1ID 3did 2Name 3DID database of 3D interacting domains 3Desc A collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 4URL http://3did.irbbarcelona.org/ 5Taxon 1 | all 6EDAMtpc 0147 | Protein-protein interactions 7EDAMtpc 0166 | Protein structural motifs and surfaces 8EDAMdat 2377 | Protein structure report (domain) 9EDAMdat 2359 | Domain-domain interaction 10EDAMdat 2378 | Protein-motif interaction 11EDAMid 1138 | Pfam accession number 12EDAMid 2757 | Pfam domain name 13EDAMid 1116 | ELM ID 14EDAMfmt 2331 | HTML 15Query Protein structure report (domain) | HTML | Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_domain_cgi.pl?draw=graph&domain=%s 16Query Protein structure report (domain) | HTML | Pfam accession number | http://3did.irbbarcelona.org/cgi-bin/query_pfamID_cgi.pl?draw=graph&id=%s 17Query 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 18Query Domain-domain interaction | HTML | Pfam domain name;Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_path_cgi.pl?domain1=%s1&domain2=%s2 19Query Protein structure report (domain) | HTML | ELM ID | http://3did.irbbarcelona.org/cgi-bin/query_peptide_cgi.pl?draw=graph&peptide=%s 20Query 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 21Example Pfam domain name | SH3_1 22Example Pfam accession number | PF00018 23Example Pfam domain name | Ank 24Example Pfam domain name | SH3_1 25Example Pfam domain name | SH2 26Example Pfam domain name | efhand 27Example ELM ID | LIG_SH3_1 28Example ELM ID | LIG_SH3_1 29 30ID abcdb 31Name Archaeal and bacterial ABC transporter database (ABCdb) 32Desc Archaeal and bacterial ABC transporter database. 33URL http://www-abcdb.biotoul.fr 34Taxon 2 | Bacteria 35Taxon 2157 | Archaea 36EDAMtpc 0820 | Membrane proteins 37 38ID ANU-2DPAGE 39Acc DB-0002 40Name Australian National University 2-DE database (ANU-2DPAGE) 41Desc 2-DE PAGE database. 42URL http://semele.anu.edu.au 43Cat 2D gel databases 44Taxon 1 | all 45EDAMtpc 0767 | Protein and peptide identification 46EDAMid 3021 | UniProt accession 47EDAMdat 2364 | Experiment annotation (2D PAGE) 48EDAMfmt 2331 | HTML 49Xref SP_explicit | UniProt accession 50Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://semele.anu.edu.au/cgi-bin/get-2d-entry?%s 51Example UniProt accession | P02930 52Example UniProt accession | Q9SIB9 53 54ID EuPathDB 55IDalt ApiDB 56Acc DB-0153 57Name Apicomplexan database resources (ApiDB) 58Desc A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Cryptosporidium, Giardia, Leishmania, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma). 59URL http://eupathdb.org/eupathdb/ 60URLrest http://eupathdb.org/eupathdb/serviceList.jsp 61Cat Not available 62Taxon 5794 | Apicomplexa 63EDAMtpc 2821 | Unicellular eukaryotes 64EDAMtpc 0783 | Pathogens 65EDAMid 1026 | Gene symbol 66EDAMdat 0916 | Gene annotation 67EDAMfmt 2331 | HTML 68Xref SP_explicit | Gene symbol 69Xref SP_FT | None 70Query Gene annotation | HTML | Gene symbol | http://www.eupathdb.org/gene/%s 71Example Gene symbol | cgd1_1090 72 73ID ApiDB_CryptoDB 74IDalt CryptoDB 75Name Cryptosporidium genome resources (CryptoDB) 76Desc Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium. 77URL http://cryptodb.org/cryptodb/ 78URLrest http://eupathdb.org/eupathdb/serviceList.jsp 79Cat Not available 80Taxon 5806 | Cryptosporidium 81EDAMtpc 2821 | Unicellular eukaryotes 82EDAMtpc 0783 | Pathogens 83EDAMdat 0916 | Gene annotation 84EDAMid 2295 | Gene ID 85EDAMfmt 2331 | HTML 86Xref SP_FT | None 87Query Gene annotation | HTML | Gene ID | http://cryptodb.org/gene/%s 88Example Gene ID | cgd7_20 89 90ID ApiDB_GiardiaDB 91IDalt GiardiaDB 92Name Giardia genome resources (GiardiaDB) 93Desc Genomic-scale datasets for the eukaryotic pathogen Giardia. 94URL http://giardiadb.org/giardiadb/ 95URLrest http://eupathdb.org/eupathdb/serviceList.jsp 96Cat Not available 97Taxon 5740 | Giardia 98EDAMtpc 2821 | Unicellular eukaryotes 99EDAMtpc 0783 | Pathogens 100EDAMdat 0916 | Gene annotation 101EDAMid 2295 | Gene ID 102EDAMfmt 2331 | HTML 103Xref SP_FT | None 104Query Gene annotation | HTML | Gene ID | http://giardiadb.org/gene/%s 105Example Gene ID | GL50803_102438 106 107ID ApiDB_PlasmoDB 108IDalt PlasmoDB 109Name Plasmodium genome resources (PlasmoDB) 110Desc Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium. 111URL http://plasmodb.org/plasmo/ 112URLrest http://eupathdb.org/eupathdb/serviceList.jsp 113Cat Not available 114Taxon 5820 | Plasmodium 115EDAMtpc 2821 | Unicellular eukaryotes 116EDAMtpc 0783 | Pathogens 117EDAMdat 0916 | Gene annotation 118EDAMid 2295 | Gene ID 119EDAMfmt 2331 | HTML 120Xref SP_FT | None 121Query Gene annotation | HTML | Gene ID | http://plasmodb.org/gene/%s 122Example Gene ID | PF11_0344 123 124ID ApiDB_ToxoDB 125IDalt ToxoDB 126Name Toxoplasma genome resources (ToxoDB) 127Desc Genomic-scale datasets associated with the eukaryotic pathogens Toxoplasma. 128URL http://toxodb.org/toxo/ 129URLrest http://eupathdb.org/eupathdb/serviceList.jsp 130Cat Not available 131Taxon 5810 | Toxoplasma 132EDAMtpc 2821 | Unicellular eukaryotes 133EDAMtpc 0783 | Pathogens 134EDAMdat 0916 | Gene annotation 135EDAMid 2295 | Gene ID 136EDAMfmt 2331 | HTML 137Xref SP_FT | None 138Query Gene annotation | HTML | Gene ID | http://toxodb.org/gene/%s 139Example Gene ID | 49.m00014 140 141ID ApiDB_TrichDB 142IDalt TrichDB 143Name Trichomonas genome resources (TrichDB) 144Desc Genomic-scale datasets associated with the eukaryotic Trichomonas. 145URL http://trichdb.org/trichdb/ 146URLrest http://eupathdb.org/eupathdb/serviceList.jsp 147Cat Not available 148Taxon 5721 | Trichomonas 149EDAMtpc 2821 | Unicellular eukaryotes 150EDAMtpc 0783 | Pathogens 151EDAMdat 0916 | Gene annotation 152EDAMid 2295 | Gene ID 153EDAMfmt 2331 | HTML 154Xref SP_FT | None 155Query Gene annotation | HTML | Gene ID | http://trichdb.org/gene/%s 156Example Gene ID | TVAG_386080 157 158ID ApiDB_TriTryPDB 159IDalt TritryPDB 160Name Kinetoplastid genome resources (TritryPDB) 161Desc Kinetoplastid genome resources. 162URL http://tritryPDB.org/tritryPDB/ 163URLrest http://eupathdb.org/eupathdb/serviceList.jsp 164Cat Not available 165Taxon 5653 | Kinetoplastida 166EDAMtpc 2821 | Unicellular eukaryotes 167EDAMtpc 0783 | Pathogens 168EDAMdat 0916 | Gene annotation 169EDAMid 2295 | Gene ID 170EDAMfmt 2331 | HTML 171Xref SP_FT | None 172Query Gene annotation | HTML | Gene ID | http://tritryPDB.org/gene/%s 173Example Gene ID | Tb927.8.620 174 175ID ArrayExpress 176Acc DB-0004 177Name ArrayExpress repository for microarray data 178Desc 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. 179URL http://www.ebi.ac.uk/arrayexpress/ 180Cat Gene expression databases 181Taxon 1 | all 182EDAMtpc 0197 | Gene expression resources 183EDAMtpc 0203 | Transcriptomics 184EDAMtpc 0200 | Microarrays 185EDAMdat 0931 | Experiment annotation (microarray) 186EDAMdat 0929 | Gene annotation (expression) 187EDAMid 0989 | Protein identifier 188EDAMid 1144 | ArrayExpress accession number 189EDAMfmt 2331 | HTML 190Xref SP_explicit | Protein identifier 191Query Gene annotation (expression) {ArrayExpress gene expression summary} | HTML | Protein identifier | http://www.ebi.ac.uk/arrayexpress/genes/uniprot/%s 192Query Experiment annotation (microarray) {ArrayExpress entry} | HTML | ArrayExpress accession number | http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=%s 193Example Protein identifier | P15455 194Example ArrayExpress accession number | E-MEXP-700 195 196ID ASTD 197Name Alternative splicing and transcript diversity (ASTD) database 198Desc Alternative splice events and the resultant isoform splice patterns of genes from human and other model species. Three databases are available: AltSplice, AltExtron, and AEdb. AltSplice and AltExtron provide information on alternative intron/exons, alternative splice events, and isoform splice patterns. AEdb contains: AEdb-Sequence (sequence and properties of alternatively splice exons), AEdb-Function (data on functional aspects of alternative splicing), AEdb-motif (data and sequence of known splice regulatory motifs), and AEdb-minigene (a collection of known minigene constructs for alternative splice events). 199URL http://www.ebi.ac.uk/astd/ 200NARid 28 201NARCat /nar/database/cat/1 | Nucleotide Sequence Databases 202NARSub /nar/database/subcat/1/3 | Gene structure, introns and exons, splice sites 203Abstrct http://nar.oupjournals.org/cgi/content/abstract/34/suppl_1/D46 204Taxon 1 | all 205EDAMtpc 0114 | Gene structure and RNA splicing 206EDAMid 2367 | ASTD ID 207EDAMid 2368 | ASTD ID (exon) 208EDAMid 2369 | ASTD ID (intron) 209EDAMid 2370 | ASTD ID (polya) 210EDAMid 2371 | ASTD ID (tss) 211EDAMdat 2397 | Gene features (exon) 212EDAMdat 0896 | Protein report 213EDAMdat 2399 | Gene annotation (transcript) 214EDAMdat 0916 | Gene annotation 215EDAMdat 1312 | Gene features (promoter) 216EDAMdat 2397 | Gene features (exon) 217EDAMdat 2754 | Gene features (intron) 218EDAMdat 1302 | Nucleic acid features (PolyA signal) 219EDAMid 1033 | Gene ID (Ensembl) 220EDAMid 2398 | Protein ID (Ensembl) 221EDAMfmt 1927 | EMBL format 222EDAMfmt 2305 | GFF 223EDAMfmt 2306 | GTF 224EDAMfmt 1929 | FASTA format 225EDAMfmt 2331 | HTML 226Query Gene annotation | HTML | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s 227Query Gene annotation | EMBL format | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=embl 228Query Gene annotation | FASTA format | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=fasta 229Query Gene annotation | GFF | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=gff 230Query Gene annotation | GTF | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=gtf 231Query Gene annotation (transcript) | HTML | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s 232Query Gene annotation (transcript) | EMBL format | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=embl 233Query Gene annotation (transcript) | GFF | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gff 234Query Gene annotation (transcript) | GTF | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gtf 235Query Protein report | HTML | Protein ID (Ensembl) | http://www.ebi.ac.uk/astd/peptideview.html?acc=%s 236Query Protein report | FASTA format | Protein ID (Ensembl) | http://www.ebi.ac.uk/astd/peptideview.html?acc=%s&export=fasta 237Query Gene features (exon) | HTML | ASTD ID (exon);ASTD ID | http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2 238Query Gene features (intron) | HTML | ASTD ID (intron);ASTD ID | http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2 239Query Gene features (promoter) {TSS} | HTML | ASTD ID (tss);ASTD ID | http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2 240Query Nucleic acid features (PolyA signal) | HTML | ASTD ID (polya) | http://www.ebi.ac.uk/astd/featureview.html?acc=%s 241Example ASTD ID (exon);ASTD ID | EXON00000830017;TRAN00000134394 242Example ASTD ID (intron);ASTD ID | INTR00000830053;TRAN00000134394 243Example ASTD ID | TRAN00000134394 244Example Gene ID (Ensembl) | ENSG00000148680 245Example Protein ID (Ensembl) | PEPT00000029170 246Example Transcript ID (Ensembl) | ENST00000229239 247 248ID Bgee 249Acc DB-0133 250Name Bgee database for gene expression evolution 251Desc 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. 252URL http://bgee.unil.ch 253Cat Gene expression databases 254Taxon 1 | all 255EDAMtpc 0623 | Genes, gene family or system 256EDAMtpc 0197 | Gene expression resources 257EDAMtpc 0203 | Transcriptomics 258EDAMdat 0929 | Gene annotation (expression) 259EDAMdat 0928 | Gene expression profile 260EDAMdat 0916 | Gene annotation 261EDAMdat 2579 | Gene annotation (expressed gene list) 262EDAMid 3021 | UniProt accession 263EDAMid 1033 | Gene ID (Ensembl) 264EDAMfmt 2331 | HTML 265Xref SP_explicit | UniProt accession 266Query Gene annotation | HTML | UniProt accession | http://bgee.unil.ch/bgee/bgee?uniprot_id=%s 267Query Gene annotation | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s 268Query Gene expression profile | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s 269Query Gene annotation (expression) | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=data&gene_id=%s 270Query 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 271Query 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 272Query 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 273Query 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 274Query 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 275Query 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 276Example Gene ID (Ensembl) | ENSG00000091831 277Example UniProt accession | P32234 278 279ID BindingDB 280Acc DB-0127 281Name BindingDB database of measured binding affinities 282Desc Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. 283URL http://www.bindingdb.org/ 284URLlink http://www.bindingdb.org/bind/SearchTemplates.jsp 285Cat Other 286Taxon 1 | all 287EDAMtpc 0148 | Protein-ligand interactions 288EDAMtpc 0620 | Drugs and targets 289EDAMdat 0962 | Small molecule report 290EDAMdat 2402 | Protein-drug interaction 291EDAMdat 0857 | Database hits (sequence) 292EDAMdat 2726 | Inhibitor annotation 293EDAMid 0842 | Identifier 294EDAMid 1127 | PDB ID 295EDAMid 1187 | PubMed ID 296EDAMid 3021 | UniProt accession 297EDAMid 2580 | BindingDB Monomer ID 298EDAMid 1009 | Protein name 299EDAMfmt 2331 | HTML 300Xref SP_explicit | UniProt accession 301Query Protein-drug interaction | HTML | UniProt accession | http://www.bindingdb.org/uniprot/%s 302Query 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 303Query 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 304Query Database hits (sequence) {BindingDB entries} | HTML | Identifier {Protein sequence} | http://www.bindingdb.org/bind/blastResult.jsp?DATASOURCE=protein&Search=B2&blastSeq=%s 305Query Small molecule report | HTML | BindingDB Monomer ID | http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=%s 306Query Small molecule report | HTML | Identifier {SMILES string} | http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=4&submit=Search&smilesStr=%s 307Query Protein-drug interaction | HTML | PDB ID | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_PDBids.jsp?PDBids_submit=Search&PDBids=%s 308Query Protein-drug interaction | HTML | PubMed ID | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=%s 309Example UniProt accession | Q29005 310Example Protein name | ABL 311Example Protein name | Ab N1G9 312Example Identifier {Protein sequence} | VKCGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLD 313Example BindingDB Monomer ID | 100 314Example Identifier {SMILES string} | CC%28C%29C1%28C%29SC%28Nc2ccccc2C%28F%29%28F%29F%29%3DNC1%3DO+%7Cc%3A18%7C 315Example PDB ID | 1OKZ 316Example PubMed ID | 17408953 317 318ID BIPA 319Name BIPA database for interaction between protein and nucleic acid 320Desc Protein-nucleic acid interactions, with various features of protein-nuleic acid interfaces. 321URL http://www-cryst.bioc.cam.ac.uk/bipa 322Taxon 1 | all 323EDAMtpc 0149 | Protein-nucleic acid interactions 324EDAMdat 1567 | Protein-nucleic acid interaction 325EDAMdat 2358 | Domain-nucleic acid interaction 326EDAMid 1042 | SCOP sunid 327EDAMid 1127 | PDB ID 328EDAMfmt 2331 | HTML 329Query Protein-nucleic acid interaction | HTML | PDB ID | http://mordred.bioc.cam.ac.uk/bipa/structures/%s 330Query Domain-nucleic acid interaction | HTML | SCOP sunid | http://mordred.bioc.cam.ac.uk/bipa/scops/%s 331Example PDB ID | 10MH 332Example SCOP sunid | 120412 333 334ID BRENDA 335Acc DB-0131 336Name BRENDA comprehensive enzyme information system 337Desc Comprehensive enzyme information. 338URL http://www.brenda-enzymes.org 339URLsoap http://www.brenda-enzymes.org/soap2 340Cat Enzyme and pathway databases 341Taxon 1 | all 342EDAMtpc 0821 | Enzymes and reactions 343EDAMdat 1509 | Protein report (enzyme) 344EDAMid 3021 | UniProt accession 345EDAMid 1011 | EC number 346EDAMid 2593 | BRENDA organism ID 347EDAMfmt 2331 | HTML 348Xref SP_explicit | EC number;BRENDA organism ID 349Query Protein report (enzyme) {BRENDA entry} | HTML | EC number | http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s 350Query 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 351Query 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 352Example EC number | 1.1.5.82 353Example EC number;UniProt accession | 1.1.5.82;P15719 354Example EC number;UniProt accession;BRENDA organism ID | 1.1.5.82;P15719;4577 355 356ID CATH 357Name CATH protein structure classification database 358Desc 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. 359URL http://www.cathdb.info/ 360URLsoap http://api.cathdb.info/api/soap/dataservices/wsdl 361Taxon 1 | all 362EDAMtpc 0736 | Protein domains and folds 363EDAMtpc 3052 | Sequence clusters and classification 364EDAMdat 0901 | Protein features (domains) 365EDAMdat 1553 | CATH node 366EDAMdat 1762 | CATH domain report 367EDAMid 1040 | CATH domain ID 368EDAMid 1008 | Polypeptide chain ID 369EDAMid 1127 | PDB ID 370EDAMid 1043 | CATH node ID 371EDAMfmt 2331 | HTML 372EDAMfmt 2332 | XML 373Query CATH domain report | HTML | CATH domain ID | http://www.cathdb.info/domain/%s 374Query CATH domain report | XML | CATH domain ID | http://www.cathdb.info/domain/%s?view=xml 375Query Protein features (domains) {CATH chain} | HTML | Polypeptide chain ID | http://www.cathdb.info/chain/%s 376Query Protein features (domains) {PDB} | HTML | PDB ID | http://www.cathdb.info/PDB/%s 377Query Protein features (domains) {PDB} | XML | PDB ID | http://www.cathdb.info/PDB/%s?view=xml 378Query CATH node | HTML | CATH node ID | http://www.cathdb.info/cathnode/%s 379Example CATH domain ID | 1cukA01 380Example Polypeptide chain ID | 1cukA 381Example PDB ID | 1cuk 382Example CATH node ID | 1.10.10.10 383 384 385ID CDD 386Name Conserved domain database (CDD) 387Desc A collection of multiple sequence alignments for ancient domains and full-length proteins. 388URL http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml 389Cat Not available 390Taxon 1 | all 391EDAMtpc 0741 | Protein sequence alignment 392EDAMtpc 3052 | Sequence clusters and classification 393EDAMtpc 0736 | Protein domains and folds 394EDAMdat 0901 | Protein features (domains) 395EDAMdat 1384 | Sequence alignment (protein) 396EDAMdat 0907 | Protein family annotation 397EDAMid 2714 | CDD PSSM-ID 398EDAMid 2666 | CDD ID 399EDAMid 2327 | GI number (protein) 400EDAMid 1096 | Sequence accession (protein) 401EDAMfmt 2331 | HTML 402EDAMfmt 2332 | XML 403Xref SP_FT | None 404Query Sequence alignment (protein) {Conserved Domain Summary} | HTML | CDD ID | http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s 405Query Sequence alignment (protein) {Conserved Domain Summary} | HTML | CDD PSSM-ID | http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s 406Query Protein family annotation {Conserved Domain Document Summary} | HTML | CDD ID | http://www.ncbi.nlm.nih.gov/sites/cdd?term=%s[Accn] 407Query Protein family annotation {Conserved Domain Document Summary} | HTML | CDD PSSM-ID | http://www.ncbi.nlm.nih.gov/cdd/%s 408Query 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 409Query Protein features (domains) {Conserved Protein structure report (domain)} | HTML | Sequence accession (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s 410Query Protein features (domains) {Conserved Protein structure report (domain)} | HTML | GI number (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s 411Query 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 412Query 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 413Example CDD PSSM-ID | 153083 414Example CDD ID | cd00576 415Example Sequence accession (protein) | P26675 416Example GI number (protein) | 76800652 417 418ID CellCycleDB 419Name Cell cycle database (CellCycleDB) 420Desc A collection of genes and proteins involved in human and yeast cell cycle. 421URL http://www.itb.cnr.it/cellcycle/index.html 422Taxon 4932 | Saccharomyces cerevisiae 423Taxon 9606 | Homo sapiens 424EDAMtpc 0635 | Specific protein resources 425EDAMtpc 2229 | Cell biology resources 426EDAMtpc 0782 | Fungi 427EDAMdat 0896 | Protein report 428EDAMdat 0916 | Gene annotation 429EDAMid 2764 | Protein name (UniProt) 430EDAMid 2300 | Gene name (NCBI) 431EDAMfmt 2331 | HTML 432Query Gene annotation | HTML | Gene name (NCBI) | http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=%s 433Query Protein report | HTML | Protein name (UniProt) | http://www.itb.cnr.it/cellcycle/protein_rep.php?protein_name=%s 434Example Gene name (NCBI) | CCND1 435Example Protein name (UniProt) | P53 436 437ID CMR 438Acc DB-0009 439Name Comprehensive microbial genome resource (CMR) 440Desc 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. 441URL http://cmr.tigr.org/ 442Cat Genome annotation databases 443Taxon 2 | Bacteria 444EDAMtpc 1811 | Prokaryotes and archae 445EDAMtpc 0622 | Genomics 446EDAMdat 0916 | Gene annotation 447EDAMdat 2711 | Genome metadata 448EDAMid 3021 | UniProt accession 449EDAMid 1179 | NCBI taxonomy ID 450EDAMid 2292 | GenBank identifier 451EDAMid 2774 | Gene ID (JCVI) 452EDAMid 2786 | NCBI Genome Project ID 453EDAMfmt 2331 | HTML 454Xref SP_implicit | UniProt accession 455Query Gene annotation | HTML | Gene ID (JCVI) | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=%s 456Query Gene annotation | HTML | GenBank identifier | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=SP&acc=%s 457Query Gene annotation | HTML | UniProt accession | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=protein_id&acc=%s 458Query Genome metadata {CMR genome page} | HTML | NCBI taxonomy ID | http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?taxon_id=%s 459Query Genome metadata {CMR genome page} | HTML | NCBI Genome Project ID | http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?ncbi_project_id=%s 460Example Gene ID (JCVI) | BA_0001 461Example GenBank identifier | AAP24059.1 462Example UniProt accession | Q81W35 463Example NCBI taxonomy ID | 198094 464Example NCBI Genome Project ID | 309 465 466ID COGEME 467Name Phytopathogenic fungi and oomycete EST database (COGEME) 468Desc Phytopathogenic fungi and oomycete EST database. 469URL http://cogeme.ex.ac.uk/ 470Taxon 4751 | Fungi 471EDAMtpc 0655 | mRNA, EST or cDNA 472EDAMtpc 0783 | Pathogens 473EDAMtpc 0782 | Fungi 474EDAMdat 0849 | Sequence record 475EDAMid 2729 | COGEME EST ID 476EDAMid 2730 | COGEME unisequence ID 477EDAMfmt 2331 | HTML 478Query Sequence record {Unisequence} | HTML | COGEME unisequence ID | http://cogeme.ex.ac.uk/cgi-bin/uni.pl?uni=x 479Query Sequence record {EST} | HTML | COGEME EST ID | http://cogeme.ex.ac.uk/cgi-bin/est.pl?est=x 480Example COGEME EST ID | Bg13901527 481Example COGEME unisequence ID | BgCon[0123] 482 483ID COMPLUYEAST-2DPAGE 484Acc DB-0010 485Name COMPLUYEAST-2DPAGE database 486Desc A two-dimensional polyacrilamide gel electrophoresis federated database. 487URL http://compluyeast2dpage.dacya.ucm.es/ 488Cat 2D gel databases 489Taxon 4932 | Saccharomyces cerevisiae 490EDAMtpc 0767 | Protein and peptide identification 491EDAMdat 2364 | Experiment annotation (2D PAGE) 492EDAMid 3021 | UniProt accession 493EDAMid 0989 | Protein identifier 494EDAMfmt 2331 | HTML 495Xref SP_explicit | UniProt accession 496Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s 497Query Experiment annotation (2D PAGE) | HTML | Protein identifier | http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s 498Example UniProt accession | P83784 499Example Protein identifier | CAP6_CANAL 500 501ID ConoServer 502Acc DB-0156 503Name Cone snail toxin database (ConoServer) 504Desc Conotoxin peptide sequences and structures. 505URL http://www.conoserver.org/ 506Cat Organism-specific databases 507Taxon 6490 | Conus 508EDAMtpc 2661 | Toxins and targets 509EDAMdat 0896 | Protein report 510EDAMid 2804 | Protein ID (ConoServer) 511EDAMfmt 2331 | HTML 512Xref SP_explicit | Protein ID (ConoServer) 513Query Protein report | HTML | Protein ID (ConoServer) | http://www.conoserver.org/?page=card&table=protein&id=%s 514Example Protein ID (ConoServer) | 3271 515 516ID Cornea-2DPAGE 517Acc DB-0011 518Name Human cornea 2-DE database (Cornea-2DPAGE) 519Desc Two-dimensional polyacrylamide gel electrophoresis federated database. 520URL http://www.cornea-proteomics.com/ 521Cat 2D gel databases 522Taxon 9606 | Homo sapiens 523EDAMtpc 0767 | Protein and peptide identification 524EDAMdat 2364 | Experiment annotation (2D PAGE) 525EDAMid 3021 | UniProt accession 526EDAMfmt 2331 | HTML 527Xref SP_explicit | UniProt accession 528Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.daimi.au.dk/cgi-jje/2d/2d.cgi#%s 529Query Experiment annotation (2D PAGE) | Text | UniProt accession | http://www.daimi.au.dk/cgi-jje/2d/2d.cgi?ac=%s&format=text&database=cornea 530Example UniProt accession | P02647 531 532ID CORUM 533Name CORUM comprehensive resource of mammalian protein complexes 534Desc 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. 535URL http://mips.gsf.de/genre/proj/corum 536Taxon 40674 | Mammalia 537EDAMtpc 0147 | Protein-protein interactions 538EDAMtpc 0140 | Protein targeting and localization 539EDAMdat 2712 | Protein structure report (protein complex) 540EDAMid 2713 | Protein ID (CORUM) 541EDAMfmt 2331 | HTML 542Query Protein structure report (protein complex) | HTML | Protein ID (CORUM) | http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=%s 543Example Protein ID (CORUM) | 178 544 545ID CuticleDB 546Name Structural proteins of the arthropod cuticle (CuticleDB) 547Desc 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. 548URL http://biophysics.biol.uoa.gr/cuticleDB/ 549Taxon 6656 | Arthropoda 550EDAMtpc 0635 | Specific protein resources 551EDAMdat 0896 | Protein report 552EDAMid 2715 | Protein ID (CuticleDB) 553EDAMfmt 2331 | HTML 554Query Protein report | HTML | Protein ID (CuticleDB) | http://bioinformatics.biol.uoa.gr/cuticleDB/protview.jsp?id=%s 555Example Protein ID (CuticleDB) | 639 556 557ID DIMA 558Name DIMA domain interaction map 559Desc Functional and physical interactions among conserved protein-domains, including experimental data and computational predictions. 560URL http://mips.gsf.de/genre/proj/dtest/index.html 561Taxon 1 | all 562EDAMtpc 0147 | Protein-protein interactions 563EDAMdat 2359 | Domain-domain interaction 564EDAMid 1138 | Pfam accession number 565EDAMfmt 2331 | HTML 566Query Domain-domain interaction | HTML | Pfam accession number | http://webclu.bio.wzw.tum.de/dima/DomQuery?domain=%s 567Example Pfam accession number | PF00419 568 569ID dbEST 570Name dbEST database of EST sequences 571Desc 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. 572URL http://www.ncbi.nlm.nih.gov/dbEST/ 573Cat Not available 574Taxon 1 | all 575EDAMtpc 0655 | mRNA, EST or cDNA 576EDAMdat 0849 | Sequence record 577EDAMid 2314 | GI number 578EDAMid 1105 | dbEST accession 579EDAMfmt 2310 | FASTA-HTML 580EDAMfmt 2532 | GenBank-HTML 581EDAMfmt 2331 | HTML 582Xref SP_FT | None 583Query Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank 584Query Sequence record | HTML {est} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est 585Query Sequence record | HTML {docsum} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum 586Query Sequence record | FASTA-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta 587Query Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank 588Query Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank 589Query Sequence record | HTML {est} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est 590Query Sequence record | HTML {docsum} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum 591Query Sequence record | FASTA-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta 592Query Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank 593Example dbEST accession | f12345 594Example GI number | 706694 595 596ID DIP 597Acc DB-0016 598Name Database of interacting proteins (DIP) 599Desc 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. 600URL http://dip.doe-mbi.ucla.edu/ 601Cat Protein-protein interaction databases 602Taxon 1 | all 603EDAMtpc 0147 | Protein-protein interactions 604EDAMtpc 3044 | Protein interaction networks 605EDAMdat 1565 | Protein-protein interaction 606EDAMid 2616 | DIP ID 607EDAMfmt 2331 | HTML 608Xref SP_explicit | DIP ID 609Query Protein-protein interaction {DIP entry} | HTML | DIP ID | dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s 610Example DIP ID | DIP-27044N 611 612ID DisProt 613Acc DB-0017 614Name Database of protein disorder (DisProt) 615Desc 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. 616URL http://www.disprot.org/ 617Cat 3D structure databases 618Taxon 1 | all 619EDAMtpc 0698 | Protein tertiary structure 620EDAMdat 2722 | Protein structure report (disordered protein) 621EDAMid 2723 | Protein ID (DisProt) 622EDAMfmt 2331 | HTML 623Xref SP_explicit | Protein ID (DisProt) 624Query Protein structure report (disordered protein) {DisProt entry} | HTML | Protein ID (DisProt) | http://www.disprot.org/protein.php?id=%s 625Example Protein ID (DisProt) | DP00001 626 627ID DOSAC-COBS-2DPAGE 628Acc DB-0018 629Name DOSAC-COBS 2D-PAGE database 630Desc Two-dimensional polyacrylamide gel electrophoresis federated database. 631URL http://www.dosac.unipa.it/2d/ 632Cat 2D gel databases 633Taxon 1 | all 634EDAMtpc 0767 | Protein and peptide identification 635EDAMdat 2364 | Experiment annotation (2D PAGE) 636EDAMid 3021 | UniProt accession 637EDAMfmt 2331 | HTML 638Xref SP_explicit | UniProt accession 639Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=O43818 640Example UniProt accession | O43818 641 642ID EcID 643Name E Coli predicted protein interactions database (EcID) 644Desc Results of running an "in silico 2 hybrid system" for all the possible pairs among E. coli proteins. 645URL http://www.pdg.cnb.uam.es/i2h/info.html 646Taxon 562 | Escherichia coli 647EDAMtpc 0147 | Protein-protein interactions 648EDAMid 1026 | Gene symbol 649EDAMdat 0896 | Protein report 650EDAMdat 1565 | Protein-protein interaction 651EDAMdat 2093 | Data reference 652EDAMid 0989 | Protein identifier 653EDAMid 2802 | Protein ID (EcID) 654EDAMfmt 2331 | HTML 655Query Data reference {Protein sequence ID table} | HTML | Protein identifier | http://ecid.bioinfo.cnio.es/Php/PreQuery.php?busca=%s 656Query 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 657Query 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 658Query Protein report | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/ProtInfo.php?busca=%s1seq=%s2&gn=%s3 659Example Protein identifier | NRDD_ECOLI 660Example Protein identifier;Protein ID (EcID);Gene symbol | NRDD_ECOLI;1639;nrdD 661 662ID ECO2DBASE 663IDalt 2DBase-Ecoli 664IDalt EC-2D-GEL 665Acc DB-0115 666Name 2D-PAGE database of Escherichia coli 667Desc 2D-PAGE database of Escherichia coli 668URL None 669Cat 2D gel databases 670Taxon 562 | Escherichia coli 671EDAMtpc 0767 | Protein and peptide identification 672EDAMid 0842 | Identifier 673Xref SP_explicit | Identifier {ECO2DBASE} 674Example Identifier | H021.1 675 676ID ELM 677Name Eukaryotic linear motif resource (ELM) 678Desc 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. 679URL http://elm.eu.org/ 680Taxon 1 | all 681EDAMtpc 0748 | Protein sites and features 682EDAMtpc 0158 | Sequence motifs 683EDAMdat 1298 | Sequence features (motifs) 684EDAMid 2705 | GO term ID (cellular compartment) 685EDAMid 2291 | UniProt ID 686EDAMid 0842 | Identifier 687EDAMid 1868 | Taxon 688EDAMfmt 2331 | HTML 689Query Sequence features (motifs) {ELM report} | HTML | UniProt ID | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s 690Query 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 691Query Sequence features (motifs) {ELM report} | HTML | Identifier {Protein sequence} | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&sequence=%s 692Example UniProt ID;Taxon;GO term ID (cellular compartment) | src_human;10116;GO:0005634 693Example UniProt ID | src_human 694Example Identifier {Protein sequence} | MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL 695 696ID Ensembl 697Acc DB-0023 698Name Ensembl eukaryotic genome annotation project 699Desc Genome databases for vertebrates and other eukaryotic species. 700URL http://www.ensembl.org/ 701Cat Genome annotation databases 702Taxon 33208 | Metazoa 703EDAMtpc 2818 | Eukaryotes 704EDAMdat 0849 | Sequence record 705EDAMdat 0916 | Gene annotation 706EDAMid 1033 | Gene ID (Ensembl) 707EDAMid 2725 | Transcript ID (Ensembl) 708EDAMfmt 1929 | FASTA format 709EDAMfmt 2331 | HTML 710Xref SP_explicit | Transcript ID (Ensembl);Protein ID (Ensembl);Gene ID (Ensembl) 711Xref SP_FT | None 712Query Gene annotation | HTML | Gene ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s 713Query 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 714Example Gene ID (Ensembl);Transcript ID (Ensembl) | ENSG00000139618;ENST00000380152 715 716ID ENZYME 717IDalt EC_number 718Acc DB-0024 719Name Enzyme nomenclature database (ENZYME) 720Desc 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. 721URL http://www.expasy.org/enzyme/ 722Cat Enzyme and pathway databases 723Taxon 1 | all 724EDAMtpc 0821 | Enzymes and reactions 725EDAMtpc 2811 | Nomenclature 726EDAMdat 1509 | Protein report (enzyme) 727EDAMid 1011 | EC number 728EDAMfmt 2331 | HTML 729Xref Other | EC number 730Query Protein report (enzyme) | Text | EC number | http://www.expasy.ch/enzyme/%s.txt 731Query Protein report (enzyme) | HTML | EC number | http://www.expasy.ch/enzyme/%s 732Example EC number | 1.5.99.11 733 734ID ERIC 735Name Enteropathogen resource integration center (ERIC) 736Desc Annotated enterobacterial genome and associated information. 737URL http://www.ericbrc.org/portal/eric/ 738Cat Not available 739Taxon 543 | Enterobacteriaceae 740EDAMtpc 1811 | Prokaryotes and archae 741EDAMtpc 0783 | Pathogens 742Xref SP_FT | None 743 744ID FusionDB 745Name FusionDB database of bacterial and archaeal gene fusion events 746Desc A database of bacterial and archaeal gene fusion events. 747URL http://www.igs.cnrs-mrs.fr/FusionDB/ 748Taxon 2 | Bacteria 749Taxon 2157 | Archaea 750EDAMtpc 0114 | Gene structure and RNA splicing 751EDAMtpc 1811 | Prokaryotes and archae 752 753ID Gene3D 754Acc DB-0029 755Name Gene3D structural and functional annotation of protein families 756Desc Gene3D structural and functional annotation of protein families incorporates several different sources including CATH, DRUGBANK, PFAM etc. 757URL http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ 758URLlink http://gene3d.biochem.ucl.ac.uk/Gene3D/linking 759URLsoap http://funcnet.eu/ 760Cat Family and domain databases 761Taxon 1 | all 762EDAMtpc 0724 | Protein families 763EDAMtpc 1775 | Protein function analysis 764EDAMdat 0907 | Protein family annotation 765EDAMid 1040 | CATH domain ID 766EDAMid 2701 | CATH node ID (family) 767EDAMfmt 2331 | HTML 768Xref SP_explicit | CATH node ID (family) 769Query Protein family annotation {Gene3D entry} | HTML | CATH node ID (family) | http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?family=%s 770Query Protein family annotation {Gene3D entry} | HTML | CATH domain ID | http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?domain_id=%s 771Query Protein family annotation {Gene3D entry} | HTML | CATH node ID (family) | http://www.cathdb.info/cgi-bin/GotoCath.pl?cath=%s 772Example CATH node ID (family) | 2.10.10.10 773Example CATH domain ID | 1cukA00 774Example CATH node ID (family) | G3DSA:3.40.30.10 775 776ID GeneCards 777Acc DB-0030 778Name GeneCards database of human genes, protein and diseases 779Desc 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. 780URL http://www.genecards.org/ 781Cat Human genes and diseases database 782Taxon 9606 | Homo sapiens 783! EDAMtpc 0803 | Human disease 784EDAMtpc 2813 | Disease genes and proteins 785EDAMtpc 3078 | Gene and protein resources 786EDAMtpc 0078 | Protein analysis 787EDAMtpc 0147 | Protein-protein interactions 788EDAMtpc 0602 | Pathways, networks and models 789EDAMtpc 0199 | Genetic variation 790EDAMtpc 2815 | Humans 791EDAMid 3021 | UniProt accession 792EDAMid 1026 | Gene symbol 793EDAMid 2298 | Gene ID (HGNC) 794EDAMid 1025 | Gene identifier 795EDAMid 1904 | Locus ID (EntrezGene) 796EDAMid 2610 | Ensembl ID 797EDAMdat 0916 | Gene annotation 798EDAMfmt 2331 | HTML 799EDAMfmt 2332 | XML 800Xref SP_explicit | Gene identifier {GeneCards} 801Query Gene annotation | HTML | Gene symbol | http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s 802Query Gene annotation | HTML | UniProt accession | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s 803Query Gene annotation | HTML | Locus ID (EntrezGene) | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s 804Query Gene annotation | HTML | Ensembl ID | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s 805Query Gene annotation | HTML | Gene ID (HGNC) | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s 806Query Gene annotation | XML | Gene symbol | http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s&format=xmlByFunction 807Query Gene annotation | HTML | Gene identifier {GeneCards} | http://www.genecards.org/cgi-bin/carddisp.pl?gc_id=%s 808Example Gene symbol | CASP3 809Example Locus ID (EntrezGene) | 1956 810Example Ensembl ID | ENSG00000146648 811Example Gene ID (HGNC) | 2041 812Example Gene identifier {GeneCards} | GC20P040256 813 814ID GeneDB 815Name GeneDB database from Sanger Institute Pathogen Sequencing Units 816Desc Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units). 817URL http://www.genedb.org/ 818Taxon 1 | all 819EDAMtpc 0783 | Pathogens 820EDAMid 1026 | Gene symbol 821EDAMdat 0916 | Gene annotation 822EDAMfmt 2331 | HTML 823Xref SP_FT | None 824Query Gene annotation | HTML | Gene symbol | http://www.genedb.org/gene/%s 825Example Gene symbol | ECA4014 826 827ID GeneFarm 828Acc DB-0032 829Name GeneFarm annotation of Arabidopsis thaliana gene and protein families 830Desc Structural and functionnal annotation of plant gene and protein families by a network of experts. 831URL http://urgi.versailles.inra.fr/Genefarm/index.htpl 832Cat Organism-specific databases 833Taxon 3702 | Arabidopsis thaliana 834EDAMtpc 3078 | Gene and protein resources 835EDAMtpc 0780 | Plants 836EDAMdat 0916 | Gene annotation 837EDAMdat 0907 | Protein family annotation 838EDAMid 2295 | Gene ID 839EDAMid 2731 | Protein family ID (GeneFarm) 840EDAMfmt 2331 | HTML 841Xref SP_explicit | Protein family ID (GeneFarm) 842Query Gene annotation | HTML | Gene ID | http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s 843Query Protein family annotation | HTML | Protein family ID (GeneFarm) | http://urgi.versailles.inra.fr/Genefarm/Family/display_family.htpl?FAM_ID=%s 844Example Protein family ID (GeneFarm) | 59 845Example Gene ID | 907 846 847ID GlycoSuiteDB 848Acc DB-0036 849Name GlycoSuiteDB glycan database 850Desc An annotated and curated relational database of glycan structures. 851URL http://glycosuitedb.expasy.org/ 852Cat PTM databases 853Taxon 1 | all 854EDAMtpc 0152 | Carbohydrates 855EDAMdat 2313 | Carbohydrate structure report 856EDAMid 3021 | UniProt accession 857EDAMfmt 2331 | HTML 858Xref SP_explicit | UniProt accession 859Query Carbohydrate structure report {GlycoSuiteDB entry} | HTML | UniProt accession | http://glycosuitedb.expasy.org/glycosuite/results?prot_swissprot=%s;results_index=protein;ig_hist=1 860Example UniProt accession | P02763 861 862ID GeneID 863Acc DB-0118 864Name GeneID database of genes from NCBI RefSeq genomes 865Desc Database of genes from NCBI RefSeq genomes 866URL http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene 867Cat Genome annotation databases 868Taxon 1 | all 869EDAMtpc 0623 | Genes, gene family or system 870EDAMtpc 0621 | Genome, proteome and model organisms 871EDAMdat 0916 | Gene annotation 872EDAMid 2339 | Ontology term name 873EDAMid 1176 | GO term ID 874EDAMid 1026 | Gene symbol 875EDAMid 1045 | Species name 876EDAMid 1011 | EC number 877EDAMid 0987 | Chromosome name 878EDAMid 1097 | Sequence accession (nucleic acid) 879EDAMid 0842 | Identifier 880EDAMid 1187 | PubMed ID 881EDAMfmt 2331 | HTML 882Xref SP_explicit | Identifier {Unique ID} 883Query Gene annotation {GeneID gene list} | HTML | Identifier {Keyword} | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=%s 884Query 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] 885Query Gene annotation {GeneID gene list} | HTML | Gene symbol | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[sym] 886Query Gene annotation {GeneID gene list} | HTML | PubMed ID | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[PMID] 887Query 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] 888Query Gene annotation {GeneID gene list} | HTML | GO term ID | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="%s"[GO] 889Query 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] 890Query Gene annotation {GeneID gene list} | HTML | EC number | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[EC] 891Query Gene annotation {GeneID gene list} | HTML | Identifier {Unique ID} | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[uid] 892Example Identifier {Keyword} | haem 893Example Sequence accession (nucleic acid) | M11313 894Example Gene symbol | BRCA1 895Example PubMed ID | 11331580 896Example Ontology term name {GO} | cell+adhesion 897Example Chromosome name | Y 898Example Species name | human 899Example EC number | 1.9.3.1 900Example Identifier {Unique ID} | 4156251 901 902ID GOA 903IDalt GOA-UniProt 904Name Gene ontology annotation database for UniProt (GOA-UniProt) 905Desc Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). 906URL http://www.ebi.ac.uk/goa 907Taxon 1 | all 908EDAMtpc 0621 | Genome, proteome and model organisms 909EDAMtpc 0089 | Ontologies 910EDAMdat 0966 | Ontology term 911EDAMdat 2093 | Data reference 912EDAMid 1009 | Protein name 913EDAMid 3021 | UniProt accession 914EDAMid 1176 | GO term ID 915EDAMid 2339 | Ontology term name 916EDAMfmt 2331 | HTML 917Xref SP_implicit | UniProt accession 918Xref EMBL_explicit | UniProt accession 919Query Data reference {GOA-UniProt protein entry} | HTML | UniProt accession | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein 920Query Data reference {GOA-UniProt protein entry} | HTML | Protein name | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein 921Query Ontology term | HTML | GO term ID | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO 922Query Ontology term | HTML | Ontology term name {GO biological process} | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO 923Example Ontology term name {GO biological process} | apoptosis 924Example GO term ID | GO:0006915 925Example Protein name | tropomyosin 926Example UniProt accession | P06727 927 928ID GPCRDB 929Acc DB-0038 930Name Information system for G protein-coupled receptors (GPCRs) 931Desc GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases. 932URL http://www.gpcr.org/7tm/ 933Cat Protein family/group databases 934Taxon 2759 | Eukaryota 935EDAMtpc 0820 | Membrane proteins 936EDAMtpc 0148 | Protein-ligand interactions 937EDAMdat 1456 | Protein report (membrane protein) 938EDAMid 1131 | Protein family name 939EDAMfmt 2331 | HTML 940Xref SP_implicit | Protein family name 941Query Protein report (membrane protein) {GPCRDB entry} | HTML | Protein family name | http://www.gpcr.org/7tm/proteins/%s 942Example Protein family name | a1kyp5_petma 943 944ID Gramene 945Acc DB-0039 946Name Gramene database for comparative grass genomics 947Desc 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. 948URL http://www.gramene.org/ 949Cat Organism-specific databases 950Taxon 4479 | Poaceae 951EDAMtpc 0797 | Comparative genomics 952EDAMtpc 0625 | Genotype and phenotype resources 953EDAMtpc 0780 | Plants 954EDAMtpc 0602 | Pathways, networks and models 955EDAMdat 0896 | Protein report 956EDAMid 3021 | UniProt accession 957EDAMfmt 2331 | HTML 958Xref SP_explicit | UniProt accession 959Query Protein report {Gramene entry} | HTML | UniProt accession | http://www.gramene.org//db/protein/protein_search?acc=%s 960Example UniProt accession | P93436 961 962ID HAMAP 963Acc DB-0041 964Name High-quality automated and manual annotation of microbial proteomes (HAMAP) 965Desc 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. 966URL http://www.expasy.org/sprot/hamap/ 967Cat Family and domain databases 968Taxon 1 | all 969EDAMtpc 0621 | Genome, proteome and model organisms 970EDAMtpc 0724 | Protein families 971EDAMdat 0896 | Protein report 972EDAMdat 0849 | Sequence record 973EDAMdat 2872 | ID list 974EDAMid 2766 | HAMAP ID 975EDAMfmt 2331 | HTML 976EDAMfmt 2188 | uniprot 977Xref SP_explicit | HAMAP ID 978Query ID list {HAMAP family members} | Text | HAMAP ID | http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=tab&columns=id 979Query Sequence record {HAMAP family sequences} | uniprot | HAMAP ID | http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=txt 980Query Protein report {HAMAP family rules} | HTML | HAMAP ID | http://www.expasy.org/unirule/MF_%s 981Query Protein report {HAMAP family rules} | Text | HAMAP ID | http://www.expasy.org/unirule/MF_%s.txt 982Example HAMAP ID | 00314 983 984ID IntAct 985Acc DB-0051 986Name IntAct protein interaction database and analysis system 987Desc Protein interaction database and analysis system. 988URL http://www.ebi.ac.uk/intact/ 989Cat Protein-protein interaction databases 990Taxon 1 | all 991EDAMtpc 0147 | Protein-protein interactions 992EDAMdat 0906 | Protein report (interaction) 993EDAMid 3021 | UniProt accession 994EDAMfmt 2331 | HTML 995Xref SP_explicit | IntAct accession number 996Query Protein report (interaction) {IntAct entry} | HTML | UniProt accession | http://www.ebi.ac.uk/intact/binary-search/faces/search.xhtml?query=%s 997Example UniProt accession | P32234 998 999ID InterPro 1000Acc DB-0052 1001Name InterPro integrated database of protein families, domains, regions, repeats and functional sites 1002Desc Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences. 1003URL http://www.ebi.ac.uk/interpro/ 1004Cat Family and domain databases 1005Taxon 1 | all 1006EDAMtpc 0724 | Protein families 1007EDAMtpc 0748 | Protein sites and features 1008EDAMtpc 0641 | Repeat sequences 1009EDAMdat 1355 | Protein signature 1010EDAMid 1133 | InterPro accession 1011EDAMfmt 2331 | HTML 1012Xref SP_explicit | InterPro accession 1013Xref SP_FT | InterPro accession 1014Xref EMBL_explicit | InterPro accession 1015Query Protein signature | HTML | InterPro accession | http://www.ebi.ac.uk/interpro/IEntry?ac=%s 1016Example InterPro accession | IPR000059 1017 1018ID IPI 1019Acc DB-0132 1020Name International protein index (IPI) 1021Desc 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. 1022URL http://www.ebi.ac.uk/IPI 1023Cat Sequence databases 1024Taxon 1 | all 1025EDAMtpc 0621 | Genome, proteome and model organisms 1026EDAMdat 0849 | Sequence record 1027EDAMid 2384 | IPI protein ID 1028EDAMfmt 2331 | HTML 1029Xref SP_explicit | IPI protein ID 1030Query Sequence record {IPI entry} | HTML | IPI protein ID | http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=%s 1031Example IPI protein ID | IPI00177866 1032 1033ID LGICdb 1034Name Ligand-gated ion channel database (LGICdb) 1035Desc 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. 1036URL http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php 1037Taxon 1 | all 1038EDAMtpc 0741 | Protein sequence alignment 1039EDAMtpc 0166 | Protein structural motifs and surfaces 1040EDAMtpc 0084 | Phylogenetics 1041EDAMdat 1456 | Protein report (membrane protein) 1042EDAMid 2797 | Protein ID (LGICdb) 1043EDAMfmt 2331 | HTML 1044EDAMfmt 2332 | XML 1045Query 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 1046Query 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 1047Example Protein ID (LGICdb) | 5HT3Arano 1048 1049ID MEROPS 1050Acc DB-0059 1051Name MEROPS peptidase database 1052Desc 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. 1053URL http://merops.sanger.ac.uk/ 1054Cat Protein family/group databases 1055Taxon 1 | all 1056EDAMtpc 0821 | Enzymes and reactions 1057EDAMtpc 2811 | Nomenclature 1058EDAMdat 0896 | Protein report 1059EDAMid 2629 | Enzyme ID (MEROPS) 1060EDAMid 0842 | Identifier 1061EDAMfmt 2331 | HTML 1062Xref SP_explicit | Enzyme ID (MEROPS) 1063Query Protein report {MEROPS page} | HTML | Identifier {Clan} | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary 1064Query Protein report {MEROPS page} | HTML | Identifier {Family} | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary 1065Query Protein report {MEROPS page} | HTML | Enzyme ID (MEROPS) | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary 1066Example Enzyme ID (MEROPS) | A01.001 1067 1068ID MINT 1069Acc DB-0158 1070Name Molecular interaction Database (MINT) 1071Desc Experimentally verified protein-protein interactions mined from the scientific literature by expert curators. 1072URL http://mint.bio.uniroma2.it/mint/ 1073Taxon 1 | all 1074EDAMtpc 0147 | Protein-protein interactions 1075EDAMdat 1565 | Protein-protein interaction 1076EDAMid 2615 | MINT ID 1077EDAMfmt 2331 | HTML 1078Query Protein-protein interaction {MINT interaction} | HTML | MINT ID | http://mint.bio.uniroma2.it/mint/search/interaction.do?ac=MINT-%s 1079Example MINT ID | 3979570 1080 1081ID NMPDR 1082Acc DB-0125 1083Name National microbial pathogen 1084Desc 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. 1085URL http://www.nmpdr.org 1086URLlink http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/LinkingToTheGenomeViewer 1087Cat Genome annotation databases 1088Taxon 2 | Bacteria 1089EDAMtpc 0783 | Pathogens 1090EDAMtpc 0797 | Comparative genomics 1091EDAMdat 0916 | Gene annotation 1092EDAMid 1179 | NCBI taxonomy ID 1093EDAMid 2737 | FIG ID 1094EDAMfmt 2331 | HTML 1095Xref SP_explicit | FIG ID 1096Query Gene annotation | HTML | NCBI taxonomy ID | http://www.nmpdr.org/linkin.cgi?genome=%s 1097Query Gene annotation {Protein encoding gene or other feature} | HTML | FIG ID | http://www.nmpdr.org/linkin.cgi?id=%s 1098Example NCBI taxonomy ID | 83333.1 1099Example FIG ID | 83333.1.peg.123 1100Example FIG ID | 83333.1.rna.1 1101 1102ID OGP 1103Acc DB-0067 1104Name Oxford glycoProteomics 2-DE database (OGP) 1105Desc Two-dimensional polyacrylamide gel electrophoresis database. 1106URL http://proteomewww.bioch.ox.ac.uk/2d/2d.html 1107Cat 2D gel databases 1108Taxon 1 | all 1109EDAMtpc 0767 | Protein and peptide identification 1110EDAMdat 2364 | Experiment annotation (2D PAGE) 1111EDAMid 3021 | UniProt accession 1112EDAMfmt 2331 | HTML 1113Xref SP_explicit | UniProt accession 1114Query Experiment annotation (2D PAGE) {OGP entry} | HTML | UniProt accession | http://proteomewww.glycob.ox.ac.uk/cgi-bin/2d-search-ac?%s 1115Example UniProt accession | P04406 1116 1117ID OMA 1118Acc DB-0137 1119Name Identification of orthologs from complete genome data (OMA database) 1120Desc Identification of orthologs from complete genome data. 1121URL http://www.omabrowser.org 1122Cat Phylogenomic databases 1123Taxon 1 | all 1124EDAMtpc 0722 | Nucleic acid classification 1125EDAMtpc 0084 | Phylogenetics 1126EDAMtpc 0194 | Phylogenomics 1127EDAMdat 2093 | Data reference 1128EDAMid 0989 | Protein identifier 1129EDAMfmt 2331 | HTML 1130Xref SP_explicit | Protein identifier {OMA} 1131Query Data reference | HTML | Protein identifier {OMA} | http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=%s 1132Example Protein identifier {OMA} | FDVARTG 1133 1134ID PANTHER 1135Acc DB-0069 1136Name Protein analysis through evolutionary relationships (PANTHER) 1137Desc 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". 1138URL http://www.pantherdb.org/ 1139Cat Family and domain databases; Protein sequence classification database 1140Taxon 1 | all 1141EDAMtpc 2225 | Protein databases 1142EDAMtpc 0602 | Pathways, networks and models 1143EDAMtpc 0724 | Protein families 1144EDAMtpc 0623 | Genes, gene family or system 1145EDAMtpc 0084 | Phylogenetics 1146EDAMdat 2984 | Pathway or network report 1147EDAMdat 0907 | Protein family annotation 1148EDAMid 1161 | Pathway ID (Panther) 1149EDAMid 2783 | Protein family ID (PANTHER) 1150EDAMfmt 2331 | HTML 1151Xref SP_explicit | Protein family ID (PANTHER) 1152Query Protein family annotation {PANTHER Family} | HTML | Protein family ID (PANTHER) | http://www.pantherdb.org/panther/family.do?clsAccession=%s 1153Query Pathway or network report | HTML | Pathway ID (Panther) | http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=%s 1154Example Protein family ID (PANTHER) | PTHR12649:SF6 1155Example Pathway ID (Panther) | P00002 1156 1157ID Pathema 1158Name Pathema: a clade-specific bioinformatics resource 1159Desc Genome database for six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica. 1160URL http://www.jcvi.org/cms/research/projects/pathema/overview/ 1161Cat Not available 1162Taxon 1 | all 1163EDAMtpc 1811 | Prokaryotes and archae 1164EDAMtpc 0783 | Pathogens 1165Xref SP_FT | None 1166 1167ID PathoPlant 1168Name PathoPlant database of plant-pathogen interactions and Arabidopsis expression 1169Desc 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. 1170URL http://www.pathoplant.de 1171Taxon 1 | all 1172EDAMtpc 0197 | Gene expression resources 1173EDAMtpc 0204 | Gene regulation resources 1174EDAMtpc 0780 | Plants 1175EDAMtpc 0754 | Signaling pathways 1176EDAMtpc 0780 | Plants 1177EDAMtpc 0783 | Pathogens 1178 1179ID PeptideAtlas 1180Acc DB-0071 1181Name PeptideAtlas peptide database 1182Desc 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. 1183URL http://www.peptideatlas.org 1184Cat Proteomic databases; Peptide identification database; Mass spectrometry database 1185Taxon 1 | all 1186EDAMtpc 0613 | Peptides and amino acids 1187EDAMtpc 0767 | Protein and peptide identification 1188EDAMdat 0896 | Protein report 1189EDAMdat 0945 | Peptide identification 1190EDAMdat 2536 | Mass spectrometry data 1191EDAMid 2384 | IPI protein ID 1192EDAMid 2398 | Protein ID (Ensembl) 1193EDAMid 0989 | Protein identifier 1194EDAMfmt 2331 | HTML 1195EDAMfmt 2332 | XML 1196Xref SP_explicit | Protein identifier {PeptideAtlas} 1197Query 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 1198Query 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 1199Query 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 1200Query 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 1201Query 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 1202Query Protein report {PeptideAtlas entry} | HTML | Protein identifier {PeptideAtlas} | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=%s 1203Example Protein ID (Ensembl) | ENSP00000374576 1204Example IPI protein ID | IPI00795032 1205Example Protein identifier {PeptideAtlas} | P62258 1206 1207ID PeroxiBase 1208Acc DB-0072 1209Name PeroxiBase peroxidase family database 1210Desc Sequences from peroxidase superfamilies with annotation on putative functions and transcription regulation. 1211URL http://peroxibase.isb-sib.ch/index.php 1212Cat Protein family/group databases 1213Taxon 1 | all 1214EDAMtpc 0635 | Specific protein resources 1215EDAMdat 0896 | Protein report 1216EDAMid 2792 | Protein ID (PeroxiBase) 1217EDAMfmt 2331 | HTML 1218Xref SP_explicit | Protein ID (PeroxiBase) 1219Query Protein report {PeroxiBase entry} | HTML | Protein ID (PeroxiBase) | http://peroxibase.isb-sib.ch/listing.php?action=view&id=%s 1220Example Protein ID (PeroxiBase) | 6846 1221 1222ID Pfam 1223Acc DB-0073 1224Name Pfam protein domain database 1225Desc Large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). 1226URL http://pfam.sanger.ac.uk/ 1227Cat Family and domain databases 1228Taxon 1 | all 1229EDAMtpc 0741 | Protein sequence alignment 1230EDAMtpc 0188 | Sequence profiles and HMMs 1231EDAMtpc 0724 | Protein families 1232EDAMtpc 0736 | Protein domains and folds 1233EDAMdat 0907 | Protein family annotation 1234EDAMid 1096 | Sequence accession (protein) 1235EDAMid 1138 | Pfam accession number 1236EDAMid 1179 | NCBI taxonomy ID 1237EDAMid 2758 | Pfam clan ID 1238EDAMfmt 2331 | HTML 1239Xref SP_explicit | Pfam accession number 1240Xref SP_FT | Pfam accession number 1241Query Protein family annotation {Pfam entry} | HTML | Sequence accession (protein) | http://pfam.sanger.ac.uk/protein/acc=%s 1242Query Protein family annotation {Pfam entry} | HTML | Pfam accession number | http://pfam.sanger.ac.uk/family?acc=%s 1243Query Protein family annotation {Pfam entry} | HTML | Pfam clan ID | http://pfam.sanger.ac.uk/clan?acc=%s 1244Query Protein family annotation {Pfam entry} | HTML | NCBI taxonomy ID | http://pfam.sanger.ac.uk/proteome?taxId=%s 1245Example Sequence accession (protein) | VAV_HUMAN 1246Example Pfam accession number | PF07388 1247Example Pfam clan ID | CL0247 1248Example NCBI taxonomy ID | 349163 1249 1250 1251ID PHCI-2DPAGE 1252Acc DB-0075 1253Name Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE) 1254Desc Two-dimensional polyacrylamide gel electrophoresis database. 1255URL http://www.gram.au.dk/2d/2d.html 1256Cat 2D gel databases 1257Taxon 1 | all 1258EDAMtpc 0767 | Protein and peptide identification 1259EDAMdat 2364 | Experiment annotation (2D PAGE) 1260EDAMid 3021 | UniProt accession 1261EDAMfmt 2331 | HTML 1262Xref SP_explicit | UniProt accession 1263Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.gram.au.dk/cgi-bin/get-2d-entry?%s 1264Example UniProt accession | P17821 1265 1266ID PHI-base 1267Name PHI-base pathogen host interactions database 1268Desc 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. 1269URL http://www.phibase.org 1270Taxon 1 | all 1271EDAMtpc 0623 | Genes, gene family or system 1272EDAMtpc 0783 | Pathogens 1273 1274ID PhosphoELM 1275Name PhosphoELM database of S/T/Y phosphorylation sites 1276Desc Experimentally verified phosphorylation sites in eukaryotic proteins. 1277URL http://phospho.elm.eu.org/ 1278Taxon 1 | all 1279EDAMtpc 0751 | Phosphorylation sites 1280EDAMdat 2071 | Sequence motif (protein) 1281EDAMid 1096 | Sequence accession (protein) 1282EDAMid 2775 | Kinase name 1283EDAMid 1009 | Protein name 1284EDAMfmt 2331 | HTML 1285Query Sequence motif (protein) {Phospho-ELM report} | HTML | Protein name {Substrate} | http://phospho.elm.eu.org/cgimodel.py?fun=Search&substrate=%s 1286Query Sequence motif (protein) {Phospho-ELM report} | HTML | Sequence accession (protein) | http://phospho.elm.eu.org/cgimodel.py?fun=Search&accession=%s 1287Query Sequence motif (protein) {Phospho-ELM report} | HTML | Kinase name | http://phospho.elm.eu.org/cgimodel.py?fun=Search&kinase=%s 1288Example Kinase | Abl2 1289Example Sequence accession (protein) | Q9H0E9 1290Example Protein name {Substrate} | Src substrate cortactin 1291 1292ID PhosphoSite 1293Acc DB-0123 1294Name Phosphorylation site database 1295Desc 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. 1296URL http://www.phosphosite.org 1297Cat PTM databases 1298Taxon 1 | all 1299EDAMtpc 0751 | Phosphorylation sites 1300EDAMdat 2071 | Sequence motif (protein) 1301EDAMid 3021 | UniProt accession 1302EDAMfmt 2331 | HTML 1303Xref SP_explicit | UniProt accession 1304Query Sequence motif (protein) {PhosphoSite entry} | HTML | UniProt accession | http://www.phosphosite.org/uniprotAccAction.do?id=%s 1305Example UniProt accession | Q92844 1306 1307ID PIR 1308Acc DB-0078 1309Name Protein sequence database of the Protein Information Resource (PIR) 1310Desc Integrated protein informatics resource for genomic, proteomic and systems biology research. 1311URL http://pir.georgetown.edu/ 1312Cat Sequence databases 1313Taxon 1 | all 1314EDAMtpc 0639 | Protein sequence analysis 1315EDAMdat 2201 | Sequence record full 1316EDAMid 0989 | Protein identifier 1317EDAMfmt 2331 | HTML 1318Xref SP_explicit | Protein identifier {PIR accession} 1319Xref SP_FT | None 1320Query Sequence record full | HTML | Protein identifier {PIR accession} | http://pir.georgetown.edu/cgi-bin/nbrfget?uid=%s 1321Example Protein identifier {PIR accession} | S12345 1322 1323ID PIRSF 1324Acc DB-0079 1325Name PIRSF whole-protein classification database 1326Desc 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. 1327URL http://pir.georgetown.edu/pirsf/ 1328Cat Family and domain databases 1329Taxon 1 | all 1330EDAMtpc 3052 | Sequence clusters and classification 1331EDAMtpc 0724 | Protein families 1332EDAMdat 0907 | Protein family annotation 1333EDAMid 1136 | PIRSF ID 1334EDAMfmt 2331 | HTML 1335Xref SP_explicit | PIRSF ID 1336Query Protein family annotation {PIRSF entry} | HTML | PIRSF ID | http://pir.georgetown.edu/cgi-bin/ipcSF?id=%s 1337Example PIRSF ID | SF000186 1338 1339ID PMAP-CutDB 1340Acc DB-0138 1341Name PMAP-CutDB proteolytic event database 1342Desc Curated proteolytic events and pathways from the literature. 1343URL http://www.proteolysis.org/ 1344Cat Other 1345Taxon 1 | all 1346EDAMtpc 0602 | Pathways, networks and models 1347EDAMid 3021 | UniProt accession 1348EDAMfmt 2331 | HTML 1349EDAMdat 2093 | Data reference 1350Xref SP_explicit | UniProt accession 1351Query Data reference | HTML | UniProt accession | http://substrate.burnham.org/lookup/uniprot/%s 1352Example UniProt accession | P05067 1353 1354ID PptaseDB 1355Acc DB-0081 1356Name Prokaryotic protein phosphatase database (PptaseDB) 1357Desc Prokaryotic protein phosphatases. 1358URL http://vigen.biochem.vt.edu/p3d/p3d.htm 1359Cat Protein family/group databases 1360Taxon 2 | Bacteria 1361EDAMtpc 0635 | Specific protein resources 1362EDAMdat 0896 | Protein report 1363EDAMid 0989 | Protein identifier 1364EDAMfmt 2331 | HTML 1365Xref SP_explicit | Protein identifier 1366Query Protein report {PptaseDB entry} | HTML | Protein identifier | http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=accession&extref=%s 1367Example Protein identifier | P3D0409136 1368 1369ID PRIDE 1370Acc DB-0130 1371Name PRIDE proteomics identifications database 1372Desc Standards compliant, public data repository for proteomics data, protein and peptide identifications together with the evidence supporting these identifications. 1373URL http://www.ebi.ac.uk/pride 1374URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do 1375Cat Proteomic databases 1376Taxon 1 | all 1377EDAMtpc 0767 | Protein and peptide identification 1378EDAMtpc 0121 | Proteomics 1379EDAMdat 2536 | Mass spectrometry data 1380EDAMid 3021 | UniProt accession 1381EDAMfmt 2331 | HTML 1382Xref SP_explicit | UniProt accession 1383Query Mass spectrometry data {PRIDE entry} | HTML | UniProt accession | http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=%s 1384Example UniProt accession | P29375 1385 1386ID PRINTS 1387Acc DB-0082 1388Name PRINTS protein motif fingerprint database 1389Desc A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family. 1390URL http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ 1391Cat Family and domain databases 1392Taxon 1 | all 1393EDAMtpc 0724 | Protein families 1394EDAMtpc 0748 | Protein sites and features 1395EDAMtpc 0158 | Sequence motifs 1396EDAMdat 1355 | Protein signature 1397EDAMid 1137 | PRINTS code 1398EDAMfmt 2331 | HTML 1399Xref SP_explicit | PRINTS code 1400Query 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 1401Example PRINTS code | pr00018 1402 1403ID ProDom 1404Acc DB-0083 1405Name ProDom protein domain database 1406Desc A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database. 1407URL http://prodom.prabi.fr/prodom/current/html/home.php 1408Cat Family and domain databases 1409Taxon 1 | all 1410EDAMtpc 0724 | Protein families 1411EDAMtpc 0736 | Protein domains and folds 1412EDAMdat 0872 | Phylogenetic tree 1413EDAMdat 1298 | Sequence features (motifs) 1414EDAMdat 0907 | Protein family annotation 1415EDAMdat 1384 | Sequence alignment (protein) 1416EDAMid 1142 | ProDom accession number 1417EDAMfmt 2331 | HTML 1418Xref SP_explicit | ProDom accession number 1419Query Protein family annotation {ProDom entry} | HTML | ProDom accession number | http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=%s 1420Query 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 1421Query Phylogenetic tree | HTML | ProDom accession number | http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent1=%s&wanted=tree 1422Query 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 1423Query Sequence alignment (protein) {ProDom family alignment} | Text | ProDom accession number | http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent0=%s 1424Example ProDom accession number | PD000023 1425 1426ID ProtoNet 1427Acc DB-0085 1428Name ProtoNet automatic hierarchical classification of proteins 1429Desc Automatic hierarchical classification of protein sequences. 1430URL http://www.protonet.cs.huji.ac.il/ 1431Cat Other 1432Taxon 1 | all 1433EDAMtpc 0724 | Protein families 1434EDAMdat 0907 | Protein family annotation 1435EDAMfmt 1978 | DASGFF 1436EDAMid 3021 | UniProt accession 1437EDAMfmt 2331 | HTML 1438Xref SP_implicit | UniProt accession 1439Query Protein family annotation {ProtoNet entry} | HTML | UniProt accession | http://www.protonet.cs.huji.ac.il/sp.php?prot=%s 1440Query Protein family annotation {ProtoNet entry} | DASGFF | UniProt accession | http://www.protonet.cs.huji.ac.il/das/protonet/features?segment=%s 1441Example UniProt accession | P01011 1442 1443ID Reactome 1444Acc DB-0088 1445Name Reactome knowledgebase of biological pathways 1446Desc Curated knowledgebase of biological pathways and processes. 1447URL http://www.reactome.org/ 1448URLlink http://www.reactome.org/referring2GK.html 1449URLsoap http://www.reactome.org/download/index.html 1450Cat Enzyme and pathway databases 1451Taxon 1 | all 1452EDAMtpc 0602 | Pathways, networks and models 1453EDAMdat 2984 | Pathway or network report 1454EDAMdat 0896 | Protein report 1455EDAMid 0989 | Protein identifier 1456EDAMid 3021 | UniProt accession 1457EDAMid 1027 | Gene ID (NCBI) 1458EDAMid 1011 | EC number 1459EDAMid 1174 | ChEBI ID 1460EDAMid 1056 | Database name 1461EDAMid 0990 | Compound name 1462EDAMid 1155 | Pathway ID (reactome) 1463EDAMid 1176 | GO term ID 1464EDAMfmt 2331 | HTML 1465EDAMfmt 2332 | XML 1466Xref SP_explicit | Pathway ID (reactome) 1467Query Pathway or network report | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%s&ZOOM=2 1468Query Pathway or network report | XML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/sbml_export?DB=gk_current&ID=%s 1469Query Protein report {Reactome entry} | HTML | Database name;Protein identifier | http://www.reactome.org/cgi-bin/link?SOURCE=%s1&ID=%s2 1470Query Protein report {Reactome entry} | HTML | UniProt accession | http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=%s 1471Query Protein report {Reactome entry} | HTML | ChEBI ID | http://www.reactome.org/cgi-bin/link?SOURCE=CHEBI&ID=%s 1472Query Protein report {Reactome entry} | HTML | Compound name | http://www.reactome.org/cgi-bin/link?SOURCE=COMPOUND&ID=%s 1473Query Protein report {Reactome entry} | HTML | GO term ID | http://www.reactome.org/cgi-bin/link?SOURCE=GO&ID=%s 1474Query Protein report {Reactome entry} | HTML | EC number | http://www.reactome.org/cgi-bin/link?SOURCE=EC&ID=%s 1475Query Protein report {Reactome entry} | HTML | Gene ID (NCBI) | http://www.reactome.org/cgi-bin/link?SOURCE=Entrez+Gene&ID=%s 1476Query Protein report {Reactome entry} | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/link?SOURCE=Reactome&ID=%s 1477Example UniProt accession | P30304 1478Example ChEBI ID | 15422 1479Example Compound name | C00002 1480Example GO term ID | 0030060 1481Example EC number | 1.1.1.37 1482Example Gene ID (NCBI) | 4171 1483Example Pathway ID (reactome) | REACT_1 1484 1485ID REBASE 1486Acc DB-0089 1487Name REBASE restriction enzymes and methylases database 1488Desc Restriction enzymes and methylases database. 1489URL http://rebase.neb.com/ 1490Cat Protein family/group databases 1491Taxon 1 | all 1492EDAMtpc 0821 | Enzymes and reactions 1493EDAMdat 1509 | Protein report (enzyme) 1494EDAMid 1012 | Enzyme name 1495EDAMid 2325 | REBASE enzyme number 1496EDAMfmt 2331 | HTML 1497Xref SP_explicit | REBASE enzyme number 1498Query Protein report (enzyme) | HTML | Enzyme name | http://rebase.neb.com/rebase/enz/%s.html 1499Query Protein report (enzyme) | HTML | REBASE enzyme number | http://rebase.neb.com/rebase/enz/%s.html 1500Example Enzyme name | EcoRI 1501Example REBASE enzyme number | 993 1502 1503ID REDIdb 1504Name RNA editing database (REDIdb) 1505Desc 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. 1506URL http://biologia.unical.it/py_script/overview.html 1507Taxon 1 | all 1508EDAMtpc 0114 | Gene structure and RNA splicing 1509EDAMdat 2043 | Sequence record lite 1510EDAMdat 1383 | Sequence alignment (nucleic acid) 1511EDAMid 2781 | REDIdb ID 1512EDAMfmt 2310 | FASTA-HTML 1513EDAMfmt 2331 | HTML 1514Query Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s 1515Query Sequence record lite {REDIdb fasta} | FASTA-HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s 1516Query Sequence alignment (nucleic acid) {REDIdb overview} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s 1517Query Sequence alignment (nucleic acid) {REDIdb alignment} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/align.py?query=%s 1518Example REDIdb ID | EDI_000000002 1519 1520ID RefSeq 1521Acc DB-0117 1522Name NCBI reference sequences 1523Desc 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. 1524URL http://www.ncbi.nlm.nih.gov/RefSeq/ 1525Cat Sequence databases 1526Taxon 1 | all 1527EDAMtpc 3041 | Sequence databases 1528EDAMtpc 0797 | Comparative genomics 1529EDAMdat 0849 | Sequence record 1530EDAMid 0989 | Protein identifier 1531EDAMfmt 2331 | HTML 1532Xref SP_explicit | Protein identifier {Refseq} 1533Query Sequence record {RefSeq entry} | HTML | Protein identifier {Refseq} | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=%s 1534Example Protein identifier {Refseq} | YP_654574.1 1535 1536ID REPRODUCTION-2DPAGE 1537IDalt REPRODUCTION2DPAGE 1538Acc DB-0090 1539Name REPRODUCTION-2DPAGE database 1540Desc REPRODUCTION-2DPAGE 2D gel protein database. 1541URL http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi 1542Cat 2D gel databases 1543Taxon 1 | all 1544EDAMtpc 0767 | Protein and peptide identification 1545EDAMid 3021 | UniProt accession 1546EDAMdat 2364 | Experiment annotation (2D PAGE) 1547EDAMfmt 2331 | HTML 1548Xref SP_explicit | UniProt accession 1549Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s&format=text 1550Query Experiment annotation (2D PAGE) | Text | UniProt accession | http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s 1551Example UniProt accession | P00352 1552 1553ID RESID 1554Name RESID database of protein modifications 1555Desc A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. 1556URL http://www.ebi.ac.uk/RESID/ 1557Taxon 1 | all 1558EDAMtpc 0601 | Protein modifications 1559EDAMtpc 0166 | Protein structural motifs and surfaces 1560EDAMdat 2191 | Protein modification annotation 1561EDAMid 2619 | RESID ID 1562EDAMfmt 2332 | XML 1563Query Protein modification annotation {RESID entry} | XML | RESID ID | http://www.ebi.ac.uk/ontology-lookup/RESIDService?resid_id=%s 1564Example RESID ID | AA0002 1565 1566ID RFAM 1567IDalt RFam 1568Name RNA families database of alignments and CMs 1569Desc 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. 1570URL http://rfam.sanger.ac.uk/ 1571Cat Not available 1572Taxon 1 | all 1573EDAMtpc 0740 | Nucleic acid sequence alignment 1574EDAMtpc 0697 | RNA structure and alignment 1575EDAMdat 2354 | RNA family annotation 1576EDAMid 2356 | RFAM accession 1577EDAMid 2606 | RFAM name 1578EDAMfmt 2331 | HTML 1579EDAMfmt 2332 | XML 1580Xref EMBL_explicit | RFAM accession 1581Query RNA family annotation | HTML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s 1582Query RNA family annotation | HTML | RFAM name | http://rfam.sanger.ac.uk/family?acc=%s 1583Query RNA family annotation | XML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s&output=xml 1584Query RNA family annotation | XML | RFAM name | http://rfam.sanger.ac.uk/family?acc=%s&output=xml 1585Example RFAM accession | RF00522 1586Example RFAM name | PreQ1 1587 1588ID SABIO-RK 1589Name Database for biochemical reactions and their kinetics. 1590Desc Biochemical pathways and reaction kinetics. 1591URL http://sabio.villa-bosch.de/SABIORK 1592Taxon 1 | all 1593EDAMtpc 0602 | Pathways, networks and models 1594EDAMdat 2093 | Data reference 1595EDAMdat 2024 | Enzyme kinetics data 1596EDAMdat 0908 | Reaction annotation 1597EDAMid 2309 | Reaction ID (SABIO-RK) 1598EDAMid 2648 | Reaction kinetics ID (SABIO-RK) 1599EDAMid 1011 | EC number 1600EDAMfmt 2331 | HTML 1601Query Reaction annotation {SABIO-RK reaction} | HTML | Reaction ID (SABIO-RK) | http://sabio.h-its.org/index2.jsp?reac=%s 1602Query Enzyme kinetics data {SABIO-RK Kinetic Record} | HTML | Reaction kinetics ID (SABIO-RK) | http://sabio.h-its.org/kineticLawEntry.jsp?kinlawid=%s 1603Query Data reference {SABIO-RK EC code} | HTML | EC number | http://sabio.h-its.org/index2.jsp?EC=%s 1604Example Reaction ID (SABIO-RK) | 75 1605Example Reaction kinetics ID (SABIO-RK) | 5046 1606Example EC number | 2.1.1.45 1607 1608ID SCOP 1609Name Structural classification of proteins (SCOP) database 1610Desc 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. 1611URL http://scop.mrc-lmb.cam.ac.uk/scop 1612Taxon 1 | all 1613EDAMtpc 0736 | Protein domains and folds 1614EDAMdat 1554 | SCOP node 1615EDAMdat 2093 | Data reference 1616EDAMid 1042 | SCOP sunid 1617EDAMid 1127 | PDB ID 1618EDAMid 0842 | Identifier 1619EDAMfmt 2331 | HTML 1620Query SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s 1621Query Data reference {PDB Entry search} | HTML | PDB ID | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?PDB=%s 1622Query Data reference | HTML | Identifier {Keyword} | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s 1623Example SCOP sunid | 47718 1624Example PDB ID | 1djh 1625Example Identifier {Keyword} | immunoglobulin 1626 1627ID SCOWL 1628Name Structural characterization of water, ligands and proteins (SCOWL) 1629Desc 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. 1630URL http://www.scowlp.org 1631Taxon 1 | all 1632EDAMtpc 0128 | Protein interactions 1633EDAMdat 2359 | Domain-domain interaction 1634EDAMid 1127 | PDB ID 1635EDAMid 1042 | SCOP sunid 1636EDAMfmt 2331 | HTML 1637Query Domain-domain interaction | HTML | PDB ID | http://www.scowlp.org/scowlp/PDB.action?show=&PDBId=%s 1638Query Domain-domain interaction | HTML | SCOP sunid {SCOP family id} | http://www.scowlp.org/scowlp/Search.action?childs=¤tChoice=SCOP_FAMILY%s 1639Example PDB ID | 1fxk 1640Example SCOP sunid | 2381635 1641 1642ID Selectome 1643Name Selectome database of positive selection 1644Desc Database of positive selection based on a rigorous branch-site specific likelihood test. 1645URL http://bioinfo.unil.ch/selectome/ 1646Taxon 1 | all 1647EDAMtpc 0084 | Phylogenetics 1648EDAMtpc 0623 | Genes, gene family or system 1649EDAMdat 0872 | Phylogenetic tree 1650EDAMdat 2093 | Data reference 1651EDAMdat 0916 | Gene annotation 1652EDAMid 1131 | Protein family name 1653EDAMid 0842 | Identifier 1654EDAMid 0989 | Protein identifier 1655EDAMid 1127 | PDB ID 1656EDAMid 1868 | Taxon 1657EDAMfmt 2331 | HTML 1658Query 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 1659Query Gene annotation {Selectome family} | HTML | Identifier {Selectome identifier} | http://bioinfo.unil.ch/cgi-bin/selectome/getFamily.cgi?query=%s 1660Query Data reference {Selectome Xref} | HTML | Protein identifier {Cross-reference} | http://bioinfo.unil.ch/cgi-bin/selectome/getXref.cgi?query=%s 1661Query Data reference {Selectome Xref} | HTML | PDB ID {Cross-reference} | http://bioinfo.unil.ch/cgi-bin/selectome/getXref.cgi?query=%s 1662Query Data reference {Selectome genes} | HTML | Identifier {Keyword} | http://bioinfo.unil.ch/cgi-bin/selectome/getGene.cgi?query=%s 1663Query Data reference {Selectome gene family} | HTML | Identifier {Keyword} | http://bioinfo.unil.ch/cgi-bin/selectome/getGeneFamily.cgi?query=%s 1664Example Identifier {Selectome identifier} | TF105041 1665Example Identifier {Selectome identifier};Protein family name;Taxon | TF105041;1;v 1666Example PDB ID | 1HCL 1667Example Protein identifier | P24941 1668Example Identifier {Keyword} | kidney 1669Example Identifier {Keyword} | Ascc3_F2 1670Example Identifier {Keyword} | BRCA2 1671 1672ID SMART 1673Acc DB-0097 1674Name Simple modular architecture research tool (SMART) 1675Desc SMART protein domain database. 1676URL http://smart.embl.de/ 1677Cat Family and domain databases 1678Taxon 1 | all 1679EDAMtpc 0724 | Protein families 1680EDAMtpc 0736 | Protein domains and folds 1681EDAMdat 2377 | Protein structure report (domain) 1682EDAMid 1139 | SMART accession number 1683EDAMid 2782 | SMART domain name 1684EDAMfmt 2331 | HTML 1685Xref SP_explicit | SMART accession number 1686Query Protein structure report (domain) {SMART entry} | HTML | SMART domain name | http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY 1687Query Protein structure report (domain) {SMART entry} | HTML | SMART accession number | http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY 1688Example SMART domain name | KISc 1689Example SMART accession number | SM00129 1690 1691ID SMR 1692Acc DB-0098 1693Name A database of annotated 3D protein structure models 1694Desc Annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. 1695URL http://swissmodel.expasy.org/repository/ 1696Cat 3D structure databases 1697Taxon 1 | all 1698EDAMtpc 0698 | Protein tertiary structure 1699EDAMdat 1460 | Protein structure 1700EDAMid 3021 | UniProt accession 1701EDAMfmt 2331 | HTML 1702Xref SP_explicit | UniProt accession 1703Query Protein structure {SMR entry} | HTML | UniProt accession | http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s 1704Example UniProt accession | P01009 1705 1706ID SpliceAid 1707Name SpliceAid database of strictly experimentally assessed target RNA sequences in humans 1708Desc Experimental RNA target motifs bound by splicing proteins in humans. 1709URL http://www.introni.it/splicing.html 1710Taxon 9606 | Homo sapiens 1711EDAMtpc 0747 | Nucleic acid sites and features 1712EDAMtpc 0114 | Gene structure and RNA splicing 1713EDAMtpc 0748 | Protein sites and features 1714EDAMtpc 0158 | Sequence motifs 1715EDAMdat 0896 | Protein report 1716EDAMid 1009 | Protein name 1717EDAMfmt 2331 | HTML 1718Query Protein report | HTML | Protein name | http://193.206.120.228/cgi-bin/SpliceAid.pl?Protein_name=%s 1719Example Protein name | 9G8 1720 1721ID STRING 1722Acc DB-0141 1723Name STRING protein-protein interaction database 1724Desc Known and predicted protein-protein interactions. 1725URL http://string-db.org/ 1726Taxon 1 | all 1727EDAMtpc 0147 | Protein-protein interactions 1728EDAMid 2302 | STRING ID 1729EDAMdat 1663 | Pathway or network (protein-protein interaction) 1730EDAMfmt 2331 | HTML 1731EDAMfmt 2332 | XML 1732Query 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 1733Query Pathway or network (protein-protein interaction) | XML | STRING ID | http://string-db.org/api/psi-mi/interactions?identifier=%s 1734Example STRING ID | 9606.ENSP00000359866 1735 1736ID SWISS-2DPAGE 1737Acc DB-0101 1738Name Two-dimensional polyacrylamide gel electrophoresis database (SWISS-2DPAGE) 1739Desc Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps. 1740URL http://www.expasy.org/ch2d/ 1741URLlink http://www.expasy.org/expasy_urls.html#ch2d 1742Cat 2D gel databases 1743Taxon 1 | all 1744EDAMtpc 0767 | Protein and peptide identification 1745EDAMdat 2364 | Experiment annotation (2D PAGE) 1746EDAMdat 2372 | 2D PAGE spot annotation 1747EDAMid 0989 | Protein identifier 1748EDAMid 2374 | Spot serial number 1749EDAMid 3021 | UniProt accession 1750EDAMid 2791 | Reference map name (SWISS-2DPAGE) 1751EDAMfmt 2331 | HTML 1752Xref SP_explicit | UniProt accession 1753Query Experiment annotation (2D PAGE) | HTML | Protein identifier | http://www.expasy.org/swiss-2dpage/%s 1754Query Experiment annotation (2D PAGE) | HTML | UniProt accession | http://www.expasy.org/swiss-2dpage/%s 1755Query Experiment annotation (2D PAGE) | Text | UniProt accession | http://www.expasy.org/swiss-2dpage/format=raw&extract&ac=%s 1756Query 2D PAGE spot annotation | HTML | Spot serial number | http://www.expasy.org/swiss-2dpage/spot=%s 1757Query 2D PAGE spot annotation {SWISS-2DPAGE protein list} | HTML | Reference map name (SWISS-2DPAGE) | http://www.expasy.org/swiss-2dpage/map=%s 1758Query 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 1759Query 2D PAGE spot annotation | HTML | Spot serial number | http://www.expasy.org/swiss-2dpage/spot=%s 1760Example UniProt accession | P01009 1761Example Spot serial number | 2D-0017PD 1762Example Reference map name (SWISS-2DPAGE) | LIVER_HUMAN 1763 1764ID TIGR 1765Acc DB-0103 1766Name The bacterial database(s) of The Institute of Genome Research 1767Desc The TIGR bacterial Genome Annotation Database. 1768Cat Genome annotation databases 1769Taxon 2 | Bacteria 1770Taxon 2157 | Archaea 1771EDAMtpc 0780 | Plants 1772EDAMdat 0916 | Gene annotation 1773EDAMid 1899 | Locus ID (CMR) 1774EDAMfmt 2331 | HTML 1775Xref SP_explicit | Locus ID 1776Query Gene annotation | HTML | Locus ID (CMR) | http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s 1777Example Locus ID (CMR) | BOV_A0688 1778 1779ID TIGRFAMs 1780Acc DB-0104 1781Name A protein family database 1782Desc Protein families based on hidden Markov models (HMMs). 1783URL http://www.tigr.org/TIGRFAMs/ 1784Cat Family and domain databases 1785Taxon 1 | all 1786EDAMtpc 0724 | Protein families 1787EDAMtpc 0188 | Sequence profiles and HMMs 1788EDAMdat 2788 | Sequence profile metadata 1789EDAMid 1141 | TIGRFam ID 1790EDAMfmt 2331 | HTML 1791Xref SP_explicit | TIGRFam ID 1792Query Sequence profile metadata {TIGRFAM entry} | HTML | TIGRFam ID | http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi?hmm_acc=%s 1793Example TIGRFam ID | TIGR01920 1794 1795ID ToPDB 1796Name Topology of transmembrane proteins 1797Desc Transmembrane protein datasets containing experimentally derived topology information. 1798URL http://toPDB.enzim.hu 1799Taxon 1 | all 1800EDAMtpc 0820 | Membrane proteins 1801EDAMdat 1456 | Protein report (membrane protein) 1802EDAMid 2789 | Protein ID (TopDB) 1803EDAMfmt 2331 | HTML 1804EDAMfmt 2332 | XML 1805Query Protein report (membrane protein) {TOPDB entry} | HTML | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=HTML&id=%s 1806Query Protein report (membrane protein) {TOPDB entry} | HTML {graphic} | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=Graph&id=%s 1807Query Protein report (membrane protein) {TOPDB entry} | HTML {flash} | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=Flash&id=%s 1808Query Protein report (membrane protein) {TOPDB entry} | XML | Protein ID (TopDB) | http://toPDB.enzim.hu/?m=show&tab=XML&id=%s 1809Example Protein ID (TopDB) | AP00085 1810 1811ID Transdab 1812Name Database of transglutaminase substrate proteins 1813Desc Database of transglutaminase substrate proteins. 1814URL http://genomics.dote.hu/wiki 1815Taxon 1 | all 1816EDAMtpc 0635 | Specific protein resources 1817EDAMdat 0896 | Protein report 1818EDAMid 1009 | Protein name 1819EDAMfmt 2331 | HTML 1820Query Protein report | HTML | Protein name | http://genomics.dote.hu/wiki/index.php/%s 1821Example Protein name | Histone_H1_%28kinase%29 1822 1823ID UniParc 1824Name UniProt Archive 1825Desc 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. 1826URL http://www.uniprot.org/ 1827Taxon 1 | all 1828EDAMtpc 0639 | Protein sequence analysis 1829EDAMdat 0849 | Sequence record 1830EDAMid 2392 | UniParc accession 1831EDAMfmt 2331 | HTML 1832Xref SP_FT | None 1833Query Sequence record {UniParc entry} | HTML | UniParc accession | http://www.uniprot.org/uniparc/%s 1834Example UniParc accession | UPI0000000001 1835 1836ID UniProt 1837IDalt UniProtKB 1838Name Universal protein resource 1839Desc A comprehensive, high-quality and freely accessible resource of protein sequence and functional information. 1840URL http://www.uniprot.org/ 1841Taxon 1 | all 1842EDAMtpc 0639 | Protein sequence analysis 1843EDAMdat 2201 | Sequence record full 1844EDAMid 3021 | UniProt accession 1845EDAMfmt 1929 | FASTA format 1846EDAMfmt 2376 | RDF 1847EDAMfmt 2188 | uniprot 1848EDAMfmt 2331 | HTML 1849EDAMfmt 2332 | XML 1850Xref SP_FT | None 1851Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s 1852Query Sequence record full | uniprot | UniProt accession | http://www.uniprot.org/uniprot/%s.txt 1853Query Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml 1854Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf 1855Query Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta 1856Example UniProt accession | P12345 1857 1858ID UniProtKB_Swiss-Prot 1859IDalt SwissProt 1860Name Universal protein resource knowledge base / Swiss-Prot 1861Desc Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature 1862URL http://www.uniprot.org 1863Taxon 1 | all 1864EDAMdat 2201 | Sequence record full 1865EDAMtpc 0639 | Protein sequence analysis 1866EDAMid 3021 | UniProt accession 1867EDAMfmt 1929 | FASTA format 1868EDAMfmt 2376 | RDF 1869EDAMfmt 2331 | HTML 1870EDAMfmt 2332 | XML 1871Xref EMBL_explicit | UniProt accession 1872Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s 1873Query Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt 1874Query Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml 1875Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf 1876Query Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta 1877Example UniProt accession | P12345 1878 1879ID UniProtKB_TrEMBL 1880IDalt TrEMBL 1881Name Universal protein resource knowledge base / Swiss-Prot 1882Desc Section of the UniProt knowledgebase, containing computationally analysed records waiting for full manual annotation 1883URL http://www.uniprot.org/ 1884Taxon 1 | all 1885EDAMdat 2201 | Sequence record full 1886EDAMtpc 0639 | Protein sequence analysis 1887EDAMid 3021 | UniProt accession 1888EDAMfmt 1929 | FASTA format 1889EDAMfmt 2376 | RDF 1890EDAMfmt 2331 | HTML 1891EDAMfmt 2332 | XML 1892Xref SP_FT | None 1893Query Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s 1894Query Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt 1895Query Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml 1896Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf 1897Query Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta 1898Example UniProt accession | Q00177 1899 1900ID UniRef 1901Name Non-redundant reference (UniRef) databases 1902Desc 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. 1903URL http://www.uniprot.org/help/uniref 1904Cat Other 1905Taxon 1 | all 1906EDAMtpc 3052 | Sequence clusters and classification 1907EDAMtpc 0114 | Gene structure and RNA splicing 1908EDAMfmt 1929 | FASTA format 1909EDAMdat 1245 | Sequence cluster (protein) 1910EDAMid 2347 | Sequence cluster ID (UniRef100) 1911EDAMid 2348 | Sequence cluster ID (UniRef90) 1912EDAMid 2349 | Sequence cluster ID (UniRef50) 1913EDAMfmt 2376 | RDF 1914EDAMfmt 2331 | HTML 1915EDAMfmt 2332 | XML 1916Xref SP_implicit | UniProt accession 1917Query Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s 1918Query Sequence cluster (protein) | XML | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.xml 1919Query Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.rdf 1920Query Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.fasta 1921Query Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s 1922Query Sequence cluster (protein) | XML | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.xml 1923Query Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.rdf 1924Query Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.fasta 1925Query Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s 1926Query Sequence cluster (protein) | XML | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.xml 1927Query Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.rdf 1928Query Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.fasta 1929Example Sequence cluster ID (UniRef100) | P02930 1930Example Sequence cluster ID (UniRef90) | P02930 1931Example Sequence cluster ID (UniRef50) | P02930 1932 1933ID VectorBase 1934Acc DB-0120 1935Name Invertebrate vectors of human pathogens 1936Desc Invertebrate vectors of human pathogens. 1937URL http://www.vectorbase.org/ 1938URLlink http://neuron.cse.nd.edu/vectorbase/index.php/Website_redirects 1939Cat Genome annotation databases 1940Taxon 1 | all 1941EDAMtpc 0783 | Pathogens 1942EDAMdat 2399 | Gene annotation (transcript) 1943EDAMdat 0895 | Peptide annotation 1944EDAMdat 0916 | Gene annotation 1945EDAMid 2759 | Gene ID (VectorBase) 1946EDAMfmt 2331 | HTML 1947Xref SP_explicit | Gene ID (VectorBase) 1948Query Gene annotation {VectorBase entry} | HTML | Gene ID (VectorBase) | http://www.vectorbase.org/Genome/BRCGene/?feature=%s 1949Query Peptide annotation {VectorBase peptide page} | HTML | Gene ID (VectorBase) | http://www.vectorbase.org/Genome/BRCGene/?feature=%s-PA 1950Query Gene annotation (transcript) | HTML | Gene ID (VectorBase) | http://www.vectorbase.org/Genome/BRCGene/?feature=%s-RA 1951Example Gene ID (VectorBase) | AGAP005025 1952 1953ID World-2DPAGE 1954Acc DB-0121 1955Name The world-2DPAGE database 1956Desc A public repository, standards compliant, for proteomics image data published in the literature. 1957URL http://world-2dpage.expasy.org/repository/ 1958Cat 2D gel databases 1959Taxon 1 | all 1960EDAMtpc 0767 | Protein and peptide identification 1961EDAMid 1096 | Sequence accession (protein) 1962EDAMfmt 2331 | HTML 1963EDAMdat 2364 | Experiment annotation (2D PAGE) 1964Xref SP_explicit | Sequence accession (protein) {World-2DPAGE} 1965Query Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) {World-2DPAGE} | http://world-2dpage.expasy.org/repository/%s 1966Example Sequence accession (protein) {World-2DPAGE} | 0020:Q20655 1967 1968ID WORLD-2DPAGE_0003 1969IDalt 0003 1970Name World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome 1971Desc World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome. 1972URL http://www.expasy.org/world-2dpage/ 1973Taxon 3702 | Arabidopsis thaliana 1974EDAMtpc 0767 | Protein and peptide identification 1975EDAMtpc 0780 | Plants 1976EDAMdat 2364 | Experiment annotation (2D PAGE) 1977EDAMid 1096 | Sequence accession (protein) 1978EDAMfmt 2331 | HTML 1979Query Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0003 1980Example Sequence accession (protein) | O65719 1981 1982ID WORLD-2DPAGE_0004 1983IDalt 0004 1984Name World-wide gel-based proteomics database (0004) for mature rat olfactory bulb 1985Desc World-wide gel-based proteomics database (0004) for mature rat olfactory bulb. 1986URL http://www.expasy.org/world-2dpage/ 1987Taxon 10114 | Rattus 1988EDAMtpc 0767 | Protein and peptide identification 1989EDAMdat 2364 | Experiment annotation (2D PAGE) 1990EDAMid 1096 | Sequence accession (protein) 1991EDAMfmt 2331 | HTML 1992Query Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0004 1993Example Sequence accession (protein) | A7VJC3 1994 1995ID WORLD-2DPAGE_0005 1996IDalt 0005 1997Name World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose 1998Desc World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose. 1999URL http://www.expasy.org/world-2dpage/ 2000Taxon 33196 | Botrytis 2001EDAMtpc 0767 | Protein and peptide identification 2002EDAMdat 2364 | Experiment annotation (2D PAGE) 2003EDAMid 1096 | Sequence accession (protein) 2004EDAMfmt 2331 | HTML 2005Query Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0005 2006Example Sequence accession (protein) | A6RHV6 2007 2008ID WORLD-2DPAGE_0006 2009IDalt 0006 2010Name World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee 2011Desc World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee. 2012URL http://www.expasy.org/world-2dpage/ 2013Taxon 7460 | Apis mellifera 2014EDAMtpc 0767 | Protein and peptide identification 2015EDAMdat 2364 | Experiment annotation (2D PAGE) 2016EDAMid 1096 | Sequence accession (protein) 2017EDAMfmt 2331 | HTML 2018Query Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0006 2019Example Sequence accession (protein) | AAP49283.1 2020 2021ID WORLD-2DPAGE_CGL14067-2DPAGE 2022IDalt CGL14067-2DPAGE 2023Name World-wide gel-based proteomics database (CGL14067-2DPAGE) 2024Desc World-wide gel-based proteomics database (CGL14067-2DPAGE) 2025URL http://www.expasy.org/world-2dpage/ 2026Taxon 1 | all 2027EDAMtpc 0767 | Protein and peptide identification 2028EDAMdat 2364 | Experiment annotation (2D PAGE) 2029EDAMid 1096 | Sequence accession (protein) 2030EDAMfmt 2331 | HTML 2031Query Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=cgl14067-2dpage 2032Example Sequence accession (protein) | O31139 2033 2034ID WORLD-2DPAGE_NIBR_2D-PAGE 2035IDalt NIBR 2D-PAGE 2036Name World-wide gel-based proteomics database (NIBR 2D-PAGE) 2037Desc World-wide gel-based proteomics database (NIBR 2D-PAGE) 2038URL http://www.expasy.org/world-2dpage/ 2039Taxon 1 | all 2040EDAMtpc 0767 | Protein and peptide identification 2041EDAMdat 2364 | Experiment annotation (2D PAGE) 2042EDAMid 1096 | Sequence accession (protein) 2043EDAMfmt 2331 | HTML 2044Query Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=nibr_2d-page 2045Example Sequence accession (protein) | O54520 2046 2047ID WormBase 2048Acc DB-0110 2049Name Caenorhabditis elegans genome database 2050Desc Caenorhabditis elegans genome database 2051URL http://www.wormbase.org/ 2052Cat Organism-specific databases 2053Taxon 6239 | Caenorhabditis elegans 2054EDAMtpc 2819 | Invertebrates 2055EDAMid 1026 | Gene symbol 2056EDAMdat 0916 | Gene annotation 2057EDAMid 2295 | Gene ID 2058EDAMid 0989 | Protein identifier 2059EDAMfmt 2331 | HTML 2060Xref SP_explicit | Protein identifier 2061Xref SP_FT | None 2062Query Gene annotation | HTML | Gene symbol | http://www.wormbase.org/db/gene/gene?name=%s 2063Query Gene annotation | HTML | Gene ID | http://www.wormbase.org/db/gene/gene?name=%s 2064Query Gene annotation | HTML | Protein identifier | http://www.wormbase.org/db/gene/gene?name=%s 2065Example Gene symbol | unc-26 2066Example Gene ID | R13A5.9 2067Example Protein identifier | CE02711 2068 2069ID YEASTRACT 2070Name Transcriptional regulators database 2071Desc 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. 2072URL http://www.yeastract.com 2073Taxon 4932 | Saccharomyces cerevisiae 2074EDAMtpc 2846 | Gene regulatory networks 2075EDAMtpc 0749 | Transcription factors and regulatory sites 2076EDAMtpc 0782 | Fungi 2077EDAMdat 0896 | Protein report 2078EDAMdat 2147 | Protein report (transcription factor) 2079EDAMdat 0916 | Gene annotation 2080EDAMdat 2223 | Ontology metadata 2081EDAMdat 0929 | Gene annotation (expression) 2082EDAMid 2755 | Transcription factor name 2083EDAMid 1009 | Protein name 2084EDAMid 1807 | ORF name 2085EDAMid 2299 | Gene name 2086EDAMid 0842 | Identifier 2087EDAMfmt 2331 | HTML 2088Query Gene annotation | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s 2089Query Protein report | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s 2090Query Ontology metadata {GO information} | HTML | ORF name | http://www.yeastract.com/view.php?existing=go&orfname=%s 2091Query Gene annotation | HTML | Gene name | http://www.yeastract.com/view.php?existing=locus&orfname=%s 2092Query Protein report | HTML | Gene name | http://www.yeastract.com/view.php?existing=locus&orfname=%s 2093Query Ontology metadata {GO information} | HTML | Gene name | http://www.yeastract.com/view.php?existing=go&orfname=%s 2094Query Gene annotation | HTML | Protein name | http://www.yeastract.com/view.php?existing=locus&orfname=%s 2095Query Protein report | HTML | Protein name | http://www.yeastract.com/view.php?existing=locus&orfname=%s 2096Query Ontology metadata {GO information} | HTML | Protein name | http://www.yeastract.com/view.php?existing=go&orfname=%s 2097Query 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 2098Query 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 2099Query 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 2100Query 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 2101Query 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 2102Example Transcription factor name | Nrg1p 2103