/usr/share/EMBOSS/test/data/DRCAT.dat

ID      3did
Name    3DID database of 3D interacting domains
Desc    A collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.
URL     http://3did.irbbarcelona.org/
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0166 | Protein structural motifs and surfaces
EDAMdat 2377 | Protein structure report (domain)
EDAMdat 2359 | Domain-domain interaction
EDAMdat 2378 | Protein-motif interaction
EDAMid  1138 | Pfam accession number
EDAMid  2757 | Pfam domain name
EDAMid  1116 | ELM ID
EDAMfmt 2331 | HTML
Query   Protein structure report (domain) | HTML | Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_domain_cgi.pl?draw=graph&domain=%s
Query   Protein structure report (domain) | HTML | Pfam accession number | http://3did.irbbarcelona.org/cgi-bin/query_pfamID_cgi.pl?draw=graph&id=%s
Query   Domain-domain interaction | HTML | Pfam domain name;Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_interaction_cgi.pl?domain1=%s1&db=Pfam&domain2=%s2
Query   Domain-domain interaction | HTML | Pfam domain name;Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_path_cgi.pl?domain1=%s1&domain2=%s2
Query   Protein structure report (domain) | HTML | ELM ID | http://3did.irbbarcelona.org/cgi-bin/query_peptide_cgi.pl?draw=graph&peptide=%s
Query   Protein-motif interaction | HTML | Pfam domain name;ELM ID | http://3did.irbbarcelona.org//cgi-bin/query_dmi_cgi.pl?domain=%s1&ddb=%&peptide=%s2&mdb=ELM
Example Pfam domain name | SH3_1
Example Pfam accession number | PF00018
Example Pfam domain name | Ank
Example Pfam domain name | SH3_1
Example Pfam domain name | SH2
Example Pfam domain name | efhand
Example ELM ID | LIG_SH3_1
Example ELM ID | LIG_SH3_1

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

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

ID      EuPathDB
IDalt   ApiDB
Acc     DB-0153
Name    Apicomplexan database resources (ApiDB)
Desc    A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Cryptosporidium, Giardia, Leishmania, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma).
URL     http://eupathdb.org/eupathdb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5794 | Apicomplexa
EDAMtpc 2821 | Unicellular eukaryotes
EDAMtpc 0783 | Pathogens
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Xref    SP_explicit | Gene symbol
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene symbol | http://www.eupathdb.org/gene/%s
Example Gene symbol | cgd1_1090

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

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

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

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

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

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

ID      ArrayExpress
Acc     DB-0004
Name    ArrayExpress repository for microarray data
Desc    A public archive for functional genomics data compliant with MIAME- and MINSEQE requirements in accordance with compliant data in accordance with MGED recommendations. Includes gene-indexed expression profiles.
URL     http://www.ebi.ac.uk/arrayexpress/
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMtpc 0200 | Microarrays
EDAMdat 0931 | Experiment annotation (microarray)
EDAMdat 0929 | Gene annotation (expression)
EDAMid  0989 | Protein identifier
EDAMid  1144 | ArrayExpress accession number
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier
Query   Gene annotation (expression) {ArrayExpress gene expression summary} | HTML | Protein identifier | http://www.ebi.ac.uk/arrayexpress/genes/uniprot/%s
Query   Experiment annotation (microarray) {ArrayExpress entry} | HTML | ArrayExpress accession number | http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=%s
Example Protein identifier | P15455
Example ArrayExpress accession number | E-MEXP-700

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

ID      Bgee
Acc     DB-0133
Name    Bgee database for gene expression evolution
Desc    Bgee is a database to retrieve and compare gene expression patterns between animal species.  Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies.  Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed.
URL     http://bgee.unil.ch
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0203 | Transcriptomics
EDAMdat 0929 | Gene annotation (expression)
EDAMdat 0928 | Gene expression profile
EDAMdat 0916 | Gene annotation
EDAMdat 2579 | Gene annotation (expressed gene list)
EDAMid  3021 | UniProt accession
EDAMid  1033 | Gene ID (Ensembl)
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Gene annotation | HTML | UniProt accession | http://bgee.unil.ch/bgee/bgee?uniprot_id=%s
Query   Gene annotation | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Query   Gene expression profile | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Query   Gene annotation (expression) | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=data&gene_id=%s
Query   Gene annotation (expressed gene list) {Bgee ID file} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv
Query   Gene annotation (expressed gene list) {Bgee ID file with expression data} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv&gene_information=2
Query   Gene annotation (expressed gene list) {Bgee ID file with expression data count} | Text | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv&gene_information=1
Query   Gene annotation (expressed gene list) {Bgee ID file} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s
Query   Gene annotation (expressed gene list) {Bgee ID file with expression data} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=2
Query   Gene annotation (expressed gene list) {Bgee ID file with expression data count} | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=1
Example Gene ID (Ensembl) | ENSG00000091831
Example UniProt accession | P32234

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

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

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

ID      CATH
Name    CATH protein structure classification database
Desc    CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis.
URL     http://www.cathdb.info/
URLsoap http://api.cathdb.info/api/soap/dataservices/wsdl
Taxon   1 | all
EDAMtpc 0736 | Protein domains and folds
EDAMtpc 3052 | Sequence clusters and classification
EDAMdat 0901 | Protein features (domains)
EDAMdat 1553 | CATH node
EDAMdat 1762 | CATH domain report
EDAMid  1040 | CATH domain ID
EDAMid  1008 | Polypeptide chain ID
EDAMid  1127 | PDB ID
EDAMid  1043 | CATH node ID
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Query   CATH domain report | HTML | CATH domain ID | http://www.cathdb.info/domain/%s
Query   CATH domain report | XML | CATH domain ID | http://www.cathdb.info/domain/%s?view=xml
Query   Protein features (domains) {CATH chain} | HTML | Polypeptide chain ID | http://www.cathdb.info/chain/%s
Query   Protein features (domains) {PDB} | HTML | PDB ID | http://www.cathdb.info/PDB/%s
Query   Protein features (domains) {PDB} | XML | PDB ID | http://www.cathdb.info/PDB/%s?view=xml
Query   CATH node | HTML | CATH node ID | http://www.cathdb.info/cathnode/%s
Example CATH domain ID | 1cukA01
Example Polypeptide chain ID | 1cukA
Example PDB ID | 1cuk
Example CATH node ID | 1.10.10.10


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

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

ID      CMR
Acc     DB-0009
Name    Comprehensive microbial genome resource (CMR)
Desc    Information on all of the publicly available, complete prokaryotic genomes.  Common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes.
URL     http://cmr.tigr.org/
Cat     Genome annotation databases
Taxon   2 | Bacteria
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0622 | Genomics
EDAMdat 0916 | Gene annotation
EDAMdat 2711 | Genome metadata
EDAMid  3021 | UniProt accession
EDAMid  1179 | NCBI taxonomy ID
EDAMid  2292 | GenBank identifier
EDAMid  2774 | Gene ID (JCVI)
EDAMid  2786 | NCBI Genome Project ID
EDAMfmt 2331 | HTML
Xref    SP_implicit | UniProt accession
Query   Gene annotation | HTML | Gene ID (JCVI) | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=%s
Query   Gene annotation | HTML | GenBank identifier | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=SP&acc=%s
Query   Gene annotation | HTML | UniProt accession | http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=protein_id&acc=%s
Query   Genome metadata {CMR genome page} | HTML | NCBI taxonomy ID | http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?taxon_id=%s
Query   Genome metadata {CMR genome page} | HTML | NCBI Genome Project ID | http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?ncbi_project_id=%s
Example Gene ID (JCVI) | BA_0001
Example GenBank identifier | AAP24059.1
Example UniProt accession | Q81W35
Example NCBI taxonomy ID | 198094
Example NCBI Genome Project ID | 309

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

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

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

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

ID      CORUM
Name    CORUM comprehensive resource of mammalian protein complexes
Desc    The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.
URL     http://mips.gsf.de/genre/proj/corum
Taxon   40674 | Mammalia
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0140 | Protein targeting and localization
EDAMdat 2712 | Protein structure report (protein complex)
EDAMid  2713 | Protein ID (CORUM)
EDAMfmt 2331 | HTML
Query   Protein structure report (protein complex) | HTML | Protein ID (CORUM) | http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=%s
Example Protein ID (CORUM) | 178

ID      CuticleDB
Name    Structural proteins of the arthropod cuticle (CuticleDB)
Desc    A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif responsible for chitin binding in Arthropod cuticle.
URL     http://biophysics.biol.uoa.gr/cuticleDB/
Taxon   6656 | Arthropoda
EDAMtpc 0635 | Specific protein resources
EDAMdat 0896 | Protein report
EDAMid  2715 | Protein ID (CuticleDB)
EDAMfmt 2331 | HTML
Query   Protein report | HTML | Protein ID (CuticleDB) | http://bioinformatics.biol.uoa.gr/cuticleDB/protview.jsp?id=%s
Example Protein ID (CuticleDB) | 639

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

ID      dbEST
Name    dbEST database of EST sequences
Desc    dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
URL     http://www.ncbi.nlm.nih.gov/dbEST/
Cat     Not available
Taxon   1 | all
EDAMtpc 0655 | mRNA, EST or cDNA
EDAMdat 0849 | Sequence record
EDAMid  2314 | GI number
EDAMid  1105 | dbEST accession
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2532 | GenBank-HTML
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query   Sequence record | HTML {est} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query   Sequence record | HTML {docsum} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query   Sequence record | FASTA-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query   Sequence record | GenBank-HTML | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query   Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query   Sequence record | HTML {est} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query   Sequence record | HTML {docsum} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query   Sequence record | FASTA-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query   Sequence record | GenBank-HTML | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Example dbEST accession | f12345
Example GI number | 706694

ID      DIP
Acc     DB-0016
Name    Database of interacting proteins (DIP)
Desc    The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
URL     http://dip.doe-mbi.ucla.edu/
Cat     Protein-protein interaction databases
Taxon   1 | all
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 3044 | Protein interaction networks
EDAMdat 1565 | Protein-protein interaction
EDAMid  2616 | DIP ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | DIP ID
Query   Protein-protein interaction {DIP entry} | HTML | DIP ID | dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s
Example DIP ID | DIP-27044N

ID      DisProt
Acc     DB-0017
Name    Database of protein disorder (DisProt)
Desc    A curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
URL     http://www.disprot.org/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure
EDAMdat 2722 | Protein structure report (disordered protein)
EDAMid  2723 | Protein ID (DisProt)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein ID (DisProt)
Query  Protein structure report (disordered protein) {DisProt entry} | HTML | Protein ID (DisProt) | http://www.disprot.org/protein.php?id=%s
Example Protein ID (DisProt) | DP00001

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

ID      EcID
Name    E Coli predicted protein interactions database (EcID)
Desc    Results of running an "in silico 2 hybrid system" for all the possible pairs among E. coli proteins.
URL     http://www.pdg.cnb.uam.es/i2h/info.html
Taxon   562 | Escherichia coli
EDAMtpc 0147 | Protein-protein interactions
EDAMid  1026 | Gene symbol
EDAMdat 0896 | Protein report
EDAMdat 1565 | Protein-protein interaction
EDAMdat 2093 | Data reference
EDAMid  0989 | Protein identifier
EDAMid  2802 | Protein ID (EcID)
EDAMfmt 2331 | HTML
Query   Data reference {Protein sequence ID table} | HTML | Protein identifier | http://ecid.bioinfo.cnio.es/Php/PreQuery.php?busca=%s
Query   Protein-protein interaction {Predictions Mode} | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/Summary.php?view=pred&ID=%s1&seq=%s2&gn=%s3
Query   Protein-protein interaction {Experimental Mode} | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/Summary.php?ID=%s1&seq=%s2&gn=%s3&view=exp
Query   Protein report | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/ProtInfo.php?busca=%s1seq=%s2&gn=%s3
Example Protein identifier | NRDD_ECOLI
Example Protein identifier;Protein ID (EcID);Gene symbol | NRDD_ECOLI;1639;nrdD

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

ID      ELM
Name    Eukaryotic linear motif resource (ELM)
Desc    A resource for predicting functional sites in eukaryotic proteins. Putative functional sites are identified by patterns (regular expressions). To improve the predictive power, context-based rules and logical filters are applied to reduce the amount of false positives.
URL     http://elm.eu.org/
Taxon   1 | all
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0158 | Sequence motifs
EDAMdat 1298 | Sequence features (motifs)
EDAMid  2705 | GO term ID (cellular compartment)
EDAMid  2291 | UniProt ID
EDAMid  0842 | Identifier
EDAMid  1868 | Taxon
EDAMfmt 2331 | HTML
Query   Sequence features (motifs) {ELM report} | HTML | UniProt ID | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s
Query   Sequence features (motifs) {ELM report} | HTML | UniProt ID;Taxon;GO term ID (cellular compartment) | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s1&userSpecies=%s2&userCC=%s3
Query   Sequence features (motifs) {ELM report} | HTML | Identifier {Protein sequence} | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&sequence=%s
Example UniProt ID;Taxon;GO term ID (cellular compartment) | src_human;10116;GO:0005634
Example UniProt ID | src_human
Example Identifier {Protein sequence} | MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL

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

ID      ENZYME
IDalt   EC_number
Acc     DB-0024
Name    Enzyme nomenclature database (ENZYME)
Desc    A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
URL     http://www.expasy.org/enzyme/
Cat     Enzyme and pathway databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 2811 | Nomenclature
EDAMdat 1509 | Protein report (enzyme)
EDAMid  1011 | EC number
EDAMfmt 2331 | HTML
Xref    Other | EC number
Query   Protein report (enzyme) | Text | EC number | http://www.expasy.ch/enzyme/%s.txt
Query   Protein report (enzyme) | HTML | EC number | http://www.expasy.ch/enzyme/%s
Example EC number | 1.5.99.11

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

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

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

ID      GeneCards
Acc     DB-0030
Name    GeneCards database of human genes, protein and diseases
Desc    GeneCards is a searchable, integrated database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs & compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.
URL     http://www.genecards.org/
Cat     Human genes and diseases database
Taxon   9606 | Homo sapiens
! EDAMtpc 0803 | Human disease
EDAMtpc 2813 | Disease genes and proteins
EDAMtpc 3078 | Gene and protein resources
EDAMtpc 0078 | Protein analysis
EDAMtpc 0147 | Protein-protein interactions
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0199 | Genetic variation
EDAMtpc 2815 | Humans
EDAMid  3021 | UniProt accession
EDAMid  1026 | Gene symbol
EDAMid  2298 | Gene ID (HGNC)
EDAMid  1025 | Gene identifier
EDAMid  1904 | Locus ID (EntrezGene)
EDAMid  2610 | Ensembl ID
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | Gene identifier {GeneCards}
Query   Gene annotation | HTML | Gene symbol | http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s
Query   Gene annotation | HTML | UniProt accession | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | HTML | Locus ID (EntrezGene) | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | HTML | Ensembl ID | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | HTML | Gene ID (HGNC) | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query   Gene annotation | XML | Gene symbol | http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s&format=xmlByFunction
Query   Gene annotation | HTML | Gene identifier {GeneCards} | http://www.genecards.org/cgi-bin/carddisp.pl?gc_id=%s
Example Gene symbol | CASP3
Example Locus ID (EntrezGene) | 1956
Example Ensembl ID | ENSG00000146648
Example Gene ID (HGNC) | 2041
Example Gene identifier {GeneCards} | GC20P040256

ID      GeneDB
Name    GeneDB database from Sanger Institute Pathogen Sequencing Units
Desc    Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units).
URL     http://www.genedb.org/
Taxon   1 | all
EDAMtpc 0783 | Pathogens
EDAMid  1026 | Gene symbol
EDAMdat 0916 | Gene annotation
EDAMfmt 2331 | HTML
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene symbol | http://www.genedb.org/gene/%s
Example Gene symbol | ECA4014

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

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

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

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

ID      GPCRDB
Acc     DB-0038
Name    Information system for G protein-coupled receptors (GPCRs)
Desc    GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases.
URL     http://www.gpcr.org/7tm/
Cat     Protein family/group databases
Taxon   2759 | Eukaryota
EDAMtpc 0820 | Membrane proteins
EDAMtpc 0148 | Protein-ligand interactions
EDAMdat 1456 | Protein report (membrane protein)
EDAMid  1131 | Protein family name
EDAMfmt 2331 | HTML
Xref    SP_implicit | Protein family name
Query   Protein report (membrane protein) {GPCRDB entry} | HTML | Protein family name | http://www.gpcr.org/7tm/proteins/%s
Example Protein family name | a1kyp5_petma

ID      Gramene
Acc     DB-0039
Name    Gramene database for comparative grass genomics
Desc    Gramene adds value to public data sets of grass genomes and helps to compare, identify and understand genes, pathways and phenotypes from different grass species.
URL     http://www.gramene.org/
Cat     Organism-specific databases
Taxon   4479 | Poaceae
EDAMtpc 0797 | Comparative genomics
EDAMtpc 0625 | Genotype and phenotype resources
EDAMtpc 0780 | Plants
EDAMtpc 0602 | Pathways, networks and models
EDAMdat 0896 | Protein report
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Protein report {Gramene entry} | HTML | UniProt accession | http://www.gramene.org//db/protein/protein_search?acc=%s
Example UniProt accession | P93436

ID      HAMAP
Acc     DB-0041
Name    High-quality automated and manual annotation of microbial proteomes (HAMAP)
Desc    A system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
URL     http://www.expasy.org/sprot/hamap/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMtpc 0724 | Protein families
EDAMdat 0896 | Protein report
EDAMdat 0849 | Sequence record
EDAMdat 2872 | ID list
EDAMid  2766 | HAMAP ID
EDAMfmt 2331 | HTML
EDAMfmt 2188 | uniprot
Xref    SP_explicit | HAMAP ID
Query   ID list {HAMAP family members} | Text | HAMAP ID | http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=tab&columns=id
Query   Sequence record {HAMAP family sequences} | uniprot | HAMAP ID | http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=txt
Query   Protein report {HAMAP family rules} | HTML | HAMAP ID | http://www.expasy.org/unirule/MF_%s
Query   Protein report {HAMAP family rules} | Text | HAMAP ID | http://www.expasy.org/unirule/MF_%s.txt
Example HAMAP ID | 00314

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

ID      InterPro
Acc     DB-0052
Name    InterPro integrated database of protein families, domains, regions, repeats and functional sites
Desc    Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.
URL     http://www.ebi.ac.uk/interpro/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0724 | Protein families
EDAMtpc 0748 | Protein sites and features
EDAMtpc 0641 | Repeat sequences
EDAMdat 1355 | Protein signature
EDAMid  1133 | InterPro accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | InterPro accession
Xref    SP_FT | InterPro accession
Xref    EMBL_explicit | InterPro accession
Query   Protein signature | HTML | InterPro accession | http://www.ebi.ac.uk/interpro/IEntry?ac=%s
Example InterPro accession | IPR000059

ID      IPI
Acc     DB-0132
Name    International protein index (IPI)
Desc    Provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases.
URL     http://www.ebi.ac.uk/IPI
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 0621 | Genome, proteome and model organisms
EDAMdat 0849 | Sequence record
EDAMid  2384 | IPI protein ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | IPI protein ID
Query   Sequence record {IPI entry} | HTML | IPI protein ID | http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=%s
Example IPI protein ID | IPI00177866

ID      LGICdb
Name    Ligand-gated ion channel database (LGICdb)
Desc    Nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.
URL     http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
Taxon   1 | all
EDAMtpc 0741 | Protein sequence alignment
EDAMtpc 0166 | Protein structural motifs and surfaces
EDAMtpc 0084 | Phylogenetics
EDAMdat 1456 | Protein report (membrane protein)
EDAMid  2797 | Protein ID (LGICdb)
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Query   Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} | HTML | Protein ID (LGICdb) | http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/%s.php
Query   Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} | XML | Protein ID (LGICdb) | http://www.ebi.ac.uk/compneur-srv/LGICdb/XML/%s.xml
Example Protein ID (LGICdb) | 5HT3Arano

ID      MEROPS
Acc     DB-0059
Name    MEROPS peptidase database
Desc    Information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. Information includes the classification and nomenclature of the peptidase and links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.
URL     http://merops.sanger.ac.uk/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMtpc 2811 | Nomenclature
EDAMdat 0896 | Protein report
EDAMid  2629 | Enzyme ID (MEROPS)
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Enzyme ID (MEROPS)
Query   Protein report {MEROPS page} | HTML | Identifier {Clan} | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Query   Protein report {MEROPS page} | HTML | Identifier {Family} | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Query   Protein report {MEROPS page} | HTML | Enzyme ID (MEROPS) | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Example Enzyme ID (MEROPS) | A01.001

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

ID      NMPDR
Acc     DB-0125
Name    National microbial pathogen
Desc    Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
URL     http://www.nmpdr.org
URLlink  http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/LinkingToTheGenomeViewer
Cat     Genome annotation databases
Taxon   2 | Bacteria
EDAMtpc 0783 | Pathogens
EDAMtpc 0797 | Comparative genomics
EDAMdat 0916 | Gene annotation
EDAMid  1179 | NCBI taxonomy ID
EDAMid  2737 | FIG ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | FIG ID
Query   Gene annotation | HTML | NCBI taxonomy ID | http://www.nmpdr.org/linkin.cgi?genome=%s
Query   Gene annotation {Protein encoding gene or other feature} | HTML | FIG ID | http://www.nmpdr.org/linkin.cgi?id=%s
Example NCBI taxonomy ID | 83333.1
Example FIG ID | 83333.1.peg.123
Example FIG ID | 83333.1.rna.1

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

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

ID      PANTHER
Acc     DB-0069
Name    Protein analysis through evolutionary relationships (PANTHER)
Desc    Classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms. PANTHER includes "PANTHER Genes" (genes, transcripts and proteins in Human, Mouse, Rat, and Drosophila melanogaster), PANTHER Families (Protein families and subfamilies and associated data such as phylogenetic trees, multiple sequence alignments and HMMs), "PANTHER Pathways" (expert-curated signaling and metabolic pathways mapped to protein sequences in PANTHER Library) and "PANTHER Ontologies".
URL     http://www.pantherdb.org/
Cat     Family and domain databases; Protein sequence classification database
Taxon   1 | all
EDAMtpc 2225 | Protein databases
EDAMtpc 0602 | Pathways, networks and models
EDAMtpc 0724 | Protein families
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0084 | Phylogenetics
EDAMdat 2984 | Pathway or network report
EDAMdat 0907 | Protein family annotation
EDAMid  1161 | Pathway ID (Panther)
EDAMid  2783 | Protein family ID (PANTHER)
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein family ID (PANTHER)
Query   Protein family annotation {PANTHER Family} | HTML | Protein family ID (PANTHER) | http://www.pantherdb.org/panther/family.do?clsAccession=%s
Query   Pathway or network report | HTML | Pathway ID (Panther) | http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=%s
Example Protein family ID (PANTHER) | PTHR12649:SF6
Example Pathway ID (Panther) | P00002

ID      Pathema
Name    Pathema: a clade-specific bioinformatics resource
Desc    Genome database for six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica.
URL     http://www.jcvi.org/cms/research/projects/pathema/overview/
Cat     Not available
Taxon   1 | all
EDAMtpc 1811 | Prokaryotes and archae
EDAMtpc 0783 | Pathogens
Xref    SP_FT | None

ID      PathoPlant
Name    PathoPlant database of plant-pathogen interactions and Arabidopsis expression
Desc    Plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. Also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.
URL     http://www.pathoplant.de
Taxon   1 | all
EDAMtpc 0197 | Gene expression resources
EDAMtpc 0204 | Gene regulation resources
EDAMtpc 0780 | Plants
EDAMtpc 0754 | Signaling pathways
EDAMtpc 0780 | Plants
EDAMtpc 0783 | Pathogens

ID      PeptideAtlas
Acc     DB-0071
Name    PeptideAtlas peptide database
Desc    A multi-organism compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences.
URL     http://www.peptideatlas.org
Cat     Proteomic databases; Peptide identification database; Mass spectrometry database
Taxon   1 | all
EDAMtpc 0613 | Peptides and amino acids
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 0896 | Protein report
EDAMdat 0945 | Peptide identification
EDAMdat 2536 | Mass spectrometry data
EDAMid  2384 | IPI protein ID
EDAMid  2398 | Protein ID (Ensembl)
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | Protein identifier {PeptideAtlas}
Query   Peptide identification | HTML | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY
Query   Peptide identification | XML | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=xml
Query   Peptide identification | Text | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=tsv
Query   Mass spectrometry data {Recommended transitions for human protein} | HTML | Protein ID (Ensembl) | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ViewMRMList?protein_name_constraint=%s&atlas_build_id=182&consensus_library_id=9&action=QUERY
Query   Protein report {PeptideAtlas entry} | HTML | IPI protein ID | http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?atlas_build_id=242&protein_name=%s&action=QUERY
Query   Protein report {PeptideAtlas entry} | HTML | Protein identifier {PeptideAtlas} | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=%s
Example Protein ID (Ensembl) | ENSP00000374576
Example IPI protein ID | IPI00795032
Example Protein identifier {PeptideAtlas} | P62258

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

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


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

ID      PHI-base
Name    PHI-base pathogen host interactions database
Desc    Curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries.
URL     http://www.phibase.org
Taxon   1 | all
EDAMtpc 0623 | Genes, gene family or system
EDAMtpc 0783 | Pathogens

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

ID      PhosphoSite
Acc     DB-0123
Name    Phosphorylation site database
Desc    A curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites. Information in PhosphoSite version 1.0 includes the phosphorylated residue and its surrounding sequence, orthologous sites in other species, the location within domains and motifs, links to other online resources and literature references.
URL     http://www.phosphosite.org
Cat     PTM databases
Taxon   1 | all
EDAMtpc 0751 | Phosphorylation sites
EDAMdat 2071 | Sequence motif (protein)
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Sequence motif (protein) {PhosphoSite entry} | HTML | UniProt accession | http://www.phosphosite.org/uniprotAccAction.do?id=%s
Example UniProt accession | Q92844

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

ID      PIRSF
Acc     DB-0079
Name    PIRSF whole-protein classification database
Desc    Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains.
URL     http://pir.georgetown.edu/pirsf/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0724 | Protein families
EDAMdat 0907 | Protein family annotation
EDAMid  1136 | PIRSF ID
EDAMfmt 2331 | HTML
Xref    SP_explicit | PIRSF ID
Query   Protein family annotation {PIRSF entry} | HTML | PIRSF ID | http://pir.georgetown.edu/cgi-bin/ipcSF?id=%s
Example PIRSF ID | SF000186

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

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

ID      PRIDE
Acc     DB-0130
Name    PRIDE proteomics identifications database
Desc    Standards compliant, public data repository for proteomics data, protein and peptide identifications together with the evidence supporting these identifications.
URL     http://www.ebi.ac.uk/pride
URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do
Cat     Proteomic databases
Taxon   1 | all
EDAMtpc 0767 | Protein and peptide identification
EDAMtpc 0121 | Proteomics
EDAMdat 2536 | Mass spectrometry data
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Mass spectrometry data {PRIDE entry} | HTML | UniProt accession | http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=%s
Example UniProt accession | P29375

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

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

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

ID      Reactome
Acc     DB-0088
Name    Reactome knowledgebase of biological pathways
Desc    Curated knowledgebase of biological pathways and processes.
URL     http://www.reactome.org/
URLlink http://www.reactome.org/referring2GK.html
URLsoap http://www.reactome.org/download/index.html
Cat     Enzyme and pathway databases
Taxon   1 | all
EDAMtpc 0602 | Pathways, networks and models
EDAMdat 2984 | Pathway or network report
EDAMdat 0896 | Protein report
EDAMid  0989 | Protein identifier
EDAMid  3021 | UniProt accession
EDAMid  1027 | Gene ID (NCBI)
EDAMid  1011 | EC number
EDAMid  1174 | ChEBI ID
EDAMid  1056 | Database name
EDAMid  0990 | Compound name
EDAMid  1155 | Pathway ID (reactome)
EDAMid  1176 | GO term ID
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_explicit | Pathway ID (reactome)
Query   Pathway or network report | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%s&ZOOM=2
Query   Pathway or network report | XML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/sbml_export?DB=gk_current&ID=%s
Query   Protein report {Reactome entry} | HTML | Database name;Protein identifier | http://www.reactome.org/cgi-bin/link?SOURCE=%s1&ID=%s2
Query   Protein report {Reactome entry} | HTML | UniProt accession | http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=%s
Query   Protein report {Reactome entry} | HTML | ChEBI ID | http://www.reactome.org/cgi-bin/link?SOURCE=CHEBI&ID=%s
Query   Protein report {Reactome entry} | HTML | Compound name | http://www.reactome.org/cgi-bin/link?SOURCE=COMPOUND&ID=%s
Query   Protein report {Reactome entry} | HTML | GO term ID | http://www.reactome.org/cgi-bin/link?SOURCE=GO&ID=%s
Query   Protein report {Reactome entry} | HTML | EC number | http://www.reactome.org/cgi-bin/link?SOURCE=EC&ID=%s
Query   Protein report {Reactome entry} | HTML | Gene ID (NCBI) | http://www.reactome.org/cgi-bin/link?SOURCE=Entrez+Gene&ID=%s
Query   Protein report {Reactome entry} | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/link?SOURCE=Reactome&ID=%s
Example UniProt accession | P30304
Example ChEBI ID | 15422
Example Compound name | C00002
Example GO term ID | 0030060
Example EC number | 1.1.1.37
Example Gene ID (NCBI) | 4171
Example Pathway ID (reactome) | REACT_1
 
ID      REBASE
Acc     DB-0089
Name    REBASE restriction enzymes and methylases database
Desc    Restriction enzymes and methylases database.
URL     http://rebase.neb.com/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0821 | Enzymes and reactions
EDAMdat 1509 | Protein report (enzyme)
EDAMid  1012 | Enzyme name
EDAMid  2325 | REBASE enzyme number
EDAMfmt 2331 | HTML
Xref    SP_explicit | REBASE enzyme number
Query   Protein report (enzyme) | HTML | Enzyme name | http://rebase.neb.com/rebase/enz/%s.html
Query   Protein report (enzyme) | HTML | REBASE enzyme number | http://rebase.neb.com/rebase/enz/%s.html
Example Enzyme name | EcoRI
Example REBASE enzyme number | 993

ID      REDIdb
Name    RNA editing database (REDIdb)
Desc    Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored.
URL     http://biologia.unical.it/py_script/overview.html
Taxon   1 | all
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMdat 2043 | Sequence record lite
EDAMdat 1383 | Sequence alignment (nucleic acid)
EDAMid  2781 | REDIdb ID
EDAMfmt 2310 | FASTA-HTML
EDAMfmt 2331 | HTML
Query   Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s
Query   Sequence record lite {REDIdb fasta} | FASTA-HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s
Query   Sequence alignment (nucleic acid) {REDIdb overview} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s
Query   Sequence alignment (nucleic acid) {REDIdb alignment} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/align.py?query=%s
Example REDIdb ID  | EDI_000000002

ID      RefSeq
Acc     DB-0117
Name    NCBI reference sequences
Desc    A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. Provides a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.
URL     http://www.ncbi.nlm.nih.gov/RefSeq/
Cat     Sequence databases
Taxon   1 | all
EDAMtpc 3041 | Sequence databases
EDAMtpc 0797 | Comparative genomics
EDAMdat 0849 | Sequence record
EDAMid  0989 | Protein identifier
EDAMfmt 2331 | HTML
Xref    SP_explicit | Protein identifier {Refseq}
Query   Sequence record {RefSeq entry} | HTML | Protein identifier {Refseq} | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=%s
Example Protein identifier {Refseq} | YP_654574.1

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

ID      RESID
Name    RESID database of protein modifications
Desc    A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
URL     http://www.ebi.ac.uk/RESID/
Taxon   1 | all
EDAMtpc 0601 | Protein modifications
EDAMtpc 0166 | Protein structural motifs and surfaces
EDAMdat 2191 | Protein modification annotation
EDAMid  2619 | RESID ID
EDAMfmt 2332 | XML
Query   Protein modification annotation {RESID entry} | XML | RESID ID | http://www.ebi.ac.uk/ontology-lookup/RESIDService?resid_id=%s
Example RESID ID | AA0002

ID      RFAM
IDalt   RFam
Name    RNA families database of alignments and CMs
Desc    Collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. The main use of Rfam is as a source of RNA multiple alignments with consensus secondary structure annotation in a consistent format.
URL     http://rfam.sanger.ac.uk/
Cat     Not available
Taxon   1 | all
EDAMtpc 0740 | Nucleic acid sequence alignment
EDAMtpc 0697 | RNA structure and alignment
EDAMdat 2354 | RNA family annotation
EDAMid  2356 | RFAM accession
EDAMid  2606 | RFAM name
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    EMBL_explicit | RFAM accession
Query   RNA family annotation | HTML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s
Query   RNA family annotation | HTML | RFAM name | http://rfam.sanger.ac.uk/family?acc=%s
Query   RNA family annotation | XML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s&output=xml
Query   RNA family annotation | XML | RFAM name | http://rfam.sanger.ac.uk/family?acc=%s&output=xml
Example RFAM accession | RF00522
Example RFAM name | PreQ1

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

ID      SCOP
Name    Structural classification of proteins (SCOP) database
Desc    The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
URL     http://scop.mrc-lmb.cam.ac.uk/scop
Taxon   1 | all
EDAMtpc 0736 | Protein domains and folds
EDAMdat 1554 | SCOP node
EDAMdat 2093 | Data reference
EDAMid  1042 | SCOP sunid
EDAMid  1127 | PDB ID
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Query   SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Query   Data reference {PDB Entry search} | HTML | PDB ID | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?PDB=%s
Query   Data reference | HTML | Identifier {Keyword} | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s
Example SCOP sunid | 47718
Example PDB ID | 1djh
Example Identifier {Keyword} | immunoglobulin

ID      SCOWL
Name    Structural characterization of water, ligands and proteins (SCOWL)
Desc    PDB interface interactions at atom, residue and domain level. The database contains protein interfaces and residue-residue interactions formed by structural units and interacting solvent.
URL     http://www.scowlp.org
Taxon   1 | all
EDAMtpc 0128 | Protein interactions
EDAMdat 2359 | Domain-domain interaction
EDAMid  1127 | PDB ID
EDAMid  1042 | SCOP sunid
EDAMfmt 2331 | HTML
Query   Domain-domain interaction | HTML | PDB ID | http://www.scowlp.org/scowlp/PDB.action?show=&PDBId=%s
Query   Domain-domain interaction | HTML | SCOP sunid {SCOP family id} | http://www.scowlp.org/scowlp/Search.action?childs=&currentChoice=SCOP_FAMILY%s
Example PDB ID | 1fxk
Example SCOP sunid | 2381635

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

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

ID      SMR
Acc     DB-0098
Name    A database of annotated 3D protein structure models
Desc    Annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
URL     http://swissmodel.expasy.org/repository/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0698 | Protein tertiary structure
EDAMdat 1460 | Protein structure
EDAMid  3021 | UniProt accession
EDAMfmt 2331 | HTML
Xref    SP_explicit | UniProt accession
Query   Protein structure {SMR entry} | HTML | UniProt accession | http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s
Example UniProt accession | P01009

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

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

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

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

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

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

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

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

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

ID      UniProtKB_Swiss-Prot
IDalt   SwissProt
Name    Universal protein resource knowledge base / Swiss-Prot
Desc    Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature
URL     http://www.uniprot.org
Taxon   1 | all
EDAMdat 2201 | Sequence record full
EDAMtpc 0639 | Protein sequence analysis
EDAMid  3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    EMBL_explicit | UniProt accession
Query   Sequence record full | HTML | UniProt accession | http://www.uniprot.org/uniprot/%s
Query   Sequence record full | Text | UniProt accession | http://www.uniprot.org/uniprot/%s.txt
Query   Sequence record full | XML | UniProt accession | http://www.uniprot.org/uniprot/%s.xml
Query   Sequence record full | RDF | UniProt accession | http://www.uniprot.org/uniprot/%s.rdf
Query   Sequence record full | FASTA format | UniProt accession | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession | P12345

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

ID      UniRef
Name    Non-redundant reference (UniRef) databases
Desc    Clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
URL     http://www.uniprot.org/help/uniref
Cat     Other
Taxon   1 | all
EDAMtpc 3052 | Sequence clusters and classification
EDAMtpc 0114 | Gene structure and RNA splicing
EDAMfmt 1929 | FASTA format
EDAMdat 1245 | Sequence cluster (protein)
EDAMid  2347 | Sequence cluster ID (UniRef100)
EDAMid  2348 | Sequence cluster ID (UniRef90)
EDAMid  2349 | Sequence cluster ID (UniRef50)
EDAMfmt 2376 | RDF
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref    SP_implicit | UniProt accession
Query   Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s
Query   Sequence cluster (protein) | XML | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.xml
Query   Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.rdf
Query   Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef100) | http://www.uniprot.org/uniref/UniRef100_%s.fasta
Query   Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s
Query   Sequence cluster (protein) | XML | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.xml
Query   Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.rdf
Query   Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef90) | http://www.uniprot.org/uniref/UniRef90_%s.fasta
Query   Sequence cluster (protein) | HTML | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s
Query   Sequence cluster (protein) | XML | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.xml
Query   Sequence cluster (protein) | RDF | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.rdf
Query   Sequence cluster (protein) | FASTA format | Sequence cluster ID (UniRef50) | http://www.uniprot.org/uniref/UniRef50_%s.fasta
Example Sequence cluster ID (UniRef100) | P02930
Example Sequence cluster ID (UniRef90) | P02930
Example Sequence cluster ID (UniRef50) | P02930

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

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

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

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

ID      WORLD-2DPAGE_0005
IDalt   0005
Name    World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose
Desc    World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose.
URL     http://www.expasy.org/world-2dpage/
Taxon   33196 | Botrytis
EDAMtpc 0767 | Protein and peptide identification
EDAMdat 2364 | Experiment annotation (2D PAGE)
EDAMid  1096 | Sequence accession (protein)
EDAMfmt 2331 | HTML
Query   Experiment annotation (2D PAGE) | HTML | Sequence accession (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0005
Example Sequence accession (protein) | A6RHV6

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

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

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

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

ID      YEASTRACT
Name    Transcriptional regulators database
Desc    A curated repository of more than 34469 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1000 bibliographic references. It also includes the description of 291 specific DNA binding sites for more than a hundred characterized TFs.
URL     http://www.yeastract.com
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 2846 | Gene regulatory networks
EDAMtpc 0749 | Transcription factors and regulatory sites
EDAMtpc 0782 | Fungi
EDAMdat 0896 | Protein report
EDAMdat 2147 | Protein report (transcription factor)
EDAMdat 0916 | Gene annotation
EDAMdat 2223 | Ontology metadata
EDAMdat 0929 | Gene annotation (expression)
EDAMid  2755 | Transcription factor name
EDAMid  1009 | Protein name
EDAMid  1807 | ORF name
EDAMid  2299 | Gene name
EDAMid  0842 | Identifier
EDAMfmt 2331 | HTML
Query   Gene annotation | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Protein report | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Ontology metadata {GO information} | HTML | ORF name | http://www.yeastract.com/view.php?existing=go&orfname=%s
Query   Gene annotation | HTML | Gene name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Protein report | HTML | Gene name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Ontology metadata {GO information} | HTML | Gene name | http://www.yeastract.com/view.php?existing=go&orfname=%s
Query   Gene annotation | HTML | Protein name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Protein report | HTML | Protein name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query   Ontology metadata {GO information} | HTML | Protein name | http://www.yeastract.com/view.php?existing=go&orfname=%s
Query   Gene annotation (expression) {Regulation reference} | HTML | Transcription factor name;Gene name {target gene} | http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Query   Gene annotation (expression) {Regulation reference} | HTML | Transcription factor name;ORF name {target ORF} | http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Query   Protein report (transcription factor) {TF binding site reference} | HTML | Transcription factor name;Identifier {Consensus sequence} | http://www.yeastract.com/view.php?existing=consensus&proteinname=%s1&consensus=%s2
Query   Protein report (transcription factor) {Documented regulators of a given set of genes} | HTML | Gene name | http://www.yeastract.com/findregulators.php?type=doc&genes=%s
Query   Gene annotation {Documented target genes of a given set of TFs} | HTML | Transcription factor name | http://www.yeastract.com/findregulated.php?type=doc&tfs=%s
Example Transcription factor name | Nrg1p
emboss-test 6.6.0-1 / usr / share / EMBOSS / test / data / DRCAT.dat
