.iastate.edu/
Cat     Not available
Taxon   3847 | Glycine max
EDAMtpc 0780 | Plants
Xref    SP_FT | None


ID      SpliceAid
Name    SpliceAid database of strictly experimentally assessed target RNA sequences in humans
Desc    Experimental RNA target motifs bound by splicing proteins in humans.
URL     http://www.introni.it/splicing.html
Taxon   9606 | Homo sapiens
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMdat 0896 | Protein report
EDAMid  1009 | Protein name
EDAMfmt 2331 | HTML
Query   Protein report | HTML | Protein name | http://193.206.120.228/cgi-bin/SpliceAid.pl?Protein_name=%s
Example Protein name | 9G8

ID      SpliceNest
Name    SpliceNest database
Desc    Visualizing splicing of genes from EST Data, based on mappings of the GeneNest EST Contigs to genomic sequence.
URL     http://splicenest.molgen.mpg.de/
Taxon   2759 | Eukaryota
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMtpc 0655 | mRNA, EST or cDNA

ID      SpodoBase
Name    Spodoptera frugiperda database (SpodoBase)
Desc    An integrated database for the genomics of the Lepidoptera Spodoptera frugiperda.
URL     http://bioweb.ensam.inra.fr/spodobase/
Taxon   7108 | Spodoptera frugiperda
EDAMtpc 2819 | Invertebrates

ID      STCDB
Name    Signal transduction classification database (STCDB)
Desc    Signal transduction classification.
URL     http://bibiserv.techfak.uni-bielefeld.de/stcdb/
Taxon   1 | all
EDAMtpc 0754 | Signaling pathways

ID      STITCH
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.
URL     http://stitch.embl.de
Taxon   1 | all
EDAMtpc 0148 | Protein-ligand interactions

ID      StrainInfo.net
Name    StrainInfo.net bioportal
Desc    Search the holdings of multiple biological resource centres (BRCs) through a single web interface.
URL     http://www.straininfo.net
Taxon   1 | all
EDAMtpc 0607 | Laboratory resources

ID      Strepto-DB
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.
URL     http://www.oger.tu-bs.de/strepto_db/
Taxon   1301 | Streptococcus
EDAMtpc 0797 | Comparative genomics

ID      STRING
Acc     DB-0141
Name    STRING protein-protein interaction database
Desc    Known and predicted protein-protein interactions.
URL     http://string-db.org/
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMid  2302 | STRING ID
EDAMdat 1663 | Pathway or network (protein-protein interaction)
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Query   Pathway or network (protein-protein interaction) | HTML | STRING ID | http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=%s&all_channels_on=1&interactive=no&network_flavor=evidence&targetmode=proteins
Query   Pathway or network (protein-protein interaction) | XML | STRING ID | http://string-db.org/api/psi-mi/interactions?identifier=%s
Example STRING ID | 9606.ENSP00000359866

ID      StructurallyConservedInterfaces
Name    Structurally conserved interfaces
Desc    Structures of protein-protein interfaces from PDB.
URL     http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0698 | Protein tertiary structure

ID      Sulfolobus
Name    Sulfolobus genome database
Desc    The three sequenced Sulfolobus genomes.
URL     http://www.sulfolobus.org
Taxon   2284 | Sulfolobus
EDAMtpc 1811 | Prokaryotes and archae

ID      SuperDrug
Name    SuperDrug drug database
Desc    Drug compounds with conformers.
URL     http://bioinformatics.charite.de/superdrug
Taxon   None
EDAMtpc 0620 | Drugs and targets

ID      SUPFAM
IDalt   SUPERFAMILY
Acc     DB-0155
Name    Superfamily database of structural and functional annotation
Desc    Structural and functional protein annotations (via HMM library) for all completely sequenced organisms.
URL     http://supfam.org
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0188 | Sequence profiles and HMMs

ID      SuperHapten
Name    SuperHapten immunogenic compound database
Desc    Database of haptens, related antibodies and carriers.
URL     http://bioinformatics.charite.de/superhapten
Cat     NoneE
Taxon   1 | all
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMtpc 0154 | Small molecules

ID      SuperNatural
Name    SuperNatural natural compound database
Desc    A searchable database of natural compounds.
URL     http://bioinformatics.charite.de/supernatural
Taxon   None
EDAMtpc 0154 | Small molecules

ID      Superscent
Name    Superscent database of scents
Desc    Database of scent molecules.
URL     http://bioinformatics.charite.de/superscent
Taxon   None
EDAMtpc 0154 | Small molecules

ID      SuperSite
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.
URL     http://bioinf-services.charite.de/supersite/
Taxon   1 | all
EDAMtpc 0620 | Drugs and targets
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0148 | Protein-ligand interactions
EDAMtpc 0079 | Metabolites

ID      SuperTarget-Matador
Name    SuperTarget and Matador database
Desc    Enzyme, drug and pathways database.
URL     http://insilico.charite.de/supertarget
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0620 | Drugs and targets
EDAMtpc 0821 | Enzymes and reactions

ID      Supertoxic
Name    Supertoxic toxic compounds database
Desc    Database of toxic compounds with synonyms.
URL     http://bioinformatics.charite.de/supertoxic
Taxon   None
EDAMtpc 0154 | Small molecules

ID      SURFACE
Name    SURFACE database of protein surface patches
Desc    Surface residues and functions, annotated, compared and evaluated.
URL     http://cbm.bio.uniroma2.it/surface
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0698 | Protein tertiary structure
EDAMtpc 0166 | Protein structural motifs and surfaces

ID      WORLD-2DPAGE_CGL14067-2DPAGE
IDalt   CGL14067-2DPAGE
Name    World-wide gel-based proteomics database (CGL14067-2DPAGE)
Desc    World-wide gel-based proteomics database (CGL14067-2DPAGE)
URL     http://www.expasy.org/world-2dpage/
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=cgl14067-2dpage
Example Sequence accession (protein) | O31139

ID      WORLD-2DPAGE_NIBR_2D-PAGE
IDalt   NIBR 2D-PAGE
Name    World-wide gel-based proteomics database (NIBR 2D-PAGE)
Desc    World-wide gel-based proteomics database (NIBR 2D-PAGE)
URL     http://www.expasy.org/world-2dpage/
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=nibr_2d-page
Example Sequence accession (protein) | O54520

ID      WORLD-2DPAGE_0003
IDalt   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.
URL     http://www.expasy.org/world-2dpage/
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0767 | Protein and peptide identification
EDAMtpc 0780 | Plants
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0003
Example Sequence accession (protein) | O65719

ID      WORLD-2DPAGE_0004
IDalt   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.
URL     http://www.expasy.org/world-2dpage/
Taxon   10114 | Rattus
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0004
Example Sequence accession (protein) | A7VJC3

ID      WORLD-2DPAGE_0005
IDalt   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.
URL     http://www.expasy.org/world-2dpage/
Taxon   33196 | Botrytis
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0005
Example Sequence accession (protein) | A6RHV6

ID      WORLD-2DPAGE_0006
IDalt   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.
URL     http://www.expasy.org/world-2dpage/
Taxon   7460 | Apis mellifera
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0006
Example Sequence accession (protein) | AAP49283.1

ID      SWISS-2DPAGE
Acc     DB-0101
Name    Two-dimensional polyacrylamide gel electrophoresis database (SWISS-2DPAGE)
Desc    Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.
URL     http://www.expasy.org/ch2d/
URLlink  http://www.expasy.org/expasy_urls.html#ch2d
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMdat 2372 | 2D PAGE spot annotation
EDAMid  0989 | Protein identifier
EDAMid  2374 | Spot serial number
EDAMid  3021 | UniProt accession
EDAMid  2791 | Reference map name (SWISS-2DPAGE)
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | Protein identifier | http://www.expasy.org/swiss-2dpage/%s
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.expasy.org/swiss-2dpage/%s
Query   Experiment annotation (2D PAGE) | Text | UniProt accession | http://www.expasy.org/swiss-2dpage/format=raw&extract&ac=%s
Query   2D PAGE spot annotation | HTML | Spot serial number | http://www.expasy.org/swiss-2dpage/spot=%s
Query   2D PAGE spot annotation {SWISS-2DPAGE protein list} | HTML | Reference map name (SWISS-2DPAGE) | http://www.expasy.org/swiss-2dpage/map=%s
Query   Experiment annotation (2D PAGE) {SWISS-2DPAGE reference map} | HTML | Reference map name (SWISS-2DPAGE) | http://www.expasy.org/swiss-2dpage/viewer&ac=all&map=%s
Query   2D PAGE spot annotation | HTML | Spot serial number | http://www.expasy.org/swiss-2dpage/spot=%s
Example UniProt accession | P01009
Example Spot serial number | 2D-0017PD
Example Reference map name (SWISS-2DPAGE) | LIVER_HUMAN

ID      SwissRegulon
Name    SwissRegulon database of regulatory site annotations
Desc    Genome-wide annotations of regulatory sites.
URL     http://www.swissregulon.unibas.ch
Taxon   1 | all
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0204 | Gene regulation resources
EDAMdat 2070 | Sequence motif (nucleic acid)
EDAMid  2735 | Database name (SwissRegulon)
EDAMid  2736 | Sequence feature ID (SwissRegulon)
EDAMfmt 2331 | HTML
Query   Sequence motif (nucleic acid) {SwissRegulon feature search results} | HTML | Database name (SwissRegulon);Sequence feature ID (SwissRegulon) | http://www.swissregulon.unibas.ch/swissregulon/cgi-bin/gbrowse/%s1/?name=%s2

ID      SYSTERS
Name    SYSTERS protein family database
Desc    Large-scale protein clustering based on sequence similarity.
URL     http://systers.molgen.mpg.de/
Taxon   1 | all
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0724 | Protein families

ID      Systomonas
Name    Systomonas database for systems biology of Pseudomonads
Desc    Molecular networks in pseudomonads with focus on Pseudomonas aeruginosa.
URL     http://www.systomonas.de/
Taxon   135621 | Pseudomondacaeae
EDAMtpc 0602 | Pathways, networks and models

ID      SysZNFC2H2
Name    C2H2 zinc finger gene database (SysZNFC2H2)
Desc    An information resource for C2H2 Zinc Finger genes in human and mouse.
URL     http://epgd.biosino.org/SysZNF
Taxon   9606 | Homo sapiens
Taxon   10088 | Mus
EDAMtpc 0623 | Genes, gene family or system

ID      T1Dbase
Name    Type 1 diabetes database (T1Dbase)
Desc    Database for type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.
URL     http://www.t1dbase.org/page/Welcome/display
Taxon   9606 | Homo sapiens
EDAMtpc 2813 | Disease genes and proteins

ID      TAED
Name    The adaptive evolution database (TAED)
Desc    Protein-encoding gene families.
URL     http://www.bioinfo.no/tools/TAED
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system

ID      TAIR
Acc     DB-0102
Name    The Arabidopsis information resource (TAIR)
Desc    Comprehensive information resources for Arabidopsis.
URL     http://www.arabidopsis.org/
URLlink  http://arabidopsis.org/about/linktotair.jsp
Cat     Organism-specific databases
Taxon   3701 | Arabidopsis
EDAMtpc 0780 | Plants
EDAMdat 0916 | Gene annotation
EDAMdat 2018 | Annotation
EDAMid  2387 | TAIR accession
EDAMid  1893 | Locus ID
EDAMid  2780 | Stock number (TAIR)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Locus ID
Query   Annotation {TAIR entry} | HTML | TAIR accession | http://arabidopsis.org/servlets/TairObject?accession=%s
Query   Gene annotation | HTML | Locus ID | http://arabidopsis.org/servlets/TairObject?type=locus&name=%s
Query   Annotation {TAIR stocks} | HTML | Stock number (TAIR) | http://arabidopsis.org/servlets/StockSearcher?action=detail&stock_number=%s
Example TAIR accession | Clone:1768
Example Locus ID | AT4G18960
Example Stock number (TAIR) | C00006

ID      TarBase
Name    miRNA target database (TarBase)
Desc    The database of experimentally supported targets.
URL     http://microrna.gr/tarbase
Taxon   1 | all
! EDAMtpc 0661 | miRNA
EDAMtpc 3060 | Regulatory RNA

ID      TassDB
Name    Tandem splice site database
Desc    TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors.
URL     http://helios.informatik.uni-freiburg.de/TassDB/
Taxon   1 | all
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMdat 1307 | Nucleic acid features (splice sites)
EDAMid  1026 | Gene symbol
EDAMfmt 2331 | HTML
Query   Nucleic acid features (splice sites) {Tandem splice site} | HTML | Gene symbol | http://gen100.imb-jena.de/TassDB2/emboss_access.pl?entry=%s
Example Gene symbol | AATF

ID      taxon
Name    NCBI's taxonomic identifier
Desc    NCBI's taxonomic identifier
URL     http://www.ncbi.nlm.nih.gov/Taxonomy/
Taxon   1 | all
EDAMtpc 0637 | Taxonomy
EDAMid  1179 | NCBI taxonomy ID
EDAMdat 3028 | Taxonomic data
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Taxonomic data {NCBI taxon} | HTML | NCBI taxonomy ID | http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s
Example NCBI taxonomy ID | 9606

ID      TBMap
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.
URL     http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap
Taxon   1 | all
EDAMtpc 0637 | Taxonomy
EDAMtpc 0084 | Phylogenetics

ID      TCACycle
Name    TCA cycle gene mutation database
Desc    TCA cycle gene mutation database.
URL     http://chromium.liacs.nl/lovd_sdh/home.php
URLrest http://www.gen2phen.org/post/development-lovd-restful-atom-webservice
Taxon   1 | all
EDAMtpc 0625 | Genotype and phenotype resources
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Query   Gene annotation | HTML | Gene symbol | http://chromium.liacs.nl/LOVDv.2.0-dev/api/rest.php/genes?search_symbol=%s
Example Gene symbol | CRYAA

ID      TCDB
Acc     DB-0135
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.
URL     http://www.tcdb.org/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0820 | Membrane proteins
EDAMtpc 0724 | Protein families
EDAMdat 1456 | Protein report (membrane protein)
EDAMid  2756 | TCID
EDAMfmt 2331 | HTML
Xref    SP_explicit | TCID
Query   Protein report (membrane protein) {TCDB entry} | HTML | TCID | http://www.tcdb.org/tcdb/index.php?tc=%s
Example TCID | 1.A.1.2.3

ID      TDR
Name    TDR targets database
Desc    Identification and ranking of targets against neglected tropical diseases.
URL     http://tdrtargets.org/
Taxon   1 | all
EDAMtpc 0202 | Pharmacoinformatics
EDAMtpc 0620 | Drugs and targets

ID      TTD
Name    Therapeutic Target Database (TTD)
Desc    A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information provided are fully referenced.
URL     http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp
Taxon   1 | all
EDAMtpc 0620 | Drugs and targets

ID      TIGR
Acc     DB-0103
Name    The bacterial database(s) of The Institute of Genome Research
Desc    The TIGR bacterial Genome Annotation Database.
Cat     Genome annotation databases
Taxon   2 | Bacteria
Taxon   2157 | Archaea
EDAMtpc 0780 | Plants
EDAMdat 0916 | Gene annotation
EDAMid  1899 | Locus ID (CMR)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Locus ID
Query   Gene annotation | HTML | Locus ID (CMR) | http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s
Example Locus ID (CMR) | BOV_A0688


ID      TIGRFAMs
Acc     DB-0104
Name    A protein family database
Desc    Protein families based on hidden Markov models (HMMs).
URL     http://www.tigr.org/TIGRFAMs/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0188 | Sequence profiles and HMMs
EDAMdat 2788 | Sequence profile metadata
EDAMid  1141 | TIGRFam ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | TIGRFam ID
Query   Sequence profile metadata {TIGRFAM entry} | HTML | TIGRFam ID | http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi?hmm_acc=%s
Example TIGRFam ID | TIGR01920

ID      TGI
Name    TIGR Gene Indices
Desc    An analysis of public Expressed Sequence Tags (EST) sequences including putative genes with functional annotation, links to mapping and genomic sequence data and links between orthologous and paralogous genes.
URL     http://www.tigr.org/tdb/tgi/
NARid   5
NARCat  /nar/database/cat/5 | Genomics Databases (non-vertebrate)
NARCat  /nar/database/cat/5 | Genomics Databases (non-vertebrate)
NARSub  /nar/database/subcat/5/17 | General genomics databases
NARCat  /nar/database/cat/7 | Human and other Vertebrate Genomes
NARSub  /nar/database/subcat/7/30 | Human ORFs
Abstrct http://nar.oupjournals.org/cgi/content/abstract/33/suppl_1/D71

ID      TmaDB
Name    Tissue microarray database
Desc    Tissue microarray (TMA) database for archiving all aspects of data associated with TMAs.
URL     http://www.bioinformatics.leeds.ac.uk/tmadb/
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0200 | Microarrays

ID      Tomatestdb
Name    An EST database from multiple Tomato species
Desc    A collection of tomato EST sequences downloaded from dbEST.
URL     http://biosrv.cab.unina.it/tomatestdb/
Taxon   4081 | Solanum lycopersicum
EDAMtpc 0655 | mRNA, EST or cDNA

ID      ToPDB
Name    Topology of transmembrane proteins
Desc    Transmembrane protein datasets containing experimentally derived topology information.
URL     http://toPDB.enzim.hu
Taxon   1 | all
EDAMtpc 0820 | Membrane proteins
EDAMdat 1456 | Protein report (membrane protein)
EDAMid  2789 | Protein ID (TopDB)
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Query   Protein report (membrane protein) {TOPDB entry} | HTML | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=HTML&id=%s
Query   Protein report (membrane protein) {TOPDB entry} | HTML {graphic} | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=Graph&id=%s
Query   Protein report (membrane protein) {TOPDB entry} | HTML {flash} | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=Flash&id=%s
Query   Protein report (membrane protein) {TOPDB entry} | XML | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=XML&id=%s
Example Protein ID (TopDB) | AP00085

ID      TOPDOM
Name    Transmembrane domains and motifs
Desc    A collection of domains and sequence motifs located conservatively in one side of transmembrane proteins.
URL     http://topdom.enzim.hu
Taxon   1 | all
EDAMtpc 0820 | Membrane proteins
EDAMtpc 0158 | Sequence motifs
EDAMtpc 0747 | Nucleic acid sites and features

ID      T3DB
Name    Toxin and Toxin Target Database (T3DB)
Desc    Toxin data with comprehensive toxin target information.  Toxins are described by synonyms and include pollutants, pesticides, drugs, and food toxins, which are linked to corresponding toxin target records. Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. 
URL     http://www.t3db.org/
Taxon   1 | all
EDAMtpc 2661 | Toxins and targets

ID      Transdab
Name    Database of transglutaminase substrate proteins
Desc    Database of transglutaminase substrate proteins.
URL     http://genomics.dote.hu/wiki
Taxon   1 | all
EDAMtpc 0635 | Specific protein resources
EDAMdat 0896 | Protein report
EDAMid  1009 | Protein name
EDAMfmt 2331 | HTML
Query   Protein report | HTML | Protein name | http://genomics.dote.hu/wiki/index.php/%s
Example Protein name | Histone_H1_%28kinase%29

ID      TRANSPATH
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.
URL     http://www.biobase.de/index.php?id=transpathdatabases
Taxon   1 | all
EDAMtpc 0754 | Signaling pathways
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0079 | Metabolites
EDAMtpc 0821 | Enzymes and reactions

ID      TranspoGene
Name    Transposed elements in proteins for 7 organisms
Desc    Data on the influence of Transposed Elements (TEs) on the transcriptome of 7 species.
URL     http://transpogene.tau.ac.il/
Taxon   1 | all
EDAMtpc 0798 | Mobile genetic elements

ID      TRBase
Name    Tandem repeats database
Desc    Tandem repeats in the human genome.
URL     http://trbase.ex.ac.uk/
Taxon   9606 | Homo sapiens
EDAMtpc 0641 | Repeat sequences

ID      TreeFam
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.
URL     http://www.treefam.org
Taxon   33208 | Metazoa
EDAMtpc 0084 | Phylogenetics
EDAMtpc 0623 | Genes, gene family or system

ID      tRNASequences
Name    tRNA sequences database
Desc    Compilation of tRNA sequences and sequence of tRNA genes.
URL     http://www.staff.uni-bayreuth.de/~btc914/search/index.html
Taxon   1 | all
EDAMtpc 0640 | Nucleic acid sequence analysis
EDAMtpc 0663 | tRNA
EDAMtpc 0623 | Genes, gene family or system

ID      TropGENE-DB
Name    TropGENE database
Desc    Genetic and genomic information about tropical crops studied by Cirad.
URL     http://tropgenedb.cirad.fr/
Taxon   58024 | Spermatophyta
EDAMtpc 0780 | Plants

ID      TrSDB
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.
URL     http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
Taxon   1 | all
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0621 | Genome, proteome and model organisms

ID      TubercuList
Acc     DB-0106
Name    Mycobacterium tuberculosis strain H37Rv genome database
Desc    Mycobacterium tuberculosis strain H37Rv genome database
URL     http://genolist.pasteur.fr/TubercuList/
Cat     Organism-specific databases
Taxon   1773 | Mycobacterium tuberculosis
EDAMtpc 1811 | Prokaryotes and archae
EDAMdat 0916 | Gene annotation
EDAMid  1097 | Sequence accession (nucleic acid)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Sequence accession (nucleic acid)
Query   Gene annotation | HTML | Sequence accession (nucleic acid) | http://genolist.pasteur.fr/TubercuList/genome.cgi?external_query+%s
Example Sequence accession (nucleic acid) | None

ID      U12DB
Name    U12-type intron database
Desc    U12-type intron database
URL     http://genome.imim.es/cgi-bin/u12db/u12db.cgi
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing

ID      UCD-2DPAGE
IDAlt   HSC-2DPAGE
Acc     DB-0047
Name    University College Dublin 2-DE Proteome Database
Desc    University College Dublin 2-DE Proteome Database
URL     http://proteomics-portal.ucd.ie:8082/cgi-bin/2d/2d.cgi
Cat     2D gel databases
Taxon   9606 | Homo sapiens
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2372 | 2D PAGE spot annotation
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   2D PAGE spot annotation | HTML | UniProt accession | http://proteomics-portal.ucd.ie:8082/cgi-bin/2d/2d.cgi?%s 

ID      UCSC
Acc     DB-0139
Name    UCSC genome browser
Desc    UCSC genome browser
URL     http://genome.ucsc.edu
Cat     Genome annotation databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMdat 0916 | Gene annotation
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Identifier {UCSC}
Query   Gene annotation | HTML | Identifier {UCSC} | http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=%s1&org=%s2
Example Identifier {UCSC}  | M117.2.2
Cmisc   Nucleic Acids Res. 37755-D761(2009); PubMed=18996895; DOI=10.1093/nar/gkn875;

ID      UMD-DMD
Name    UMD-DMD France genotype-phenotype dystrophinopathy patients
Desc    Knowledgebase related to mutations of the DMD gene.
URL     http://www.umd.be/DMD/
Taxon   9606 | Homo sapiens
EDAMtpc 0625 | Genotype and phenotype resources
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      UniGene
Acc     DB-0107
Name    UniGene gene-oriented nucleotide sequence clusters
Desc    Each UniGene entry is a set of transcript (expressed sequence tag) 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.
URL     http://www.ncbi.nlm.nih.gov/sites/entrez?db=UniGene
NARid   6
NARCat  /nar/database/cat/7 | Human and other Vertebrate Genomes
NARSub  /nar/database/subcat/7/30 | Human ORFs
Abstrct http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D35
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0722 | Nucleic acid classification
EDAMtpc 0197 | Gene expression resources
EDAMdat 2399 | Gene annotation (transcript)
EDAMid  2594 | UniGene taxon
EDAMid  1104 | Sequence cluster ID (UniGene)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Sequence cluster ID (UniGene)
Query   Gene annotation (transcript) | HTML | UniGene taxon;Sequence cluster ID (UniGene) | http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s1&CID=%s2
Example UniGene taxon | None
Example Sequence cluster ID (UniGene) | None

ID      UniHI
Name    Unified human interactome database
Desc    Protein interaction analysis.
URL     http://www.mdc-berlin.de/unihi
Taxon   9606 | Homo sapiens
EDAMtpc 0147 | Protein-protein interactions

ID      UNILIB
Name    Unified library database
Desc    A library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap.
URL     http://binfo.ym.edu.tw/edu/seminars/clho/UniLib Browser_kidney.htm
Taxon   1 | all
EDAMtpc 0655 | mRNA, EST or cDNA
Xref    SP_FT | None

ID      Unipathway
Name    Unipathway
Desc    A manually curated database of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway.
URL     http://www.grenoble.prabi.fr/obiwarehouse/unipathway
Taxon   1 | all
EDAMtpc 0753 | Metabolic pathways

ID      UniSave
Name    Uniprot version archive
Desc    A repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions.
URL     http://www.ebi.ac.uk/uniprot/unisave/
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis

ID      UniSTS
Name    NCBI database of sequence tagged sites
Desc    A comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.
URL     http://www.ncbi.nlm.nih.gov/unists
Taxon   1 | all
EDAMtpc 0796 | Genetic mapping and linkage
EDAMdat 0916 | Gene annotation
EDAMid  2389 | UniSTS accession
EDAMfmt 2331 | HTML
Query   Gene annotation {UniSTS entry} | HTML | UniSTS accession | http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=%s
Example UniSTS accession | 2019

ID      UNITE
Name    UNITE rDNA sequences from ectomycorrhizal asco- and basidiomycetes
Desc    UNITE is a rDNA sequence database focused on ectomycorrhizal asco- and basidiomycetes.
URL     http://unite.ut.ee/
Taxon   4751 | Fungi
EDAMtpc 0654 | DNA
EDAMdat 0855 | Sequence metadata
EDAMid  2390 | UNITE accession
EDAMfmt 2331 | HTML
Query   Sequence metadata {UNITE entry} | HTML | UNITE accession | http://unite.ut.ee/bl_forw.php?nimi=%s
Example UNITE accession | UDB000215

ID      UniTrap
Name    UniTrap gene trap clones
Desc    Tools for the biologist enabling optimized use of gene trap clones.
URL     http://unitrap.cbm.fvg.it/
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMdat 0916 | Gene annotation
EDAMid  1033 | Gene ID (Ensembl)
EDAMfmt 2331 | HTML
Query   Gene annotation {UniTrap entry} | HTML | Gene ID (Ensembl) | http://unitrap.cbm.fvg.it/gene.php?show_unitraps=1&show_domains=1&show_genes=1&ensembl_id=%s
Example Gene ID (Ensembl) | ENSMUSG00000025903

ID      UMD
Name    Universal mutation database
Desc    Collection of mutations in human genes associated with genetic diseases.
URL     http://umd.be
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins

ID      UniParc
Name    UniProt Archive
Desc    Part of UniProt project - a non-redundant archive of protein sequences extracted from public databases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, PIR-PSD, EMBL, EMBL WGS, Ensembl, IPI, PDB, PIR-PSD, RefSeq, FlyBase, WormBase, H-Invitational Database, TROME database, European Patent Office proteins, United States Patent and Trademark Office proteins (USPTO) and Japan Patent Office proteins.
URL     http://www.uniprot.org/
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 0849 | Sequence record
EDAMid  2392 | UniParc accession
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Sequence record {UniParc entry} | HTML | UniParc accession | http://www.uniprot.org/uniparc/%s
Example UniParc accession | UPI0000000001

ID      UniProt
IDalt   UniProtKB
Name    Universal protein resource
Desc    A comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
URL     http://www.uniprot.org/
Taxon   1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid  3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2188 | uniprot
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_FT | None
Query   Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query   Sequence record full | uniprot | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query   Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query   Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query   Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | P12345

ID      UniProtKB_Swiss-Prot
IDalt   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
URL     http://www.uniprot.org
Taxon   1 | all
EDAMdat 2201 | Sequence record full
EDAMtpc 0639 | Protein sequence analysis
EDAMid  3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    EMBL_explicit | UniProt accession
Query   Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query   Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query   Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query   Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query   Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | P12345

ID      UniProtKB_TrEMBL
IDalt   TrEMBL
Name    Universal protein resource knowledge base / Swiss-Prot
Desc    Section of the UniProt knowledgebase, containing computationally analysed records waiting for full manual annotation
URL     http://www.uniprot.org/
Taxon   1 | all
EDAMdat 2201 | Sequence record full
EDAMtpc 0639 | Protein sequence analysis
EDAMid  3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_FT | None
Query   Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query   Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query   Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query   Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query   Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | Q00177

ID      UniRef
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.
URL     http://www.uniprot.org/help/uniref
Cat     Other
Taxon   1 | all
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMfmt 1929 | FASTA format
EDAMdat 1245 | Sequence cluster (protein)
EDAMid  2347 | Sequence cluster ID (UniRef100)
EDAMid  2348 | Sequence cluster ID (UniRef90)
EDAMid  2349 | Sequence cluster ID (UniRef50)
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_implicit | UniProt accession
Query   Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s
Query   Sequence cluster (protein) | XML | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.xml
Query   Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.rdf
Query   Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.fasta
Query   Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s
Query   Sequence cluster (protein) | XML | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.xml
Query   Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.rdf
Query   Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.fasta
Query   Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s
Query   Sequence cluster (protein) | XML | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.xml
Query   Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.rdf
Query   Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.fasta
Example Sequence cluster ID (UniRef100) | P02930
Example Sequence cluster ID (UniRef90) | P02930
Example Sequence cluster ID (UniRef50) | P02930

ID      UTILLdb
Name    URGV TILLING platform databases
Desc    Lines, phenotype categories, sequences and mutations for pea and tomatoe.
URL     http://urgv.evry.inra.fr/UTILLdb
Taxon   3888 | Pisum sativum
Taxon   4081 | Solanum lycopersicum
EDAMtpc 0625 | Genotype and phenotype resources

ID      UTRdb
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.
URL     http://www.ba.itb.cnr.it/UTR/
Taxon   1 | all
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0158 | Sequence motifs
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMdat 0916 | Gene annotation
EDAMid  1026 | Gene symbol
EDAMid  2391 | UTR accession
EDAMid  2595 | UTRdb taxon
EDAMid  2745 | Locus ID (UTR)
EDAMfmt 2331 | HTML
Query   Gene annotation {UTR report} | HTML | Locus ID (UTR) | http://utrdb.ba.itb.cnr.it/getutr/%s
Query   Gene annotation {UTR report} | HTML | UTR accession | http://utrdb.ba.itb.cnr.it/getutra/%s
Query   Gene annotation {UTR gene report} | HTML | UTRdb taxon;Gene symbol | http://utrdb.ba.itb.cnr.it/getgene/%s1/%s2
Query   Gene annotation {UTR full report} | HTML | Locus ID (UTR) | http://utrdb.ba.itb.cnr.it/getutr/%s/1
Query   Gene annotation {UTR full report} | HTML | UTR accession | http://utrdb.ba.itb.cnr.it/getutra/%s/1
Query   Gene annotation {UTR full report} | HTML | UTR accession | http://utrdb.ba.itb.cnr.it/getutra/BA064434/1
Query   Gene annotation {UTR full gene report} | HTML | UTRdb taxon;Gene symbol | http://utrdb.ba.itb.cnr.it/getgene/%s1/%s2/1
Example UTR accession | CR478594
Example Locus ID (UTR) | 3HSAR031240
Example UTRdb taxon;Gene symbol | hs;MDM2

ID      UTRsite
Name    Regulatory motifs in eukaryotic UTRs
Desc    UTRSite is a collection of functional sequence patterns located in 5' or 3' UTR sequences.
URL     http://www.ba.itb.cnr.it/UTR/
Taxon   1 | all
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0747 | Nucleic acid sites and features
EDAMtpc 0158 | Sequence motifs
EDAMdat 2762 | Sequence motif metadata
EDAMid  2761 | UTRSite ID
EDAMfmt 2331 | HTML
Query   Sequence motif metadata {UTR site} | HTML | UTRSite ID | URL: http://utrsite.ba.itb.cnr.it/index.php/UTRSite signal/Signal/frmID/%s
Example UTRSite ID | U0001

ID      VBASE2
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.
URL     http://www.vbase2.org/
Taxon   9606 | Homo sapiens
Taxon   10888 |  Mus
EDAMtpc 0213 | Mice or rats
EDAMtpc 2815 | Humans
EDAMtpc 2830 | Immunity genes, immunoproteins and antigens
EDAMdat 0916 | Gene annotation
EDAMid  2835 | Gene ID (VBASE2)
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation {VBASE2 entry} | HTML | Gene ID (VBASE2) | http://vbase2.org/vgene.php?id=%s
Example Gene ID (VBASE2) | musIGHV028

ID      VectorBase
Acc     DB-0120
Name    Invertebrate vectors of human pathogens
Desc    Invertebrate vectors of human pathogens.
URL     http://www.vectorbase.org/
URLlink http://neuron.cse.nd.edu/vectorbase/index.php/Website_redirects
Cat     Genome annotation databases
Taxon   1 | all
EDAMtpc 0783 | Pathogens
EDAMdat 2399 | Gene annotation (transcript)
EDAMdat 0895 | Peptide annotation
EDAMdat 0916 | Gene annotation
EDAMid  2759 | Gene ID (VectorBase)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene ID (VectorBase)
Query   Gene annotation {VectorBase entry} | HTML | Gene ID (VectorBase) | http://www.vectorbase.org/Genome/BRCGene/?feature=%s
Query   Peptide annotation {VectorBase peptide page} | HTML | Gene ID (VectorBase) | http://www.vectorbase.org/Genome/BRCGene/?feature=%s-PA
Query   Gene annotation (transcript) | HTML | Gene ID (VectorBase) | http://www.vectorbase.org/Genome/BRCGene/?feature=%s-RA
Example Gene ID (VectorBase) | AGAP005025

ID      VEGA
Name    Vertebrate Genome Annotation (VEGA) database
Desc    A central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence.
URL     http://vega.sanger.ac.uk/
Taxon   9711 | Chordata
EDAMtpc 2820 | Vertebrates

ID      VIDA
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.
URL     http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA3/VIDA.html
Taxon   10239 | Viruses
EDAMtpc 0781 | Viruses
EDAMtpc 0741 | Protein sequence alignment
EDAMtpc 0724 | Protein families

ID      VirusMINT
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.
URL     http://mint.bio.uniroma2.it/virusmint/
Taxon   10239 | Viruses
EDAMtpc 0781 | Viruses
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 3044 | Protein interaction networks

ID      VSGdb
Name    A database of trypanosomal variant surface glycoproteins
Desc    A database of trypanosomal variant surface glycoproteins.
URL     http://leishman.cent.gla.ac.uk/pward001/vsgdb/kook_index.html
Taxon   5654 | Trypanosomatidae
EDAMtpc 0635 | Specific protein resources

ID      WorfDB
Name    The C.elegans ORFeome cloning project
Desc    The Caenorhabditis elegans ORFeome cloning project
URL     http://worfdb.dfci.harvard.edu/
Cat     Organism-specific databases
Taxon   6239 | Caenorhabditis elegans
EDAMtpc 0215 | Worms
EDAMdat 0916 | Gene annotation
EDAMid  1807 | ORF name
EDAMfmt 2331 | HTML
Xref    SP_implicit | ORF name
Query   Gene annotation {WorfDB entry} | HTML | ORF name | http://worfdb.dfci.harvard.edu/searchallwormorfs.pl?by=name&sid=%s
Example ORF name | pos-1


ID      World-2DPAGE
Acc     DB-0121
Name    The world-2DPAGE database
Desc    A public repository, standards compliant, for proteomics image data published in the literature.
URL     http://world-2dpage.expasy.org/repository/
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
EDAMdat 2364 | Experiment annotation (2D PAGE)
Xref    SP_explicit | Sequence accession (protein) {World-2DPAGE}
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) {World-2DPAGE} | http://world-2dpage.expasy.org/repository/%s
Example Sequence accession (protein) {World-2DPAGE} | 0020:Q20655


ID      WormBase
Acc     DB-0110
Name    Caenorhabditis elegans genome database
Desc    Caenorhabditis elegans genome database
URL     http://www.wormbase.org/
Cat     Organism-specific databases
Taxon   6239 | Caenorhabditis elegans
EDAMtpc 2819 | Invertebrates
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene symbol | http://www.wormbase.org/db/gene/gene?name=%s
Query   Gene annotation | HTML | Gene ID | http://www.wormbase.org/db/gene/gene?name=%s
Query   Gene annotation | HTML | Protein identifier | http://www.wormbase.org/db/gene/gene?name=%s
Example Gene symbol | unc-26
Example Gene ID | R13A5.9
Example Protein identifier | CE02711

ID      Xenbase
Acc     DB-0129
Name    Xenopus laevis and tropicalis biology and genomics resource
Desc    Xenopus laevis and tropicalis biology and genomics resource
URL     http://www.xenbase.org/
Cat     Organism-specific databases
Taxon   8353 | Xenopus
EDAMdat 0916 | Gene annotation
EDAMid  2295 | Gene ID
EDAMid  2738 | Gene ID (Xenbase)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene ID (Xenbase)
Query   Gene annotation | HTML | Gene ID (Xenbase) | http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=%s
Query   Gene annotation | HTML | Gene ID | http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=%s
Example Gene ID (Xenbase) | XB-GENE-1006026


ID      Yeast_complexes
Name    Yeast complexes database
Desc    Information on protein-protein interactions and protein complexes in yeast.
URL     http://yeast-complexes.embl.de/
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0782 | Fungi

ID      Yeast-GFP
Name    Yeast GFP fusion localization database
Desc    Yeast GFP fusion localization database
URL     http://yeastgfp.ucsf.edu
Cat     Organism-specific databases
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMtpc 0782 | Fungi
EDAMdat 0916 | Gene annotation
EDAMid  1807 | ORF name
EDAMfmt 2331 | HTML
Query   Gene annotation {Yeast-GFP entry} | HTML | ORF name | http://yeastgfp.ucsf.edu/getOrf.php?orf=%s


ID      YEASTRACT
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.
URL     http://www.yeastract.com
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 2846 | Gene regulatory networks
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0782 | Fungi
EDAMdat 0896 | Protein report
EDAMdat 2147 | Protein report (transcription factor)
EDAMdat 0916 | Gene annotation
EDAMdat 2223 | Ontology metadata
EDAMdat 0929 | Gene annotation (expression)
EDAMid  2755 | Transcription factor name
EDAMid  1009 | Protein name
EDAMid  1807 | ORF name
EDAMid  2299 | Gene name
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Query   Gene annotation | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Protein report | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Ontology metadata {GO information} | HTML | ORF name | http://www.yeastract.com/view.php?existing=go&orfname=%s
Query   Gene annotation | HTML | Gene name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Protein report | HTML | Gene name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Ontology metadata {GO information} | HTML | Gene name | http://www.yeastract.com/view.php?existing=go&orfname=%s
Query   Gene annotation | HTML | Protein name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Protein report | HTML | Protein name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Ontology metadata {GO information} | HTML | Protein name | http://www.yeastract.com/view.php?existing=go&orfname=%s
Query   Gene annotation (expression) {Regulation reference} | HTML | Transcription factor name;Gene name {target gene} | http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Query   Gene annotation (expression) {Regulation reference} | HTML | Transcription factor name;ORF name {target ORF} | http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Query   Protein report (transcription factor) {TF binding site reference} | HTML | Transcription factor name;Identifier {Consensus sequence} | http://www.yeastract.com/view.php?existing=consensus&proteinname=%s1&consensus=%s2
Query   Protein report (transcription factor) {Documented regulators of a given set of genes} | HTML | Gene name | http://www.yeastract.com/findregulators.php?type=doc&genes=%s
Query   Gene annotation {Documented target genes of a given set of TFs} | HTML | Transcription factor name | http://www.yeastract.com/findregulated.php?type=doc&tfs=%s
Example Transcription factor name | Nrg1p

ID      YGOB
Name    Yeast gene order browser
Desc    Tool for visualising the syntenic context of any gene from several yeast genomes.
URL     http://wolfe.gen.tcd.ie/ygob
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0796 | Genetic mapping and linkage
EDAMtpc 0782 | Fungi
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Query   Gene annotation {YGOB entry} | HTML | Gene symbol | http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=%s
Example Gene symbol | YAL068C

ID      yMGV
Name    Yeast microarray global viewer
Desc    Transcriptional expression profiles of yeast genes among most of the published expression datasets.
URL     http://transcriptome.ens.fr/ymgv/
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMtpc 0200 | Microarrays
EDAMtpc 0782 | Fungi

ID      ZFIN
Acc     DB-0113
Name    Zebrafish information network genome database
Desc    Zebrafish information network genome database
URL     http://zfin.org/
Cat     Organism-specific databases
Taxon   7955 | Danio rerio
EDAMtpc 2820 | Vertebrates
EDAMdat 0916 | Gene annotation
EDAMid  2643 | Gene ID (ZFIN)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene ID (ZFIN)
Query   Gene annotation {ZFIN entry} | HTML | Gene ID (ZFIN) | http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=%s
Example Gene ID (ZFIN) | ZDB-GENE-011205-17
