# 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 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 0000133 | Two-dimensional gel electrophoresis EDAMtpc 0000134 | Mass spectrometry 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 0000644 | Proteome 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 0000147 | Protein-protein interactions EDAMdat 0002377 | Protein structure report (domain) EDAMdat 0002359 | Domain-domain interaction EDAMdat 0002378 | Protein-motif interaction EDAMid 0001138 | Pfam accession number EDAMid 0002757 | Pfam domain name EDAMid 0001116 | ELM ID EDAMfmt 0002331 | 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 0000154 | Small molecules EDAMtpc 0000079 | 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 0000197 | Gene expression and regulation EDAMid 0001033 | Gene ID (Ensembl) EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0000660 | rRNA EDAMtpc 0000623 | 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 0000803 | Human disease 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 0000133 | Two-dimensional gel electrophoresis EDAMid 0000842 | 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 0000820 | Membrane protein 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMdat 0001312 | Gene features (promoter) EDAMid 0002741 | ABS ID EDAMfmt 0002331 | 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000623 | Gene family or system EDAMdat 0000916 | Gene annotation EDAMdat 0000929 | Gene annotation (expression) EDAMdat 0002394 | Gene annotation (functional) EDAMdat 0001300 | Nucleic acid features (gene structure) EDAMdat 0002703 | Gene annotation (clone or EST) EDAMid 0001045 | Species name EDAMid 0001108 | GenBank accession EDAMid 0002296 | Gene name (AceView) EDAMid 0001027 | Gene ID (NCBI) EDAMid 0002704 | Clone ID (IMAGE) EDAMid 0002803 | Clone ID (RefSeq) EDAMfmt 0002331 | 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 0000798 | 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 0000148 | 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 0000782 | Fungal EDAMid 0001045 | Species name EDAMid 0001870 | Genus name EDAMdat 0002395 | Fungi annotation EDAMdat 0002396 | Fungi annotation (anamorph) EDAMfmt 0002331 | 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 0000782 | Fungal EDAMtpc 0000643 | Genomes EDAMtpc 0000797 | Comparative genomics EDAMtpc 0000197 | Gene expression and regulation EDAMtpc 0000621 | Organism EDAMid 0001026 | Gene symbol EDAMid 0001045 | Species name EDAMdat 0000916 | Gene annotation EDAMdat 0002397 | Gene features (exon) EDAMdat 0000896 | Protein report EDAMdat 0002399 | Gene annotation (transcript) EDAMfmt 0002331 | 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 0000634 | Disease EDAMdat 0002018 | Metadata and annotation EDAMid 0000842 | Identifier EDAMfmt 0002331 | HTML Xref SP_explicit | Identifier {Allergome} Query Metadata and 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 0000634 | Disease 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 0000644 | Proteome EDAMtpc 0000780 | Plant EDAMtpc 0000797 | 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 0002830 | Immune-related proteins and peptides 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 0002830 | Immune-related proteins and peptides EDAMtpc 0000147 | Protein-protein interactions EDAMtpc 0000613 | 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 0000133 | Two-dimensional gel electrophoresis EDAMid 0003021 | UniProt accession EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMfmt 0002331 | 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 0002819 | Invertebrate EDAMtpc 0000643 | Genomes 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 0000147 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | 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 0002820 | Vertebrate EDAMtpc 0000643 | Genomes EDAMtpc 0000796 | Genetic mapping and linkage EDAMtpc 0000655 | 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 0000621 | Organism EDAMtpc 0002661 | Toxins and targets EDAMdat 0002400 | Toxin annotation EDAMid 0002578 | ArachnoServer ID EDAMfmt 0002331 | 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 0000635 | Specific protein EDAMtpc 0000811 | Transcription factor and binding site EDAMtpc 0000724 | Protein families EDAMdat 0002147 | Protein report (transcription factor) EDAMid 0002742 | AraC-XylS ID EDAMfmt 0002331 | 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 0000820 | Membrane protein EDAMtpc 0000780 | Plant EDAMdat 0001456 | Protein report (membrane protein) EDAMid 0001895 | Locus ID (AGI) EDAMfmt 0002331 | 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 0000166 | Protein structural motifs EDAMdat 0000899 | Protein structure report (3D motif) EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0000661 | miRNA EDAMtpc 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMtpc 0002846 | 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 0000197 | Gene expression and regulation EDAMtpc 0000203 | Gene expression profiling EDAMtpc 0000200 | Microarrays EDAMdat 0000931 | Experiment annotation (microarray) EDAMdat 0000929 | Gene annotation (expression) EDAMid 0000989 | Protein identifier EDAMid 0001144 | ArrayExpress accession number EDAMfmt 0002331 | 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes 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 0000639 | Protein sequences EDAMtpc 0000613 | 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 0000630 | Gene structure EDAMdat 0002399 | Gene annotation (transcript) EDAMdat 0000896 | Protein report EDAMid 0001026 | Gene symbol EDAMfmt 0002331 | 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 splicing and transcript diversity. URL http://www.ebi.ac.uk/astd/ Taxon 1 | all EDAMtpc 0000630 | Gene structure EDAMid 0002367 | ASTD ID EDAMid 0002368 | ASTD ID (exon) EDAMid 0002369 | ASTD ID (intron) EDAMid 0002370 | ASTD ID (polya) EDAMid 0002371 | ASTD ID (tss) EDAMdat 0002397 | Gene features (exon) EDAMdat 0000896 | Protein report EDAMdat 0002399 | Gene annotation (transcript) EDAMdat 0000916 | Gene annotation EDAMdat 0001312 | Gene features (promoter) EDAMdat 0002397 | Gene features (exon) EDAMdat 0002754 | Gene features (intron) EDAMdat 0001302 | Nucleic acid features (PolyA signal) EDAMid 0001033 | Gene ID (Ensembl) EDAMid 0002398 | Protein ID (Ensembl) EDAMfmt 0001927 | EMBL format EDAMfmt 0002305 | GFF EDAMfmt 0002306 | GTF EDAMfmt 0001929 | FASTA format EDAMfmt 0002331 | 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 0000608 | Cell lines and culture EDAMdat 0000963 | Cell line annotation EDAMid 0000842 | 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 0000608 | Cell lines and culture 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 0000608 | Cell lines and culture 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 0000635 | Specific protein 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMtpc 0000811 | Transcription factor and binding site EDAMtpc 0000780 | Plant 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 0000724 | Protein families ID Axeldb Name Axeldb database of gene expression in Xenopus laevis Desc Gene expression in Xenopus laevis. URL http://www.dkfz.de/en/mol_embryology/axeldb.html Taxon 8355 | Xenopus laevis EDAMtpc 0000197 | Gene expression and regulation 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 0000741 | 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 0000152 | 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 0000655 | mRNA, EST or cDNA 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 0002819 | Invertebrate EDAMtpc 0000643 | Genomes 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 0000623 | Gene family or system EDAMtpc 0000197 | Gene expression and regulation EDAMtpc 0000203 | Gene expression profiling EDAMdat 0000929 | Gene annotation (expression) EDAMdat 0000928 | Gene expression profile EDAMdat 0000916 | Gene annotation EDAMdat 0002579 | Gene annotation (expressed gene list) EDAMid 0003021 | UniProt accession EDAMid 0001033 | Gene ID (Ensembl) EDAMfmt 0002331 | 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 0000148 | Protein-ligand interactions EDAMtpc 0000620 | Drugs and targets EDAMdat 0000962 | Small molecule report EDAMdat 0002402 | Protein-drug interaction EDAMdat 0000857 | Database hits (sequence) EDAMdat 0002726 | Inhibitor annotation EDAMid 0000842 | Identifier EDAMid 0001127 | PDB ID EDAMid 0001187 | PubMed ID EDAMid 0003021 | UniProt accession EDAMid 0002580 | BindingDB Monomer ID EDAMid 0001009 | Protein name EDAMfmt 0002331 | 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 0000643 | Genomes EDAMtpc 0000821 | Enzymes EDAMtpc 0000753 | Metabolic pathways EDAMdat 0001509 | Protein report (enzyme) EDAMdat 0001288 | Genome map EDAMdat 0001283 | Cytogenetic map EDAMdat 0000962 | Small molecule report EDAMdat 0002984 | Pathway or network report EDAMdat 0000908 | Reaction annotation EDAMid 0001795 | Gene ID (EcoGene) EDAMid 0002106 | Reaction ID (BioCyc) EDAMid 0002107 | Enzyme ID (BioCyc) EDAMid 0002105 | Compound ID (BioCyc) EDAMid 0001157 | Pathway ID (BioCyc) EDAMid 0000987 | Chromosome name EDAMid 0000842 | Identifier EDAMfmt 0002331 | HTML Xref SP_explicit | Identifier {BioCyc} Query Metadata and report | 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 0000128 | Protein interactions EDAMtpc 0000197 | Gene expression and regulation 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 0000771 | Biological models EDAMdat 0000950 | Biological model EDAMid 0001171 | BioModel ID EDAMfmt 0002585 | SBML EDAMfmt 0002331 | 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 0000091 | Data handling EDAMtpc 0000088 | Literature and documentation 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 0000602 | Pathways, networks and models EDAMtpc 0000634 | Disease 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 0000149 | Protein-nucleic acid interactions EDAMdat 0001567 | Protein-nucleic acid interaction EDAMdat 0002358 | Domain-nucleic acid interaction EDAMid 0001042 | SCOP sunid EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0000197 | Gene expression and regulation EDAMtpc 0000200 | Microarrays ID BlotBase Name BlotBase Northern blots database Desc Northern blots database. URL http://www.medicalgenomics.org/Databases/BlotBase Taxon 1 | all EDAMtpc 0000197 | Gene expression and regulation EDAMdat 0002586 | Northern blot image EDAMid 0001026 | Gene symbol EDAMid 0002588 | BlotBase blot ID EDAMfmt 0002331 | 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 0000602 | Pathways, networks and models 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 0000625 | Genotype and phenotype 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 0000821 | Enzymes EDAMdat 0001509 | Protein report (enzyme) EDAMid 0003021 | UniProt accession EDAMid 0001011 | EC number EDAMid 0002593 | BRENDA organism ID EDAMfmt 0002331 | 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 0002844 | Structural clustering 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes 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 0002819 | Invertebrate EDAMtpc 0000643 | Genomes EDAMtpc 0000797 | 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 0000607 | Laboratory resources EDAMdat 0000963 | Cell line annotation EDAMid 0002380 | CABRI accession EDAMid 0002597 | 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 0000621 | Organism 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 0000197 | Gene expression and regulation EDAMtpc 0000200 | Microarrays EDAMtpc 0002640 | Cancer 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 0000197 | Gene expression and regulation EDAMtpc 0000780 | Plant EDAMdat 0000916 | Gene annotation EDAMdat 0000929 | Gene annotation (expression) EDAMdat 0002093 | Data reference EDAMid 0002388 | TAIR accession (At gene) EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000736 | Protein domains EDAMtpc 0000164 | Sequence clustering EDAMdat 0000901 | Protein features (domains) EDAMdat 0001553 | CATH node EDAMdat 0001762 | CATH domain report EDAMid 0001040 | CATH domain ID EDAMid 0001008 | Polypeptide chain ID EDAMid 0001127 | PDB ID EDAMid 0001043 | CATH node ID EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000197 | Gene expression and regulation EDAMtpc 0000200 | Microarrays EDAMtpc 0000780 | Plant 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 0000821 | Enzymes EDAMtpc 0000724 | Protein families EDAMdat 0001509 | Protein report (enzyme) EDAMid 0002702 | Enzyme ID (CAZy) EDAMfmt 0002331 | 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 0000622 | 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 0000166 | Protein structural motifs 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 0000608 | Cell lines and culture EDAMdat 0000963 | Cell line annotation EDAMid 0002778 | CCAP strain number EDAMfmt 0002331 | 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 0000635 | Specific protein EDAMtpc 0000612 | Cell cycle and development EDAMtpc 0000782 | Fungal EDAMdat 0000896 | Protein report EDAMdat 0000916 | Gene annotation EDAMid 0002764 | Protein name (UniProt) EDAMid 0002300 | Gene name (NCBI) EDAMfmt 0002331 | 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 0000607 | Laboratory resources EDAMtpc 0000608 | Cell lines and culture 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 0000147 | Protein-protein interactions EDAMtpc 0000140 | 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 0000635 | Specific protein 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 0000796 | Genetic mapping and linkage EDAMtpc 0000625 | Genotype and phenotype 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 0000797 | Comparative genomics EDAMtpc 0000624 | Chromosomes EDAMtpc 0000097 | Nucleic acid structure EDAMdat 0002086 | Nucleic acid structure report EDAMid 0002787 | NCBI genome accession EDAMfmt 0002331 | 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 0000741 | Protein sequence alignment EDAMtpc 0000164 | Sequence clustering EDAMtpc 0000736 | Protein domains EDAMdat 0000901 | Protein features (domains) EDAMdat 0001384 | Sequence alignment (protein) EDAMdat 0000907 | Protein family annotation EDAMid 0002714 | CDD PSSM-ID EDAMid 0002666 | CDD ID EDAMid 0002327 | GI number (protein) EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0002817 | Yeast EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001898 | Locus ID (CGD) EDAMid 0002794 | ORF ID EDAMfmt 0002331 | 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 0000154 | Small molecules EDAMdat 0000962 | Small molecule report EDAMid 0001174 | ChEBI ID EDAMfmt 0002331 | 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 0000620 | Drugs and targets EDAMtpc 0000154 | Small molecules 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 0000154 | Small molecules EDAMtpc 0002811 | 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 0000088 | Literature and documentation EDAMdat 0000970 | Bibliographic reference EDAMid 0001187 | PubMed ID EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000197 | Gene expression and regulation EDAMtpc 0000203 | Gene expression profiling EDAMdat 0000931 | Experiment annotation (microarray) EDAMdat 0000928 | Gene expression profile EDAMid 0002709 | CleanEx entry name EDAMid 0002710 | CleanEx dataset code EDAMfmt 0002331 | 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 0000608 | Cell lines and culture EDAMdat 0000963 | Cell line annotation EDAMid 0002317 | Cell line name (exact) EDAMid 0002318 | Cell line name (truncated) EDAMid 0002319 | Cell line name (no punctuation) EDAMid 0002320 | Cell line name (assonant) EDAMfmt 0002331 | 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 0000724 | Protein families EDAMtpc 0000164 | Sequence clustering 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000622 | Genomics EDAMdat 0000916 | Gene annotation EDAMdat 0002711 | Genome metadata EDAMid 0003021 | UniProt accession EDAMid 0001179 | NCBI taxonomy ID EDAMid 0002292 | GenBank identifier EDAMid 0002774 | Gene ID (JCVI) EDAMid 0002786 | NCBI Genome Project ID EDAMfmt 0002331 | 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 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000783 | Pathogen EDAMtpc 0000782 | Fungal EDAMdat 0000849 | Sequence record EDAMid 0002729 | COGEME EST ID EDAMid 0002730 | COGEME unisequence ID EDAMfmt 0002331 | 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 0000797 | Comparative genomics EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes 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 0000803 | Human disease EDAMdat 0000918 | Sequence variation annotation EDAMid 0002747 | Database name (CMD) EDAMfmt 0002331 | 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 0002814 | Protein 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0003021 | UniProt accession EDAMid 0000989 | Protein identifier EDAMfmt 0002331 | 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 0000621 | Organism EDAMtpc 0002661 | Toxins and targets EDAMdat 0000896 | Protein report EDAMid 0002804 | Protein ID (ConoServer) EDAMfmt 0002331 | 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 0002846 | Gene regulatory networks EDAMtpc 0000147 | Protein-protein interactions EDAMtpc 0000602 | Pathways, networks and models EDAMtpc 0000197 | Gene expression and regulation EDAMdat 0002984 | Pathway or network report EDAMdat 0002767 | Identifier metadata EDAMdat 0000906 | Protein interaction report EDAMid 0002342 | Pathway or network name EDAMid 0002345 | Pathway ID (ConsensusPathDB) EDAMid 0002776 | ConsensusPathDB entity ID EDAMid 0002777 | ConsensusPathDB entity name EDAMid 0002091 | Accession EDAMfmt 0002331 | 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 metadata {Physical entities} | HTML | ConsensusPathDB entity name | http://cPDB.molgen.mpg.de/CPDB/search?nameacc=name&keywords=%s&searchspace=PhysicalEntity Query Identifier 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 interaction report {Interactions of pathway} | HTML | Pathway ID (ConsensusPathDB) | http://cPDB.molgen.mpg.de/CPDB/getInteractionsOfObjs?objs:list=%s&objtype=p Query Protein interaction report {Interactions of physical entity} | HTML | ConsensusPathDB entity ID | http://cPDB.molgen.mpg.de/CPDB/getInteractionsOfObjs?objs:list=%s&objtype=e Query Protein interaction report {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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription 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 0000147 | Protein-protein interactions EDAMtpc 0000140 | Protein targeting and localization EDAMdat 0002712 | Protein structure report (protein complex) EDAMid 0002713 | Protein ID (CORUM) EDAMfmt 0002331 | 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 0002846 | Gene regulatory networks EDAMtpc 0000197 | Gene expression and regulation EDAMtpc 0000811 | Transcription factor and binding site 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 0002640 | Cancer 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000164 | Sequence clustering EDAMtpc 0000722 | 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 0000641 | Repeat sequence EDAMtpc 0000164 | Sequence clustering EDAMtpc 0000722 | 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 0000748 | Protein functional sites EDAMtpc 0000821 | Enzymes 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 0000635 | Specific protein 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 0002661 | Toxins and targets EDAMtpc 0000625 | Genotype and phenotype EDAMdat 0000916 | Gene annotation EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 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 0000635 | Specific protein EDAMdat 0000896 | Protein report EDAMid 0002715 | Protein ID (CuticleDB) EDAMfmt 0002331 | 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 0000612 | Cell cycle and development 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 0000602 | Pathways, networks and models EDAMtpc 0000782 | Fungal EDAMtpc 0000797 | Comparative genomics EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0000635 | Specific protein EDAMtpc 0000084 | 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 0000199 | Mutation and polymorphism EDAMtpc 0000803 | Human disease 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 0002826 | 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 0002826 | 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 0000811 | Transcription factor and binding site EDAMdat 0002147 | Protein report (transcription factor) EDAMid 0002716 | DBD ID EDAMfmt 0002331 | 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 0000655 | mRNA, EST or cDNA EDAMdat 0000849 | Sequence record EDAMid 0002314 | GI number EDAMid 0001105 | dbEST accession EDAMfmt 0002310 | FASTA-HTML EDAMfmt 0002532 | GenBank-HTML EDAMfmt 0002331 | 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 0000607 | Laboratory resources EDAMtpc 0000632 | Molecular probes or primers EDAMdat 0002717 | Oligonucleotide probe annotation EDAMid 0002719 | dbProbe ID EDAMfmt 0002331 | 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 0000199 | Mutation and polymorphism EDAMdat 0002092 | SNP annotation EDAMid 0001106 | dbSNP ID EDAMfmt 0002331 | 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 databank of Japan (DDBJ) Desc A nucleotide sequence database. URL http://www.ddbj.nig.ac.jp/ Cat Sequence databases Taxon 1 | all EDAMtpc 0000640 | Nucleic acid sequences EDAMdat 0002201 | Sequence record full EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0001936 | GenBank format EDAMfmt 0002532 | 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 0000634 | Disease ID Diamond Name Blackfan Anemia mutation database (Diamond) Desc Blackfan Anemia mutation database. URL http://www.dbagenes.unito.it Taxon 9606 | Homo sapiens EDAMtpc 0000803 | Human disease EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0002818 | Eukaryote EDAMtpc 0000643 | Genomes 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 0000655 | 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 0000621 | Organism EDAMtpc 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMfmt 0002331 | 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 0000147 | Protein-protein interactions EDAMdat 0002359 | Domain-domain interaction EDAMid 0001138 | Pfam accession number EDAMfmt 0002331 | 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 0000147 | Protein-protein interactions EDAMdat 0001565 | Protein-protein interaction EDAMid 0002616 | DIP ID EDAMfmt 0002331 | 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 0000094 | Nucleic acid physicochemistry EDAMtpc 0000097 | Nucleic acid structure EDAMdat 0002720 | Dinucleotide property EDAMdat 0002086 | Nucleic acid structure report EDAMid 0002721 | DiProDB ID EDAMfmt 0002331 | 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 0000698 | Protein tertiary structure EDAMdat 0002722 | Protein structure report (disordered protein) EDAMid 0002723 | Protein ID (DisProt) EDAMfmt 0002331 | 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 0000654 | 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 0000147 | 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 0000147 | 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000199 | Mutation and polymorphism 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 0000781 | Virus EDAMtpc 0000780 | Plant EDAMdat 0002307 | Virus annotation EDAMdat 0002308 | Virus annotation (taxonomy) EDAMid 0002733 | Genus name (virus) EDAMid 0002734 | Family name (virus) EDAMid 0002836 | DPVweb ID EDAMfmt 0002331 | 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 0000754 | Signalling 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 0000617 | Ribosomes 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 0000620 | Drugs and targets EDAMdat 0001696 | Drug annotation EDAMid 0002326 | DrugBank ID EDAMfmt 0002331 | 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 0000821 | Enzymes 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 0000145 | Molecular flexibility and motion 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 0002814 | Protein structure EDAMtpc 0000694 | Protein secondary structure EDAMdat 0000876 | Protein features (secondary structure) EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis ID EASED Name EASED database Desc Extended Alternatively Spliced EST Database URL http://eased.bioinf.mdc-berlin.de/ Taxon 1 | all EDAMtpc 0000655 | mRNA, EST or cDNA 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 0000147 | Protein-protein interactions EDAMid 0001026 | Gene symbol EDAMdat 0000896 | Protein report EDAMdat 0001565 | Protein-protein interaction EDAMdat 0002093 | Data reference EDAMid 0000989 | Protein identifier EDAMid 0002802 | Protein ID (EcID) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMid 0000842 | 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 varios 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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. A major EcoGene focus has been the re-evaluation of translation start sites. URL http://ecogene.org/ Cat Organism-specific databases Taxon 562 | Escherichia coli EDAMtpc 0000110 | Transcription EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000644 | Proteome EDAMtpc 0001811 | Prokaryote EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001795 | Gene ID (EcoGene) EDAMfmt 0002331 | 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 0000621 | Organism EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0001026 | Gene symbol EDAMfmt 0002331 | 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 emap Name Edinburgh Mouse Atlas project database (emap) Desc The emap Atlas is a digital Atlas of mouse embryonic development. It is based on the definitive books of mouse embryonic development by Theiler (1989) and Kaufman (1992) yet extends these studies by creating a series of interactive three-dimensional computer models of mouse embryos at successive stages of development with defined anatomical domains linked to a stage-by-stage ontology of anatomical names. URL http://genex.hgu.mrc.ac.uk/ Taxon 10088 | Mus EDAMtpc 0000612 | Cell cycle and development EDAMdat 0002724 | Embryo annotation EDAMid 0001149 | EMAGE ID EDAMfmt 0002331 | 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 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 0000081 | Structure EDAMdat 0000896 | Protein report EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0000625 | Genotype and phenotype EDAMdat 0002381 | Experiment annotation (genotype) EDAMid 0002383 | EGA accession EDAMfmt 0002331 | 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 0000722 | Nucleic acid classification EDAMtpc 0000623 | 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 0000158 | Sequence motifs EDAMtpc 0000748 | Protein functional sites EDAMtpc 0000158 | Sequence motifs EDAMdat 0001298 | Sequence features (motifs) EDAMid 0002705 | GO term ID (cellular compartment) EDAMid 0002291 | UniProt ID EDAMid 0000842 | Identifier EDAMid 0001868 | Taxon EDAMfmt 0002331 | 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 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 0002201 | Sequence record full EDAMtpc 0000640 | Nucleic acid sequences EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0001927 | EMBL format EDAMfmt 0002311 | 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 0000611 | Electron microscopy 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 0002817 | Yeast EDAMtpc 0000643 | Genomes EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes ID ENA Name European nucleotide short read and trace archive (ENA) Desc European nucleotide short read and trace archive (ENA). URL http://www.ebi.ac.uk/ena Taxon 1 | all EDAMtpc 0000640 | Nucleic acid sequences 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 0000754 | Signalling 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 0000643 | Genomes EDAMtpc 0002818 | Eukaryote EDAMtpc 0000643 | Genomes EDAMdat 0000849 | Sequence record EDAMdat 0000916 | Gene annotation EDAMid 0001033 | Gene ID (Ensembl) EDAMid 0002725 | Transcript ID (Ensembl) EDAMfmt 0001929 | FASTA format EDAMfmt 0002331 | 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 0000643 | Genomes 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 0000643 | Genomes EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002725 | Transcript ID (Ensembl) EDAMfmt 0002331 | 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 0000643 | Genomes EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002725 | Transcript ID (Ensembl) EDAMfmt 0002331 | 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 0000643 | Genomes EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002725 | Transcript ID (Ensembl) EDAMfmt 0002331 | 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 0000643 | Genomes EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002725 | Transcript ID (Ensembl) EDAMfmt 0002331 | 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 0000643 | Genomes EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002725 | Transcript ID (Ensembl) EDAMfmt 0002331 | 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 0000821 | Enzymes EDAMtpc 0002811 | Nomenclature EDAMdat 0001509 | Protein report (enzyme) EDAMid 0001011 | EC number EDAMfmt 0002331 | 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 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMdat 0001312 | Gene features (promoter) EDAMid 0002386 | EPD ID EDAMfmt 0002331 | 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen 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 0000820 | Membrane protein EDAMtpc 0000140 | 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 0000780 | Plant EDAMtpc 0000643 | Genomes 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 0000635 | Specific protein 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 0000781 | Virus EDAMtpc 0000621 | Organism EDAMdat 0000849 | Sequence record EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002331 | 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 0000625 | Genotype and phenotype 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 0000736 | Protein domains 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 0000821 | Enzymes EDAMtpc 0002811 | 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 0000644 | Proteome EDAMtpc 0001811 | Prokaryote EDAMtpc 0000639 | Protein sequences 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 0000820 | Membrane protein 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 0000635 | Specific protein EDAMtpc 0000724 | Protein families EDAMtpc 0000164 | Sequence clustering 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 0002640 | Cancer 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 0000643 | Genomes 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 0000630 | Gene structure 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 0000644 | Proteome 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 0000602 | Pathways, networks and models EDAMtpc 0000782 | Fungal EDAMtpc 0000643 | Genomes 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 0000803 | Human disease 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 0000748 | Protein functional sites EDAMtpc 0000148 | Protein-ligand interactions 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 0000643 | Genomes EDAMtpc 0000780 | Plant 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 0000147 | Protein-protein interactions EDAMtpc 0000197 | Gene expression and regulation EDAMtpc 0000625 | Genotype and phenotype 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 0002819 | Invertebrate EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001796 | Gene ID (FlyBase) EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0002819 | Invertebrate EDAMtpc 0000643 | Genomes 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 0000199 | Mutation and polymorphism EDAMtpc 0000643 | Genomes 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 0000811 | Transcription factor and binding site 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/ Taxon 7215 | Drosophila EDAMtpc 0000621 | Organism EDAMtpc 0000612 | Cell cycle and development EDAMtpc 0000197 | Gene expression and regulation 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 0000748 | Protein functional sites 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 0000602 | Pathways, networks and models EDAMtpc 0000197 | Gene expression and regulation EDAMtpc 0000140 | 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 0000622 | Genomics EDAMtpc 0000782 | Fungal 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 0000642 | Low complexity sequence 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 0000724 | 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 0000724 | Protein families 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 0000644 | Proteome EDAMtpc 0000724 | Protein families EDAMtpc 0000164 | Sequence clustering EDAMtpc 0000782 | Fungal EDAMtpc 0000194 | 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 0000630 | Gene structure 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 0000803 | Human disease 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 0000780 | Plant 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 0000796 | 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 0000610 | Ecoinformatics ID GDB Name Human Genome Database (GDB) Desc Community curated collection of human genomic data - now obsolete. Taxon 9606 | Homo sapiens EDAMtpc 0002815 | Human EDAMtpc 0000643 | Genomes Xref EMBL_explicit | Identifier {GDB} Example Identifier {GDB} | 4466301 ID GenAtlas Acc DB-0027 Name GenAtlas human gene database Desc Information on gene apping and genetic diseases. URL http://www.dsi.univ-paris5.fr/genatlas/ Cat Organism-specific databases Taxon 9606 | Homo sapiens EDAMtpc 0000803 | Human disease EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001026 | Gene symbol EDAMfmt 0002331 | 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 Nucleotide sequence database. URL http://www.ncbi.nlm.nih.gov/ Cat Sequence databases Taxon 1 | all EDAMtpc 0000640 | Nucleic acid sequences EDAMdat 0002201 | Sequence record full EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002532 | 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 0000796 | Genetic mapping and linkage EDAMdat 0002201 | Sequence record full EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002532 | 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 0000724 | Protein families EDAMdat 0000907 | Protein family annotation EDAMid 0001040 | CATH domain ID EDAMid 0002701 | CATH node ID (family) EDAMfmt 0002331 | 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 0000632 | Molecular probes or 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 0000803 | Human disease EDAMtpc 0000586 | Proteins EDAMtpc 0000147 | Protein-protein interactions EDAMtpc 0000602 | Pathways, networks and models EDAMtpc 0000199 | Mutation and polymorphism EDAMtpc 0000643 | Genomes EDAMid 0003021 | UniProt accession EDAMid 0001026 | Gene symbol EDAMid 0002298 | Gene ID (HGNC) EDAMid 0001025 | Gene identifier EDAMid 0001904 | Locus ID (EntrezGene) EDAMid 0002610 | Ensembl ID EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0000643 | Genomes EDAMtpc 0002817 | Yeast EDAMtpc 0000659 | Functional RNA EDAMtpc 0000621 | Organism EDAMtpc 0000798 | Mobile genetic elements EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0000197 | Gene expression and regulation 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 0000724 | Protein families EDAMtpc 0000780 | Plant EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMdat 0000907 | Protein family annotation EDAMid 0002295 | Gene ID EDAMid 0002731 | Protein family ID (GeneFarm) EDAMfmt 0002331 | 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 0000623 | Gene family or system EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002339 | Ontology term name EDAMid 0001176 | GO term ID EDAMid 0001026 | Gene symbol EDAMid 0001045 | Species name EDAMid 0001011 | EC number EDAMid 0000987 | Chromosome name EDAMid 0001097 | Sequence accession (nucleic acid) EDAMid 0000842 | Identifier EDAMid 0001187 | PubMed ID EDAMfmt 0002331 | 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 0000643 | Genomes EDAMtpc 0000624 | 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 0000630 | Gene structure EDAMtpc 0000722 | Nucleic acid classification EDAMtpc 0000164 | Sequence clustering EDAMtpc 0000655 | 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 0000197 | Gene expression and regulation EDAMtpc 0000203 | Gene expression profiling EDAMtpc 0000803 | Human disease ID GeneSapiens Name GeneSapiens human transcriptome database Desc Human transcriptome database. URL http://www.genesapiens.org/ Taxon 9606 | Homo sapiens EDAMtpc 0000197 | Gene expression and regulation 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 0000199 | Mutation and polymorphism EDAMtpc 0000643 | Genomes EDAMtpc 0000803 | Human disease EDAMdat 0002092 | SNP annotation EDAMid 0002805 | GeneSNP ID EDAMfmt 0002331 | 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 0000655 | 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 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0002817 | Yeast EDAMtpc 0000643 | Genomes EDAMtpc 0000722 | 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000797 | Comparative genomics EDAMdat 0003028 | Taxonomic data EDAMdat 0000916 | Gene annotation EDAMid 0001868 | Taxon EDAMid 0001026 | Gene symbol EDAMid 0002739 | Gene ID (Genolist) EDAMfmt 0002331 | 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 0000643 | Genomes EDAMdat 0002711 | Genome metadata EDAMid 0002751 | GenomeReviews ID EDAMfmt 0002331 | 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 0000644 | Proteome 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 0000625 | Genotype and phenotype 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 0002640 | Cancer 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 0000197 | Gene expression and regulation EDAMdat 0000916 | Gene annotation EDAMid 0001026 | Gene symbol EDAMid 0001045 | Species name EDAMid 0001033 | Gene ID (Ensembl) EDAMfmt 0002331 | 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 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 0000748 | Protein functional sites 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 0000152 | 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 0000152 | Carbohydrates EDAMdat 0002313 | Carbohydrate structure report EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000089 | Ontologies EDAMdat 0000966 | Ontology term EDAMid 0001176 | GO term ID EDAMfmt 0002331 | 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 0000644 | Proteome EDAMtpc 0000219 | Annotation EDAMdat 0000966 | Ontology term EDAMdat 0002093 | Data reference EDAMid 0001009 | Protein name EDAMid 0003021 | UniProt accession EDAMid 0001176 | GO term ID EDAMid 0002339 | Ontology term name EDAMfmt 0002331 | 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 0000622 | 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 0000803 | Human disease ID GoPubMed Name GoPubMed ontology-based literature search Desc Ontology-based literature search. URL http://www.gopubmed.org Taxon None EDAMtpc 0000088 | Literature and documentation EDAMtpc 0000089 | 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 0000820 | Membrane protein EDAMtpc 0000148 | Protein-ligand interactions EDAMdat 0001456 | Protein report (membrane protein) EDAMid 0001131 | Protein family name EDAMfmt 0002331 | 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 0000820 | Membrane protein ID GlycosciencesDB IDalt DBGLYCOSCIENCES.de Name Glycosciences database Desc Carbohydrate structure database. URL http://www.glycosciences.de/sweetdb/index.php Taxon None EDAMtpc 0000152 | Carbohydrates EDAMdat 0002753 | Carbohydrate conformational map EDAMdat 0002313 | Carbohydrate structure report EDAMid 0001127 | PDB ID EDAMid 0002752 | GlycoMap ID EDAMid 0002796 | Linucs ID EDAMfmt 0002331 | 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 0000820 | Membrane protein 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 0000797 | Comparative genomics EDAMtpc 0000625 | Genotype and phenotype EDAMtpc 0000621 | Organism EDAMtpc 0000602 | Pathways, networks and models EDAMdat 0000896 | Protein report EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000797 | Comparative genomics EDAMtpc 0000084 | Phylogenetics EDAMtpc 0000194 | Phylogenomics EDAMtpc 0000780 | Plant 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 0000780 | Plant EDAMtpc 0002811 | Nomenclature Xref SP_FT | None Example Identifier | 1005973 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 0000781 | Virus EDAMtpc 0000798 | 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 0000197 | Gene expression and regulation EDAMtpc 0000203 | Gene expression profiling EDAMtpc 0000199 | Mutation and polymorphism EDAMtpc 0000753 | Metabolic pathways EDAMtpc 0000803 | Human disease EDAMtpc 0000621 | Organism EDAMtpc 0000659 | Functional RNA EDAMtpc 0000630 | Gene structure EDAMtpc 0000140 | Protein targeting and localization EDAMdat 0002399 | Gene annotation (transcript) EDAMdat 0000916 | Gene annotation EDAMid 0002770 | HIT ID EDAMid 0002771 | HIX ID EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000803 | Human disease 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 0000644 | Proteome EDAMtpc 0000724 | Protein families EDAMdat 0000896 | Protein report EDAMdat 0000849 | Sequence record EDAMdat 0002872 | ID list EDAMid 0002766 | HAMAP ID EDAMfmt 0002331 | HTML EDAMfmt 0002188 | 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 0000803 | Human disease 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 0000624 | 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 0000781 | Virus 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 0000781 | Virus EDAMtpc 0000640 | Nucleic acid sequences 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 0000796 | 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 0000803 | Human disease 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 0000621 | Organism EDAMtpc 0000622 | Genomics EDAMtpc 0002811 | Nomenclature EDAMdat 0000916 | Gene annotation EDAMid 0002298 | Gene ID (HGNC) EDAMfmt 0002331 | 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 0000084 | Phylogenetics EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes 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 0000625 | Genotype and phenotype 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 0000154 | 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 0000779 | Mitochondria EDAMtpc 0000643 | Genomes 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 0000740 | Nucleic acid sequence alignment EDAMtpc 0000623 | Gene family or system EDAMtpc 0000084 | Phylogenetics EDAMtpc 0000797 | Comparative genomics EDAMtpc 0000194 | Phylogenomics EDAMdat 0000872 | Phylogenetic tree EDAMdat 0002925 | Sequence data EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000623 | Gene family or system EDAMtpc 0000740 | Nucleic acid sequence alignment EDAMtpc 0000084 | Phylogenetics EDAMtpc 0000797 | 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 0000623 | Gene family or system EDAMtpc 0000740 | Nucleic acid sequence alignment EDAMtpc 0000084 | Phylogenetics EDAMtpc 0000797 | Comparative genomics EDAMtpc 0000194 | Phylogenomics EDAMdat 0002201 | Sequence record full EDAMdat 0000916 | Gene annotation EDAMdat 0000872 | Phylogenetic tree EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000623 | 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 0000147 | Protein-protein interactions EDAMtpc 0000602 | Pathways, networks and models 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 0000741 | Protein sequence alignment EDAMtpc 0000724 | 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 0000623 | 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 0000635 | Specific protein EDAMtpc 0000623 | Gene family or system EDAMtpc 0000630 | Gene structure 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 0000147 | 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 0000197 | Gene expression and regulation EDAMtpc 0002640 | Cancer EDAMtpc 0000611 | Electron microscopy EDAMtpc 0000621 | Organism EDAMtpc 0000140 | Protein targeting and localization EDAMtpc 0000644 | Proteome EDAMtpc 0002815 | Human EDAMdat 0002394 | Gene annotation (functional) EDAMid 0001791 | Gene name (HGNC) EDAMid 0001033 | Gene ID (Ensembl) EDAMid 0002772 | HPA antibody id EDAMfmt 0002331 | 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 0000630 | Gene structure EDAMtpc 0000747 | Nucleic acid functional sites EDAMtpc 0000114 | 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 0000694 | Protein secondary structure EDAMdat 0000876 | Protein features (secondary structure) EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0000811 | Transcription factor and binding site 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000621 | Organism EDAMdat 0000896 | Protein report EDAMid 0002393 | mFLJ/mKIAA number EDAMfmt 0002331 | 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 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 0000625 | Genotype and phenotype 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 0000154 | Small molecules EDAMtpc 0000079 | 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 0000779 | Mitochondria EDAMtpc 0002815 | Human EDAMtpc 0000643 | Genomes 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 0000662 | siRNA ID HvrBase++ Name HvrBase++ phylogenetic database for primate species Desc Hypervariable regions database. URL http://www.hvrbase.org Taxon 9443 | Primates EDAMtpc 0000084 | 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 0000199 | Mutation and polymorphism EDAMtpc 0000625 | Genotype and phenotype 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 0000608 | Cell lines and culture 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 0002640 | Cancer 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 0000803 | Human disease EDAMdat 0000918 | Sequence variation annotation EDAMid 0001097 | Sequence accession (nucleic acid) EDAMid 0001025 | 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 0000803 | Human disease EDAMdat 0000918 | Sequence variation annotation EDAMid 0001097 | 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 0002830 | Immune-related proteins and peptides EDAMdat 0000849 | Sequence record EDAMid 0002773 | IMGT/HLA ID EDAMfmt 0001927 | 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 0002830 | Immune-related proteins and peptides EDAMtpc 0002811 | Nomenclature EDAMdat 0000896 | Protein report EDAMid 0002773 | IMGT/HLA ID EDAMfmt 0002331 | 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 0002830 | Immune-related proteins and peptides EDAMtpc 0000698 | 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 0000804 | Immunoinformatics 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 0002830 | Immune-related proteins and peptides EDAMtpc 0000639 | Protein sequences EDAMid 0001097 | 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 0002830 | Immune-related proteins and peptides EDAMtpc 0000632 | Molecular probes or 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 0000803 | Human disease ID InParanoid Acc DB-0146 Name Inparanoid orthologs database Desc Eukaryotic orthholog groups. URL http://InParanoid.sbc.su.se Taxon 1 | all EDAMtpc 0000722 | 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 0000147 | Protein-protein interactions EDAMdat 0000906 | Protein interaction report EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | HTML Xref SP_explicit | IntAct accession number Query Protein interaction report {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 0000644 | Proteome EDAMtpc 0000643 | Genomes 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 0000630 | Gene structure 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 0000821 | Enzymes EDAMtpc 0002811 | 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 0000724 | Protein families EDAMtpc 0000748 | Protein functional sites EDAMtpc 0000641 | Repeat sequence EDAMdat 0001355 | Protein signature EDAMid 0001133 | InterPro accession EDAMfmt 0002331 | 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 0000634 | Disease ID ICDS Name Interrupted coding sequences (ICDS) Desc Interrupted coding sequences. URL http://www-bio3d-igbmc.u-strasbg.fr/ICDS/ Taxon 1 | all EDAMtpc 0000630 | Gene structure 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 0000199 | Mutation and polymorphism EDAMtpc 0000804 | Immunoinformatics 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 0002640 | Cancer EDAMtpc 0000199 | Mutation and polymorphism EDAMtpc 0000655 | 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 0000199 | Mutation and polymorphism 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 0000199 | Mutation and polymorphism EDAMtpc 0002830 | Immune-related proteins and peptides EDAMtpc 0000639 | Protein sequences 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 0000199 | Mutation and polymorphism 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 0000644 | Proteome EDAMdat 0000849 | Sequence record EDAMid 0002384 | IPI protein ID EDAMfmt 0002331 | 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 0000147 | 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 0000747 | Nucleic acid functional sites EDAMtpc 0000617 | Ribosomes 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 0000617 | Ribosomes EDAMtpc 0000110 | Transcription 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 0000798 | Mobile genetic elements Xref SP_FT | None Example Identifier | ISA1083-2 ID ISOLA Name Italian Solanaceae genome resource (ISOLA) Desc Solanaceae genome resource. URL http://biosrv.cab.unina.it/isola Taxon 4070 | Solanaceae EDAMtpc 0000780 | Plant EDAMtpc 0000643 | Genomes EDAMtpc 0000780 | Plant 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 0000740 | Nucleic acid sequence alignment EDAMtpc 0000697 | 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 0000197 | Gene expression and regulation EDAMtpc 0002640 | Cancer 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 0002811 | 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 0000620 | Drugs and targets EDAMtpc 0002811 | 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 0000624 | 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 0000128 | Protein interactions EDAMtpc 0000081 | Structure 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 0000811 | Transcription factor and binding site EDAMtpc 0000188 | 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 0000637 | 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 0000081 | Structure 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 0000643 | Genomes 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 0000602 | Pathways, networks and models 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 0000624 | 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 0000643 | Genomes EDAMtpc 0000623 | Gene family or system EDAMtpc 0000622 | Genomics EDAMdat 0002984 | Pathway or network report EDAMdat 0002589 | Hierarchy annotation EDAMdat 0002018 | Metadata and annotation EDAMid 0002891 | Biological model accession EDAMid 0001154 | KEGG object identifier EDAMid 0002343 | Pathway ID (KEGG) EDAMfmt 0002331 | 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 Metadata and 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 Taxon 9711 | Chordata EDAMtpc 0000612 | Cell cycle and development 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 0002640 | Cancer 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 0000748 | Protein functional sites EDAMtpc 0000158 | Sequence motifs EDAMtpc 0000635 | Specific protein 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 0000202 | Pharmacoinformatics EDAMtpc 0000698 | Protein tertiary structure EDAMtpc 0000635 | Specific protein 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 0000798 | Mobile genetic elements 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000197 | Gene expression and regulation EDAMtpc 0000140 | 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001026 | Gene symbol EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002331 | 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001026 | Gene symbol EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002331 | 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 0000182 | Sequence alignment EDAMtpc 0000084 | Phylogenetics EDAMdat 0001456 | Protein report (membrane protein) EDAMid 0002797 | Protein ID (LGICdb) EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000748 | Protein functional sites EDAMtpc 0000148 | Protein-ligand interactions 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 0000153 | 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 0000153 | 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 0000635 | Specific protein 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 0002819 | Invertebrate EDAMtpc 0000643 | Genomes 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/ PMID 18628892 Cat Organism-specific databases Taxon 4577 | Zea mays EDAMtpc 0000780 | Plant EDAMtpc 0000621 | Organism EDAMdat 0002703 | Gene annotation (clone or EST) EDAMid 0002798 | MaizeDB ID EDAMfmt 0002331 | 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 0000612 | Cell cycle and development 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 0000199 | Mutation and polymorphism 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 0000644 | Proteome 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 0000780 | Plant EDAMtpc 0000643 | Genomes EDAMtpc 0000780 | Plant ID MatrixDB Name MatrixDB Desc A database of interactions established by extracellular proteins and polysaccharides. URL http://matrixdb.ibcp.fr/ Taxon 1 | all EDAMtpc 0000128 | 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 0000821 | Enzymes 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 0000610 | Ecoinformatics ID MeGX IDalt MegDB Name MeGX marine microbial ecological genomics database Desc Specialized database for genome-wide analysis of marine bacteria and metagenomics. Taxon 1 | all URL http://www.megx.net EDAMtpc 0000610 | 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 0002640 | Cancer 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 0000197 | Gene expression and regulation 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 0000821 | Enzymes EDAMtpc 0002811 | Nomenclature EDAMdat 0000896 | Protein report EDAMid 0002629 | Enzyme ID (MEROPS) EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000753 | Metabolic pathways EDAMtpc 0000780 | Plant 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 0000608 | Cell lines and culture 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 0000821 | Enzymes ID MethDB Name MethDB DNA methylation database Desc DNA methylation and environmental epigenetic effects. URL http://www.methdb.de Taxon 1 | all EDAMtpc 0000654 | 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 0002820 | Vertebrate EDAMtpc 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0002799 | Gene ID (MfunGD) EDAMfmt 0002331 | 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 0002820 | Vertebrate EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0002093 | Data reference EDAMid 0001792 | Gene name (MGD) EDAMfmt 0002331 | 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0002093 | Data reference EDAMid 0001026 | Gene symbol EDAMfmt 0002331 | 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 0000771 | 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 0000698 | 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 0000641 | Repeat sequence 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 0000803 | Human disease EDAMtpc 0000621 | Organism EDAMtpc 0000625 | Genotype and phenotype EDAMdat 0000920 | Genotype/phenotype annotation EDAMid 0001153 | OMIM ID EDAMfmt 0002331 | 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 0000147 | Protein-protein interactions EDAMdat 0001565 | Protein-protein interaction EDAMid 0002615 | MINT ID EDAMfmt 0002331 | 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 0000780 | Plant EDAMtpc 0000643 | Genomes EDAMtpc 0000797 | Comparative genomics EDAMtpc 0000780 | Plant 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 0000661 | miRNA EDAMtpc 0000623 | 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 0000770 | Data types and objects ID miROrtho Name miROrtho animal microRNA database Desc Catalogue of animal microRNA genes. URL http://cegg.unige.ch/mirortho Taxon 33208 | Metazoa EDAMtpc 0000661 | miRNA EDAMtpc 0000623 | 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 0000152 | Carbohydrates EDAMdat 0002313 | Carbohydrate structure report EDAMid 0002746 | MonosaccharideDB ID EDAMfmt 0002331 | 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 0000199 | Mutation and polymorphism 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 0000779 | Mitochondria EDAMtpc 0000623 | Gene family or system EDAMtpc 0000655 | mRNA, EST or cDNA ID MITOP2 Name Mitochondrial proteome database Desc Mitochondria-related genes, proteins and diseases. URL http://www.mitop.de:8080/mitop2/ Taxon 2759 | Eukaryota EDAMtpc 0000779 | Mitochondria EDAMtpc 0000644 | Proteome EDAMtpc 0000634 | Disease 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 0000779 | Mitochondria EDAMtpc 0000644 | Proteome ID MLVAbank Name Bacterial MLVA-genotyping service (MLVAbank) Desc Bacterial MLVA-genotyping service. URL http://mlva.u-psud.fr/ Taxon 2 | Bacteria EDAMtpc 0000625 | Genotype and phenotype ID MMsINC Name MMsINC chemoinformatics database Desc Chemoinformatics database. URL http://mms.dsfarm.unipd.it/MMsINC/search/ Taxon None EDAMtpc 0000154 | 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 0000602 | Pathways, networks and models EDAMtpc 0000782 | Fungal EDAMtpc 0000643 | Genomes 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 0000698 | Protein tertiary structure EDAMdat 0002092 | SNP annotation EDAMdat 0001537 | Protein structure report EDAMid 0003021 | UniProt accession EDAMid 0001106 | dbSNP ID EDAMfmt 0002331 | 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 0000602 | 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 0002640 | Cancer EDAMtpc 0000625 | Genotype and phenotype ID MolliGen Name MolliGen Mollicutes database Desc Comparative genomics of Mollicutes. URL http://cbi.labri.fr/outils/molligen/ Taxon 31969 | Mollicutes EDAMtpc 0000797 | 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 0000797 | 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 0000780 | Plant EDAMtpc 0000643 | Genomes EDAMtpc 0000780 | Plant 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 0000197 | Gene expression and regulation 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 0000621 | Organism 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 0000128 | 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 0000804 | Immunoinformatics EDAMtpc 0000634 | Disease 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 0000602 | Pathways, networks and models EDAMtpc 0000782 | Fungal EDAMtpc 0000643 | Genomes 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 0000748 | Protein functional sites EDAMtpc 0000158 | Sequence motifs EDAMtpc 0000736 | Protein domains EDAMtpc 0000188 | 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 0000154 | Small molecules EDAMtpc 0000593 | NMR 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 0000796 | 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 0000608 | Cell lines and culture 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 0000623 | Gene family or system EDAMtpc 0000199 | Mutation and polymorphism 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 0000197 | Gene expression and regulation EDAMtpc 0000659 | 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 0000655 | 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 0000635 | Specific protein 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 0002229 | Cell biology informatics 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 0002229 | Cell biology informatics 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 0000643 | Genomes EDAMtpc 0000797 | Comparative genomics EDAMdat 0000916 | Gene annotation EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000197 | Gene expression and regulation 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 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000655 | 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 0000643 | Genomes EDAMtpc 0000783 | Pathogen EDAMtpc 0000797 | Comparative genomics EDAMdat 0000916 | Gene annotation EDAMid 0001179 | NCBI taxonomy ID EDAMid 0002737 | FIG ID EDAMfmt 0002331 | 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 0000593 | NMR 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 0000134 | Mass spectrometry ID NORINE Name NORINE database of nonribosomal peptides Desc Database of nonribosomal peptides. URL http://bioinfo.lifl.fr/norine/ Taxon 1 | all EDAMtpc 0000613 | 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 0000803 | Human disease 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 0000635 | Specific protein 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 0000655 | 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 0000643 | Genomes EDAMtpc 0001811 | Prokaryote 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 0000635 | Specific protein 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 0000748 | Protein functional sites EDAMtpc 0000635 | Specific protein 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000722 | Nucleic acid classification EDAMtpc 0000084 | Phylogenetics EDAMtpc 0000194 | Phylogenomics EDAMdat 0002093 | Data reference EDAMid 0000989 | Protein identifier EDAMfmt 0002331 | 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 0000722 | 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 0000821 | Enzymes 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 0000620 | Drugs and targets EDAMtpc 0000634 | Disease EDAMid 0002800 | Orpha number EDAMfmt 0002331 | HTML EDAMdat 0001622 | 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 0000722 | Nucleic acid classification EDAMtpc 0000623 | 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000640 | Nucleic acid sequences EDAMtpc 0000780 | Plant 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 0000625 | Genotype and phenotype EDAMtpc 0000780 | Plant EDAMtpc 0000643 | Genomes 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 0000803 | Human disease EDAMdat 0000918 | Sequence variation annotation EDAMid 0002748 | Database name (Osteogenesis) EDAMfmt 0002331 | 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 0000623 | Gene family or system EDAMtpc 0000197 | Gene expression and regulation 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 0000741 | 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 0000748 | Protein functional sites 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 0000586 | Proteins 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 0000602 | Pathways, networks and models EDAMtpc 0000724 | Protein families EDAMtpc 0000623 | Gene family or system EDAMtpc 0000084 | Phylogenetics EDAMdat 0002984 | Pathway or network report EDAMdat 0000907 | Protein family annotation EDAMid 0001161 | Pathway ID (Panther) EDAMid 0002783 | Protein family ID (PANTHER) EDAMfmt 0002331 | 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 0002821 | Unicellular eukaryote EDAMtpc 0000643 | Genomes 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000783 | Pathogen 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 0000197 | Gene expression and regulation EDAMtpc 0000780 | Plant EDAMtpc 0000754 | Signalling pathways EDAMtpc 0000780 | Plant EDAMtpc 0000783 | Pathogen 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 0000602 | Pathways, networks and models 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 0000754 | Signalling pathways EDAMdat 0002984 | Pathway or network report EDAMid 0002344 | Pathway ID (NCI-Nature) EDAMfmt 0002331 | 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 0000081 | Structure EDAMdat 0000883 | Structure EDAMdat 0002085 | Structure report EDAMid 0001127 | PDB ID EDAMfmt 0001476 | PDB format EDAMfmt 0001478 | PDBML EDAMfmt 0001477 | mmCIF EDAMfmt 0002331 | 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 0000081 | Structure 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 0002814 | Protein structure EDAMdat 0002085 | Structure report EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0002814 | 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 0000081 | Structure EDAMdat 0000883 | Structure EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0002814 | 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 0000698 | 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 0002814 | Protein structure EDAMdat 0002085 | Structure report EDAMid 0001127 | PDB ID EDAMfmt 0002331 | 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 0000820 | Membrane protein 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 0002640 | Cancer EDAMtpc 0000197 | Gene expression and regulation 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 0000643 | Genomes 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 0000767 | Peptide identification and proteolysis ID Peptaibol Name Peptaibol database of natural fungal peptides Desc Natural fungal peptides. URL http://peptaibol.cryst.bbk.ac.uk Taxon 4751 | Fungi EDAMtpc 0000613 | Peptides and amino acids EDAMtpc 0000782 | Fungal 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 0000613 | Peptides and amino acids EDAMtpc 0000767 | Peptide identification and proteolysis EDAMdat 0000896 | Protein report EDAMdat 0000945 | Peptide identification EDAMdat 0002536 | Mass spectrometry data EDAMid 0002384 | IPI protein ID EDAMid 0002398 | Protein ID (Ensembl) EDAMid 0000989 | Protein identifier EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000635 | Specific protein EDAMtpc 0000613 | 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 0000635 | Specific protein EDAMdat 0000896 | Protein report EDAMid 0002792 | Protein ID (PeroxiBase) EDAMfmt 0002331 | 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 0000753 | Metabolic pathways EDAMtpc 0000635 | Specific protein EDAMtpc 0000644 | Proteome 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 0000767 | Peptide identification and proteolysis 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 0000741 | Protein sequence alignment EDAMtpc 0000188 | Sequence profiles and HMMs EDAMtpc 0000724 | Protein families EDAMtpc 0000736 | Protein domains EDAMdat 0000907 | Protein family annotation EDAMid 0001096 | Sequence accession (protein) EDAMid 0001138 | Pfam accession number EDAMid 0001179 | NCBI taxonomy ID EDAMid 0002758 | Pfam clan ID EDAMfmt 0002331 | 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000780 | Plant 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 0000625 | Genotype and phenotype EDAMtpc 0000202 | Pharmacoinformatics EDAMtpc 0000208 | Pharmacogenomics EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0002649 | PharmGKB ID EDAMfmt 0002331 | 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 0000625 | Genotype and phenotype 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000623 | Gene family or system EDAMtpc 0000783 | Pathogen 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 0000751 | Phosphorylation EDAMtpc 0000780 | Plant EDAMtpc 0000134 | Mass spectrometry EDAMtpc 0000767 | Peptide identification and proteolysis 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 0000751 | Phosphorylation EDAMdat 0002071 | Sequence motif (protein) EDAMid 0001096 | Sequence accession (protein) EDAMid 0002775 | Kinase name EDAMid 0001009 | Protein name EDAMfmt 0002331 | 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 0000751 | Phosphorylation EDAMtpc 0000698 | Protein tertiary structure 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 0000751 | Phosphorylation 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 0000751 | Phosphorylation EDAMdat 0002071 | Sequence motif (protein) EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000751 | Phosphorylation EDAMdat 0002071 | Sequence motif (protein) EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000741 | Protein sequence alignment EDAMtpc 0000084 | 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 0000084 | 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 0000724 | Protein families EDAMtpc 0000164 | Sequence clustering 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 0000147 | 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 0000639 | Protein sequences EDAMdat 0002201 | Sequence record full EDAMid 0000989 | Protein identifier EDAMfmt 0002331 | 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 0000164 | Sequence clustering EDAMtpc 0000724 | Protein families EDAMdat 0000907 | Protein family annotation EDAMid 0001136 | PIRSF ID EDAMfmt 0002331 | 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 0000780 | Plant 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 0000665 | snoRNA EDAMtpc 0000780 | Plant 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMtpc 0000780 | Plant 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 0000796 | Genetic mapping and linkage EDAMtpc 0000780 | Plant 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 0000635 | Specific protein EDAMtpc 0000780 | Plant 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMtpc 0000780 | Plant 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 lake GO annotation, and the genes that are already annotated in GeneDB. Predictions of PlasmoDraft are based on transcriptome, proteome, and interactome data, and are thus complementary to predictions achieved by sequence homology. URL http://www.atgc-montpellier.fr/PlasmoDraft/ Taxon 5820 | Plasmodium EDAMtpc 0000219 | Annotation EDAMtpc 0000643 | Genomes 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 0000779 | Mitochondria EDAMtpc 0000663 | tRNA EDAMtpc 0000623 | Gene family or system EDAMtpc 0000780 | Plant 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 0000635 | Specific protein EDAMtpc 0000644 | Proteome EDAMtpc 0000616 | Organelles 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 0000602 | Pathways, networks and models EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | HTML EDAMdat 0002093 | 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 0000698 | 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 0000199 | Mutation and polymorphism 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 0000643 | Genomes ID PPD Name PPD protein pKa values database Desc Protein pKa values. URL http://www.darrenflower.info/PPD/pKahomepage.htm Taxon 1 | all EDAMtpc 0000123 | Protein physicochemistry 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 0000660 | rRNA EDAMtpc 0000623 | 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 0000635 | Specific protein EDAMdat 0000896 | Protein report EDAMid 0000989 | Protein identifier EDAMfmt 0002331 | 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 0000202 | 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 0000767 | Peptide identification and proteolysis EDAMtpc 0000121 | Proteomics EDAMdat 0002536 | Mass spectrometry data EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000724 | Protein families EDAMtpc 0000748 | Protein functional sites EDAMtpc 0000158 | Sequence motifs EDAMdat 0001355 | Protein signature EDAMid 0001137 | PRINTS code EDAMfmt 0002331 | 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 0000147 | 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 0000632 | Molecular probes or primers EDAMtpc 0000660 | 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 0000803 | Human disease EDAMtpc 0000634 | Disease EDAMtpc 0000625 | Genotype and phenotype 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 0000821 | Enzymes EDAMtpc 0000148 | Protein-ligand interactions EDAMtpc 0000154 | 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 0000724 | Protein families EDAMtpc 0000736 | Protein domains EDAMdat 0000872 | Phylogenetic tree EDAMdat 0001298 | Sequence features (motifs) EDAMdat 0000907 | Protein family annotation EDAMdat 0001384 | Sequence alignment (protein) EDAMid 0001142 | ProDom accession number EDAMfmt 0002331 | 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 0000197 | Gene expression and regulation EDAMtpc 0000811 | Transcription factor and binding site 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription 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 0000767 | Peptide identification and proteolysis EDAMtpc 0000134 | Mass spectrometry EDAMtpc 0000780 | Plant EDAMdat 0000943 | Mass spectrometry spectra EDAMid 0001895 | Locus ID (AGI) EDAMfmt 0002331 | 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 0000625 | Genotype and phenotype EDAMtpc 0000782 | Fungal 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 0000748 | Protein functional sites EDAMtpc 0000158 | Sequence motifs EDAMtpc 0000188 | 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 0000630 | Gene structure EDAMtpc 0002814 | 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 0002814 | Protein structure 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 0000724 | Protein families EDAMtpc 0000736 | Protein domains EDAMtpc 0000748 | Protein functional sites EDAMtpc 0000158 | Sequence motifs EDAMtpc 0000188 | Sequence profiles and HMMs EDAMdat 0002071 | Sequence motif (protein) EDAMid 0001117 | Prosite accession number EDAMfmt 0002331 | 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 0000724 | Protein families EDAMtpc 0000164 | Sequence clustering EDAMdat 0000907 | Protein family annotation EDAMid 0001075 | 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 0000736 | Protein domains EDAMdat 0000896 | Protein report EDAMid 0003021 | 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 0000724 | Protein families EDAMdat 0000907 | Protein family annotation EDAMfmt 0001978 | DASGFF EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000586 | Proteins 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 0000748 | Protein functional sites EDAMtpc 0000158 | 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 0000697 | 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0002314 | GI number EDAMid 0002744 | Locus ID (PseudoCAP) EDAMfmt 0002331 | 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 0002846 | Gene regulatory networks EDAMtpc 0000128 | Protein interactions EDAMtpc 0000602 | 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 0000199 | Mutation and polymorphism EDAMtpc 0002640 | Cancer 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 0000154 | 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 0002640 | Cancer EDAMtpc 0000654 | DNA EDAMid 0001026 | Gene symbol EDAMid 0000976 | Identifier (typed) EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002372 | 2D PAGE spot annotation EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002372 | 2D PAGE spot annotation EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0002820 | Vertebrate EDAMtpc 0000643 | Genomes 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 0002820 | Vertebrate EDAMtpc 0000643 | Genomes 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 0000803 | Human disease 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 0000602 | Pathways, networks and models EDAMdat 0002984 | Pathway or network report EDAMdat 0000896 | Protein report EDAMid 0000989 | Protein identifier EDAMid 0003021 | UniProt accession EDAMid 0001027 | Gene ID (NCBI) EDAMid 0001011 | EC number EDAMid 0001174 | ChEBI ID EDAMid 0001056 | Database name EDAMid 0000990 | Compound name EDAMid 0001155 | Pathway ID (reactome) EDAMid 0001176 | GO term ID EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000821 | Enzymes EDAMdat 0001509 | Protein report (enzyme) EDAMid 0001012 | Enzyme name EDAMid 0002325 | REBASE enzyme number EDAMfmt 0002331 | 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 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 0000630 | Gene structure EDAMdat 0002043 | Sequence record lite EDAMdat 0001383 | Sequence alignment (nucleic acid) EDAMid 0002781 | REDIdb ID EDAMfmt 0002310 | FASTA-HTML EDAMfmt 0002331 | 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 0000080 | Sequence EDAMtpc 0000797 | Comparative genomics EDAMdat 0000849 | Sequence record EDAMid 0000989 | Protein identifier EDAMfmt 0002331 | 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 0000602 | 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 0000133 | Two-dimensional gel electrophoresis EDAMid 0003021 | UniProt accession EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMfmt 0002331 | 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 0000601 | Protein modifications EDAMdat 0002191 | Protein modification annotation EDAMid 0002619 | RESID ID EDAMfmt 0002332 | 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 0000798 | Mobile genetic elements EDAMtpc 0000780 | Plant 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 0000740 | Nucleic acid sequence alignment EDAMtpc 0000697 | RNA structure and alignment EDAMdat 0002354 | RNA family annotation EDAMid 0002356 | RFAM accession EDAMid 0002606 | RFAM name EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0002820 | Vertebrate EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0002620 | RGD ID EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000821 | Enzymes 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 0000639 | Protein sequences EDAMtpc 0000621 | Organism EDAMdat 0002394 | Gene annotation (functional) EDAMid 0002393 | mFLJ/mKIAA number EDAMfmt 0002331 | 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 0000617 | Ribosomes 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 0000697 | 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 0000781 | Virus EDAMtpc 0000643 | Genomes EDAMdat 0002307 | Virus annotation EDAMid 0002784 | RNAVirusDB ID EDAMfmt 0002331 | 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 0000635 | Specific protein EDAMtpc 0000698 | 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 0000747 | Nucleic acid functional sites EDAMtpc 0000149 | 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 0000635 | Specific protein 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 0000632 | Molecular probes or 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 0000635 | Specific protein 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 0000741 | 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 0000602 | Pathways, networks and models EDAMdat 0002093 | Data reference EDAMdat 0002024 | Enzyme kinetics data EDAMdat 0000908 | Reaction annotation EDAMid 0002309 | Reaction ID (SABIO-RK) EDAMid 0002648 | Reaction kinetics ID (SABIO-RK) EDAMid 0001011 | EC number EDAMfmt 0002331 | 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000623 | 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 0000736 | Protein domains EDAMdat 0001554 | SCOP node EDAMdat 0002093 | Data reference EDAMid 0001042 | SCOP sunid EDAMid 0001127 | PDB ID EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000147 | 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 0000128 | Protein interactions EDAMdat 0002359 | Domain-domain interaction EDAMid 0001127 | PDB ID EDAMid 0001042 | SCOP sunid EDAMfmt 0002331 | 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=¤tChoice=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 0000199 | Mutation and polymorphism EDAMtpc 0000602 | Pathways, networks and models EDAMtpc 0000625 | Genotype and phenotype EDAMdat 0000916 | Gene annotation EDAMid 0001791 | Gene name (HGNC) EDAMfmt 0002331 | 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 0000623 | Gene family or system EDAMtpc 0000197 | Gene expression and regulation 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 0000797 | Comparative genomics EDAMdat 0002711 | Genome metadata EDAMdat 0002394 | Gene annotation (functional) EDAMdat 0000916 | Gene annotation EDAMid 0002737 | FIG ID EDAMfmt 0002331 | 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 0000084 | Phylogenetics EDAMtpc 0000623 | Gene family or system EDAMdat 0000872 | Phylogenetic tree EDAMdat 0002093 | Data reference EDAMdat 0000916 | Gene annotation EDAMid 0001131 | Protein family name EDAMid 0000842 | Identifier EDAMid 0000989 | Protein identifier EDAMid 0001127 | PDB ID EDAMid 0001868 | Taxon EDAMfmt 0002331 | 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 0002817 | Yeast EDAMtpc 0000643 | Genomes EDAMtpc 0000782 | Fungal EDAMdat 0000916 | Gene annotation EDAMid 0001026 | Gene symbol EDAMid 0001807 | ORF name EDAMid 0001901 | Locus ID (SGD) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002372 | 2D PAGE spot annotation EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000754 | Signalling 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 0000660 | rRNA EDAMtpc 0000640 | Nucleic acid sequences EDAMdat 0000855 | Sequence metadata EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002331 | 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 0000660 | rRNA EDAMtpc 0000640 | Nucleic acid sequences EDAMdat 0000855 | Sequence metadata EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002331 | 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 0000724 | Protein families EDAMdat 0000896 | Protein report EDAMdat 0000857 | Database hits (sequence) EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000662 | siRNA 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 0002826 | Protein structure alignment EDAMdat 0001481 | Structure alignment (protein) EDAMid 0002793 | SISYPHUS ID EDAMfmt 0002332 | 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 0000748 | Protein functional sites EDAMtpc 0000148 | Protein-ligand interactions EDAMtpc 0000741 | 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 0000602 | Pathways, networks and models EDAMtpc 0000079 | 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 0000724 | Protein families EDAMtpc 0000736 | Protein domains EDAMdat 0002377 | Protein structure report (domain) EDAMid 0001139 | SMART accession number EDAMid 0002782 | SMART domain name EDAMfmt 0002331 | 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 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 0000698 | Protein tertiary structure EDAMdat 0001460 | Protein structure EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000199 | Mutation and polymorphism 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 0000147 | Protein-protein interactions EDAMtpc 0000698 | Protein tertiary structure EDAMtpc 0000741 | 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 0000664 | snRNA 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 0000665 | snoRNA 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 0000199 | Mutation and polymorphism EDAMtpc 0000803 | Human disease EDAMtpc 0000625 | Genotype and phenotype ID SNPnexus Name SNPnexus database for SNP selection Desc SNP selection database. URL http://www.snp-nexus.org Taxon 9606 | Homo sapiens EDAMtpc 0000199 | Mutation and polymorphism 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 0000796 | Genetic mapping and linkage EDAMtpc 0000199 | Mutation and polymorphism 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 0000655 | mRNA, EST or cDNA EDAMdat 0002703 | Gene annotation (clone or EST) EDAMid 0001108 | GenBank accession EDAMid 0002704 | Clone ID (IMAGE) EDAMfmt 0002331 | 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 0000780 | Plant EDAMtpc 0000643 | Genomes 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 0000630 | Gene structure EDAMtpc 0000747 | Nucleic acid functional sites EDAMtpc 0000114 | RNA splicing EDAMtpc 0000748 | Protein functional sites EDAMtpc 0000158 | Sequence motifs EDAMdat 0000896 | Protein report EDAMid 0001009 | Protein name EDAMfmt 0002331 | 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 0000655 | mRNA, EST or cDNA EDAMtpc 0000630 | Gene structure 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 0000621 | Organism EDAMtpc 0002819 | Invertebrate EDAMtpc 0000643 | Genomes ID STCDB Name Signal transduction classification database (STCDB) Desc Signal transduction classification. URL http://bibiserv.techfak.uni-bielefeld.de/stcdb/ Taxon 1 | all EDAMtpc 0000754 | Signalling 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 0000148 | 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 0000607 | 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 0000797 | 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 0000147 | Protein-protein interactions EDAMid 0002302 | STRING ID EDAMdat 0001663 | Pathway or network (protein-protein interaction) EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000147 | Protein-protein interactions EDAMtpc 0000698 | Protein tertiary structure ID Sulfolobus Name Sulfolobus genome database Desc The three sequenced Sulfolobus genomes. URL http://www.sulfolobus.org Taxon 2284 | Sulfolobus EDAMtpc 0001811 | Prokaryote EDAMtpc 0000643 | Genomes ID SuperDrug Name SuperDrug drug database Desc Drug compounds with conformers. URL http://bioinformatics.charite.de/superdrug Taxon None EDAMtpc 0000620 | 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 0000724 | Protein families EDAMtpc 0000644 | Proteome EDAMtpc 0000188 | 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 0002830 | Immune-related proteins and peptides EDAMtpc 0000154 | 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 0000154 | Small molecules ID Superscent Name Superscent database of scents Desc Database of scent molecules. URL http://bioinformatics.charite.de/superscent Taxon None EDAMtpc 0000618 | Scents 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 0000620 | Drugs and targets EDAMtpc 0000748 | Protein functional sites EDAMtpc 0000148 | Protein-ligand interactions EDAMtpc 0000079 | 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 0000602 | Pathways, networks and models EDAMtpc 0000620 | Drugs and targets EDAMtpc 0000821 | Enzymes ID Supertoxic Name Supertoxic toxic compounds database Desc Database of toxic compounds with synonyms. URL http://bioinformatics.charite.de/supertoxic Taxon None EDAMtpc 0000154 | 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 0000748 | Protein functional sites EDAMtpc 0000698 | Protein tertiary structure 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMtpc 0000780 | Plant EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002364 | Experiment annotation (2D PAGE) EDAMdat 0002372 | 2D PAGE spot annotation EDAMid 0000989 | Protein identifier EDAMid 0002374 | Spot serial number EDAMid 0003021 | UniProt accession EDAMid 0002791 | Reference map name (SWISS-2DPAGE) EDAMfmt 0002331 | 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 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMdat 0002070 | Sequence motif (nucleic acid) EDAMid 0002735 | Database name (SwissRegulon) EDAMid 0002736 | Sequence feature ID (SwissRegulon) EDAMfmt 0002331 | 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 0000164 | Sequence clustering EDAMtpc 0000724 | 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 0000602 | 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 0000623 | 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 0000634 | Disease ID TAED Name The adaptive evolution database (TAED) Desc Protein-encoding gene families. URL http://www.bioinfo.no/tools/TAED Taxon 1 | all EDAMtpc 0000623 | 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 0000780 | Plant EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMdat 0002018 | Metadata and annotation EDAMid 0002387 | TAIR accession EDAMid 0001893 | Locus ID EDAMid 0002780 | Stock number (TAIR) EDAMfmt 0002331 | HTML Xref SP_explicit | Locus ID Query Metadata and 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 Metadata and 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 0000661 | miRNA 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 0000747 | Nucleic acid functional sites EDAMtpc 0000114 | RNA splicing EDAMtpc 0000630 | Gene structure EDAMdat 0001307 | Nucleic acid features (splice sites) EDAMid 0001026 | Gene symbol EDAMfmt 0002331 | 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 0000637 | Taxonomy EDAMid 0001179 | NCBI taxonomy ID EDAMdat 0003028 | Taxonomic data EDAMfmt 0002331 | 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 0000637 | Taxonomy EDAMtpc 0000084 | 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 0000625 | Genotype and phenotype EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0000820 | Membrane protein EDAMtpc 0000724 | Protein families EDAMdat 0001456 | Protein report (membrane protein) EDAMid 0002756 | TCID EDAMfmt 0002331 | 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 0000202 | Pharmacoinformatics EDAMtpc 0000620 | Drugs and targets ID 1000Genomes Name The 1000 Genomes project Desc Database of human genetic variation. URL http://1000genomes.org/page.php Taxon 9606 | Homo sapiens EDAMtpc 0000199 | Mutation and polymorphism 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 0000620 | 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 0000643 | Genomes EDAMtpc 0000780 | Plant EDAMdat 0000916 | Gene annotation EDAMid 0001899 | Locus ID (CMR) EDAMfmt 0002331 | 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 0000724 | Protein families EDAMtpc 0000188 | Sequence profiles and HMMs EDAMdat 0002788 | Sequence profile metadata EDAMid 0001141 | TIGRFam ID EDAMfmt 0002331 | 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 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 0000197 | Gene expression and regulation EDAMtpc 0000200 | 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 0000655 | 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 0000820 | Membrane protein EDAMdat 0001456 | Protein report (membrane protein) EDAMid 0002789 | Protein ID (TopDB) EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000820 | Membrane protein EDAMtpc 0000158 | Sequence motifs EDAMtpc 0000747 | Nucleic acid functional sites EDAMtpc 0000158 | Sequence motifs 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 0002661 | 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 0000635 | Specific protein EDAMdat 0000896 | Protein report EDAMid 0001009 | Protein name EDAMfmt 0002331 | 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 0000754 | Signalling pathways EDAMtpc 0000602 | Pathways, networks and models EDAMtpc 0000079 | Metabolites EDAMtpc 0000821 | Enzymes 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 0000798 | 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 0000641 | Repeat sequence 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 0000084 | Phylogenetics EDAMtpc 0000623 | 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 0000640 | Nucleic acid sequences EDAMtpc 0000663 | tRNA EDAMtpc 0000623 | 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 0000643 | Genomes 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 0000811 | Transcription factor and binding site EDAMtpc 0000644 | Proteome 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 0001811 | Prokaryote EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001097 | Sequence accession (nucleic acid) EDAMfmt 0002331 | 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 0000630 | Gene structure 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 0000133 | Two-dimensional gel electrophoresis EDAMdat 0002372 | 2D PAGE spot annotation EDAMid 0003021 | UniProt accession EDAMfmt 0002331 | 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 0000643 | Genomes EDAMdat 0000916 | Gene annotation EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000625 | Genotype and phenotype EDAMtpc 0000803 | Human disease ID UniGene Acc DB-0107 Name UniGene gene-oriented nucleotide sequence clusters Desc Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. URL http://www.ncbi.nlm.nih.gov/sites/entrez?db=UniGene Cat Sequence databases Taxon 1 | all EDAMtpc 0000655 | mRNA, EST or cDNA EDAMtpc 0000164 | Sequence clustering EDAMtpc 0000722 | Nucleic acid classification EDAMtpc 0000197 | Gene expression and regulation EDAMdat 0002399 | Gene annotation (transcript) EDAMid 0002594 | UniGene taxon EDAMid 0001104 | Sequence cluster ID (UniGene) EDAMfmt 0002331 | 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 0000147 | 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 0000655 | 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 0000753 | 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 0000639 | Protein sequences 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 0000796 | Genetic mapping and linkage EDAMdat 0000916 | Gene annotation EDAMid 0002389 | UniSTS accession EDAMfmt 0002331 | 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 0000666 | rDNA EDAMdat 0000855 | Sequence metadata EDAMid 0002390 | UNITE accession EDAMfmt 0002331 | 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 0000630 | Gene structure EDAMdat 0000916 | Gene annotation EDAMid 0001033 | Gene ID (Ensembl) EDAMfmt 0002331 | 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 0000803 | Human disease 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 0000639 | Protein sequences EDAMdat 0000849 | Sequence record EDAMid 0002392 | UniParc accession EDAMfmt 0002331 | 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 0000639 | Protein sequences EDAMdat 0002201 | Sequence record full EDAMid 0003021 | UniProt accession EDAMfmt 0001929 | FASTA format EDAMfmt 0002376 | RDF EDAMfmt 0002188 | uniprot EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0002201 | Sequence record full EDAMtpc 0000639 | Protein sequences EDAMid 0003021 | UniProt accession EDAMfmt 0001929 | FASTA format EDAMfmt 0002376 | RDF EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0002201 | Sequence record full EDAMtpc 0000639 | Protein sequences EDAMid 0003021 | UniProt accession EDAMfmt 0001929 | FASTA format EDAMfmt 0002376 | RDF EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000164 | Sequence clustering EDAMfmt 0001929 | FASTA format EDAMdat 0001245 | Sequence cluster (protein) EDAMid 0002347 | Sequence cluster ID (UniRef100) EDAMid 0002348 | Sequence cluster ID (UniRef90) EDAMid 0002349 | Sequence cluster ID (UniRef50) EDAMfmt 0002376 | RDF EDAMfmt 0002331 | HTML EDAMfmt 0002332 | 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 0000625 | Genotype and phenotype 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 0000110 | Transcription EDAMtpc 0000747 | Nucleic acid functional sites EDAMtpc 0000158 | Sequence motifs EDAMtpc 0000655 | mRNA, EST or cDNA EDAMdat 0000916 | Gene annotation EDAMid 0001026 | Gene symbol EDAMid 0002391 | UTR accession EDAMid 0002595 | UTRdb taxon EDAMid 0002745 | Locus ID (UTR) EDAMfmt 0002331 | 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 0000110 | Transcription EDAMtpc 0000747 | Nucleic acid functional sites EDAMtpc 0000158 | Sequence motifs EDAMdat 0002762 | Sequence motif metadata EDAMid 0002761 | UTRSite ID EDAMfmt 0002331 | 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 0000804 | Immunoinformatics EDAMdat 0000916 | Gene annotation EDAMid 0002835 | Gene ID (VBASE2) EDAMfmt 0002331 | 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 0000783 | Pathogen EDAMdat 0002399 | Gene annotation (transcript) EDAMdat 0000895 | Peptide annotation EDAMdat 0000916 | Gene annotation EDAMid 0002759 | Gene ID (VectorBase) EDAMfmt 0002331 | 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 0000643 | Genomes 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 0000781 | Virus EDAMtpc 0000741 | Protein sequence alignment EDAMtpc 0000724 | 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 0000781 | Virus EDAMtpc 0000147 | Protein-protein interactions 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 0000635 | Specific protein 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 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0001807 | ORF name EDAMfmt 0002331 | 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 0000133 | Two-dimensional gel electrophoresis EDAMid 0001096 | Sequence accession (protein) EDAMfmt 0002331 | HTML EDAMdat 0002364 | 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 0002819 | Invertebrate EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMid 0000989 | Protein identifier EDAMfmt 0002331 | 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 EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0002295 | Gene ID EDAMid 0002738 | Gene ID (Xenbase) EDAMfmt 0002331 | 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 0000147 | Protein-protein interactions EDAMtpc 0000782 | Fungal 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 0000621 | Organism EDAMtpc 0000630 | Gene structure EDAMtpc 0000782 | Fungal EDAMdat 0000916 | Gene annotation EDAMid 0001807 | ORF name EDAMfmt 0002331 | 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 0002846 | Gene regulatory networks EDAMtpc 0000747 | Nucleic acid functional sites EDAMtpc 0000110 | Transcription EDAMtpc 0000811 | Transcription factor and binding site EDAMtpc 0000782 | Fungal EDAMdat 0000896 | Protein report EDAMdat 0002147 | Protein report (transcription factor) EDAMdat 0000916 | Gene annotation EDAMdat 0002223 | Ontology metadata EDAMdat 0000929 | Gene annotation (expression) EDAMid 0002755 | Transcription factor name EDAMid 0001009 | Protein name EDAMid 0001807 | ORF name EDAMid 0002299 | Gene name EDAMid 0000842 | Identifier EDAMfmt 0002331 | 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 0000796 | Genetic mapping and linkage EDAMtpc 0000782 | Fungal EDAMid 0001026 | Gene symbol EDAMdat 0000916 | Gene annotation EDAMfmt 0002331 | 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 0000197 | Gene expression and regulation EDAMtpc 0000203 | Gene expression profiling EDAMtpc 0000200 | Microarrays EDAMtpc 0000782 | Fungal 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 0002820 | Vertebrate EDAMtpc 0000643 | Genomes EDAMtpc 0000621 | Organism EDAMdat 0000916 | Gene annotation EDAMid 0002643 | Gene ID (ZFIN) EDAMfmt 0002331 | 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