/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 0000719 | Protein-protein interaction
EDAMdat 0002377 | Domain annotation
EDAMdat 0002359 | Domain-domain interaction
EDAMdat 0002378 | Domain-motif interaction
EDAMdat 0002360 | Domain-domain interaction (indirect)
EDAMid  0001138 | Pfam accession number
EDAMid  0002757 | Pfam domain name
EDAMid  0001116 | ELM ID
EDAMfmt 0002331 | HTML
Query    Domain annotation | HTML | Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_domain_cgi.pl?draw=graph&domain=%s
Query    Domain annotation | 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 (indirect) | HTML | Pfam domain name;Pfam domain name | http://3did.irbbarcelona.org/cgi-bin/query_path_cgi.pl?domain1=%s1&domain2=%s2
Query    Domain annotation | HTML | ELM ID | http://3did.irbbarcelona.org/cgi-bin/query_peptide_cgi.pl?draw=graph&peptide=%s
Query    Domain-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 0000820 | Membrane protein

ID      anu_2dpage
Acc     DB-0002
Name    Australian National University 2-DE database (ANU-2DPAGE)
Desc    2-DE PAGE database.
URL     http://semele.anu.edu.au
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit Uniprot accession number
Query    2D PAGE annotation | HTML | UniProt accession number | http://semele.anu.edu.au/cgi-bin/get-2d-entry?%s
Example UniProt accession number | P02930
Example UniProt accession number | Q9SIB9


ID      apidb
IDalt   EuPathDB
Acc     DB-0153
Name    Apicomplexan database resources (ApiDB)
Desc    A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Cryptosporidium, Giardia, Leishmania, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma).
URL     http://eupathdb.org/eupathdb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5794 | Apicomplexa
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0001026 | Gene symbol
EDAMfmt 0002331 | HTML
Xref    SP_explicit Gene symbol
Xref    SP_FT None
Query    Gene annotation | HTML | Gene symbol | http:www.eupathdb.org/gene/%s
Example Gene symbol | cgd1_1090


ID      apidb_cryptodb
IDalt   CryptoDB
Name    Cryptosporidium genome resources (CryptoDB)
Desc    Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium.
URL     http://cryptodb.org/cryptodb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5806 | Cryptosporidium
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Gene annotation | HTML | Gene ID | http://cryptodb.org/gene/%s


ID      apidb_giardiadb
IDalt   GiardiaDB
Name    Giardia genome resources (GiardiaDB)
Desc    Genomic-scale datasets for the eukaryotic pathogen Giardia.
URL     http://giardiadb.org/giardiadb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5740 | Giardia
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Gene annotation | HTML | Gene ID | http://giardiadb.org/gene/%s


ID      apidb_plasmodb
IDalt   PlasmoDB
Name    Plasmodium genome resources (PlasmoDB)
Desc    Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium.
URL     http://plasmodb.org/plasmo/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5820 | Plasmodium
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Gene annotation | HTML | Gene ID | http://plasmodb.org/gene/%s


ID      apidb_toxodb
IDalt   ToxoDB
Name    Toxoplasma genome resources (ToxoDB)
Desc    Genomic-scale datasets associated with the eukaryotic pathogens Toxoplasma.
URL     http://toxodb.org/toxo/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5810 | Toxoplasma
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Gene annotation | HTML | Gene ID | http://toxodb.org/gene/%s


ID      apidb_trichdb
IDalt   TrichDB
Name    Trichomonas genome resources (TrichDB)
Desc    Genomic-scale datasets associated with the eukaryotic Trichomonas.
URL     http://trichdb.org/trichdb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5721 | Trichomonas
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Gene annotation | HTML | Gene ID | http://trichdb.org/gene/%s


ID      apidb_tritrypdb
IDalt   TritrypDB
Name    Kinetoplastid genome resources (TritrypDB)
Desc    Kinetoplastid genome resources.
URL     http://tritrypdb.org/tritrypdb/
URLrest http://eupathdb.org/eupathdb/serviceList.jsp
Cat     Not available
Taxon   5653 | Kinetoplastida
EDAMtpc 0002821 | Unicellular eukaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0002295 | Gene ID
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Gene annotation | HTML | Gene ID | http://tritrypdb.org/gene/%s


ID      arrayexpress
Acc     DB-0004
Name    ArrayExpress repository for microarray data
Desc    A public archive for functional genomics data compliant with MIAME- and MINSEQE requirements in accordance with compliant data in accordance with MGED recommendations. Includes gene-indexed expression profiles.
URL     http://www.ebi.ac.uk/arrayexpress/
Cat     Gene expression databases
Taxon   1 | all
EDAMtpc 0000197 | Gene expression and regulation
EDAMtpc 0000203 | Gene expression profiling
EDAMtpc 0000200 | Microarrays
EDAMdat 0000931 | Microarray experiment annotation
EDAMdat 0000929 | Gene expression annotation
EDAMid  0000989 | Protein identifier
EDAMid  0001144 | ArrayExpress accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit Protein identifier
Query    Gene expression annotation {ArrayExpress gene expression summary} | HTML | Protein identifier | http://www.ebi.ac.uk/arrayexpress/genes/uniprot/%s
Query    Microarray experimental data {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 splicing and transcript diversity.
URL     http://www.ebi.ac.uk/astd/
Taxon   1 | all
EDAMtpc 0000630 | Gene structure
EDAMdat 0002397 | Gene features (exon)
EDAMdat 0000896 | Protein annotation
EDAMdat 0002399 | Transcript annotation
EDAMdat 0000916 | Gene annotation
EDAMdat 0001312 | Gene features (promoter)
EDAMdat 0002397 | Gene features (exon)
EDAMdat 0002754 | Gene features (intron)
EDAMdat 0001302 | Nucleic acid features (PolyA signal)
EDAMid  0002367 | ASTD ID
EDAMid  0002368 | ASTD ID (exon)
EDAMid  0002369 | ASTD ID (intron)
EDAMid  0002370 | ASTD ID (polya)
EDAMid  0002371 | ASTD ID (tss)
EDAMid  0001033 | Gene ID (Ensembl)
EDAMid  0002398 | Protein ID (Ensembl)
EDAMfmt 0001927 | embl
EDAMfmt 0002305 | gff
EDAMfmt 0002306 | gtf
EDAMfmt 0001929 | fasta
EDAMfmt 0002331 | HTML
Query    Gene annotation | HTML | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s
Query    Gene annotation | embl | Gene ID (Ensembl) | http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=embl
Query    Gene annotation | fasta | 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    Transcript annotation | HTML | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s
Query    Transcript annotation | embl | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=embl
Query    Transcript annotation | gff | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gff
Query    Transcript annotation | gtf | ASTD ID | http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gtf
Query    Protein annotation | HTML | Protein ID (Ensembl) | http://www.ebi.ac.uk/astd/peptideview.html?acc=%s
Query    Protein annotation | fasta | 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 | 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 0000623 | Gene family or system
EDAMtpc 0000197 | Gene expression and regulation
EDAMtpc 0000203 | Gene expression profiling
EDAMdat 0000929 | Gene expression annotation
EDAMdat 0000928 | Gene expression profile
EDAMdat 0000916 | Gene annotation
EDAMdat 0002579 | Gene expression annotation (expressed genes)
EDAMid  0001099 | UniProt accession number
EDAMid  0001033 | Gene ID (Ensembl)
EDAMfmt 0002331 | HTML
Xref    SP_explicit UniProt accession number
Query    Gene annotation | HTML | UniProt accession number | 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 expression annotation | HTML | Gene ID (Ensembl) | http://bgee.unil.ch/bgee/bgee?page=expression&action=data&gene_id=%s
Query    Gene expression annotation (expressed genes) {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 expression annotation (expressed genes) {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 expression annotation (expressed genes) {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 expression annotation (expressed genes) {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 expression annotation (expressed genes) {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 expression annotation (expressed genes) {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 number | 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 0000717 | Protein-ligand interaction
EDAMtpc 0000620 | Drugs and targets
EDAMdat 0002301 | SMILES string
EDAMdat 0000962 | Small molecule annotation
EDAMdat 0002402 | Protein-drug interaction annotation
EDAMdat 0000857 | Sequence database hits
EDAMdat 0002726 | Inhibitor annotation
EDAMid  0001208 | Protein sequence
EDAMid  0001127 | PDB ID
EDAMid  0001187 | PubMed unique identifier
EDAMid  0001099 | UniProt accession number
EDAMid  0002301 | SMILES string
EDAMid  0002580 | BindingDB Monomer ID
EDAMid  0001009 | Protein name
EDAMfmt 0002331 | HTML
Xref    SP_explicit UniProt accession number
Query    Protein-drug interaction annotation | HTML | UniProt accession number | 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    Compound annotation {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    Sequence database hits {BindingDB entries} | HTML | Protein sequence | http://www.bindingdb.org/bind/blastResult.jsp?DATASOURCE=protein&Search=B2&blastSeq=%s
Query    Compound annotation | HTML | BindingDB Monomer ID | http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=%s
Query    Compound annotation | HTML | SMILES string | http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=4&submit=Search&smilesStr=%s
Query    Protein-drug interaction annotation | HTML | PDB ID | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pdbids.jsp?pdbids_submit=Search&pdbids=%s
Query    Protein-drug interaction annotation | HTML | PubMed unique identifier | http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=%s
Example UniProt accession number | Q29005
Example Protein name | ABL
Example Protein name | Ab N1G9
Example Protein sequence | VKCGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLD
Example BindingDB Monomer ID | 100
Example SMILES string | CC%28C%29C1%28C%29SC%28Nc2ccccc2C%28F%29%28F%29F%29%3DNC1%3DO+%7Cc%3A18%7C
Example PDB ID | 1OKZ
Example PubMed unique identifier | 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 0000718 | Protein-nucleic acid interaction
EDAMdat 0001567 | Protein-nucleic acid interaction
EDAMdat 0002358 | Protein domain-nucleic acid interaction
EDAMid  0001042 | SCOP sunid
EDAMid  0001127 | PDB ID
EDAMfmt 0002331 | HTML
Query    Protein-nucleic acid interaction | HTML | PDB ID | http://mordred.bioc.cam.ac.uk/bipa/structures/%s
Query    Protein 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 0000821 | Enzymes
EDAMdat 0001509 | Enzyme annotation
EDAMid  0001099 | UniProt accession number
EDAMid  0001011 | EC number
EDAMid  0002593 | BRENDA organism ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit EC number;BRENDA organism ID
Query    Enzyme annotation {BRENDA entry} | HTML | EC number | http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s
Query    Enzyme annotation {BRENDA entry} | HTML | EC number;BRENDA organism ID | http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s1&&OrganismID=&s3&ShowAll=True
Query    Enzyme annotation {BRENDA entry} | HTML | EC number;UniProt accession number;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 number | 1.1.5.82;P15719
Example EC number;UniProt accession number;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 0000736 | Protein domains
EDAMtpc 0000703 | CATH domain structure
EDAMtpc 0000164 | Sequence clustering
EDAMdat 0000901 | Protein features (domain composition)
EDAMdat 0001553 | CATH node
EDAMdat 0001762 | CATH domain report
EDAMid  0001040 | CATH domain ID
EDAMid  0001008 | Polypeptide chain ID
EDAMid  0001127 | PDB ID
EDAMid  0001043 | CATH node ID
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Query    CATH domain report | HTML | CATH domain ID | http://www.cathdb.info/domain/%s
Query    CATH domain report | XML | CATH domain ID | http://www.cathdb.info/domain/%s?view=xml
Query    Protein features (domain composition) {CATH chain} | HTML | Polypeptide chain ID | http://www.cathdb.info/chain/%s
Query    Protein features (domain composition) {Pdb} | HTML | PDB ID | http://www.cathdb.info/pdb/%s
Query    Protein features (domain composition) {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 0000741 | Protein sequence alignment
EDAMtpc 0000164 | Sequence clustering
EDAMtpc 0000736 | Protein domains
EDAMdat 0000901 | Protein features (domain composition)
EDAMdat 0001382 | Sequence alignment (multiple)
EDAMdat 0000907 | Protein family annotation
EDAMid  0002714 | CDD PSSM-ID
EDAMid  0002666 | CDD ID
EDAMid  0002327 | GI number (protein)
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_FT None
Query    Sequence alignment (multiple) {Conserved Domain Summary} | HTML | CDD ID | http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s
Query    Sequence alignment (multiple) {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 (domain composition) {Conserved Domain annotation} | HTML | Sequence accession number (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s
Query    Protein features (domain composition) {Conserved Domain annotation} | HTML | GI number (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s
Query    Protein features (domain composition) {Conserved Domain annotation} | XML | Sequence accession number (protein) | http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s&output=xml
Query    Protein features (domain composition) {Conserved Domain annotation} | 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 number (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 0000635 | Specific protein
EDAMtpc 0000612 | Cell cycle and development
EDAMtpc 0000782 | Fungal
EDAMdat 0000896 | Protein annotation
EDAMdat 0000916 | Gene annotation
EDAMid  0002764 | Protein name (UniProt)
EDAMid  0002300 | Gene name (NCBI)
EDAMfmt 0002331 | HTML
Query    Gene annotation | HTML | Gene name (NCBI) | http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=%s
Query    Protein annotation | 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 0001811 | Prokaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000622 | Genomics
EDAMdat 0000916 | Gene annotation
EDAMdat 0002711 | Genome metadata
EDAMid  0001099 | UniProt accession number
EDAMid  0001179 | NCBI taxonomy ID
EDAMid  0002292 | GenBank identifier
EDAMid  0002774 | Gene ID (JCVI)
EDAMid  0002786 | NCBI Genome Project ID
EDAMfmt 0002331 | HTML
Xref    SP_implicit None
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 number | 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 number | Q81W35
Example NCBI taxonomy ID | 198094
Example NCBI Genome Project ID | 309


ID      cogeme
Name    Phytopathogenic fungi and oomycete EST database (COGEME)
Desc    Phytopathogenic fungi and oomycete EST database.
URL     http://cogeme.ex.ac.uk/
Taxon   4751 | Fungi
EDAMtpc 0000655 | mRNA, EST or cDNA
EDAMtpc 0000783 | Pathogen
EDAMtpc 0000782 | Fungal
EDAMdat 0000849 | Sequence record
EDAMid  0002729 | COGEME EST ID
EDAMid  0002730 | COGEME unisequence ID
EDAMfmt 0002331 | HTML
Query    Sequence record {Unisequence} | HTML | COGEME unisequence ID | http://cogeme.ex.ac.uk/cgi-bin/uni.pl?uni=x
Query    Sequence record {EST} | HTML | COGEME EST ID | http://cogeme.ex.ac.uk/cgi-bin/est.pl?est=x
Example COGEME EST ID | Bg13901527
Example COGEME unisequence ID | BgCon[0123]


ID      compluyeast_2dpage
Acc     DB-0010
Name    COMPLUYEAST-2DPAGE database
Desc    A two-dimensional polyacrilamide gel electrophoresis federated database.
URL     http://compluyeast2dpage.dacya.ucm.es/
Cat     2D gel databases
Taxon   4932 | Saccharomyces cerevisiae
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001099 | UniProt accession number
EDAMid  0000989 | Protein identifier
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation | HTML | UniProt accession number | http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s
Query    2D PAGE annotation | HTML | Protein identifier | http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s
Example UniProt accession number | P83784
Example Protein identifier | CAP6_CANAL


ID      conoserver
Acc     DB-0156
Name    Cone snail toxin database (ConoServer)
Desc    Conotoxin peptide sequences and structures.
URL     http://www.conoserver.org/
Cat     Organism-specific databases
Taxon   6490 | Conus
EDAMtpc 0000621 | Organism
EDAMtpc 0002661 | Toxins and targets
EDAMdat 0000896 | Protein annotation
EDAMid  0002804 | Protein ID (ConoServer)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein annotation | 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 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation | HTML | UniProt accession number | http://www.daimi.au.dk/cgi-jje/2d/2d.cgi#%s
Query    2D PAGE annotation | Text | UniProt accession number | http://www.daimi.au.dk/cgi-jje/2d/2d.cgi?ac=%s&format=text&database=cornea
Example UniProt accession number | 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 0000719 | Protein-protein interaction
EDAMtpc 0000140 | Protein targeting and localization
EDAMdat 0002712 | Protein complex annotation
EDAMid  0002713 | Protein ID (CORUM)
EDAMfmt 0002331 | HTML
Query    Protein complex annotation | 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 0000635 | Specific protein
EDAMdat 0000896 | Protein annotation
EDAMid  0002715 | Protein ID (CuticleDB)
EDAMfmt 0002331 | HTML
Query    Protein annotation | HTML | Protein ID (CuticleDB) | http://bioinformatics.biol.uoa.gr/cuticleDB/protview.jsp?id=%s
Example Protein ID (CuticleDB) | 639


ID      dbest
Name    dbEST database of EST sequences
Desc    dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.
URL     http://www.ncbi.nlm.nih.gov/dbEST/
Cat     Not available
Taxon   1 | all
EDAMtpc 0000655 | mRNA, EST or cDNA
EDAMdat 0000849 | Sequence record
EDAMid  0002314 | GI number
EDAMid  0001105 | dbEST accession
EDAMfmt 0002310 | fasta-html
EDAMfmt 0002532 | genbank-html
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Sequence record | genbank-html | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query    Sequence record | HTML {est} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query    Sequence record | HTML {docsum} | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query    Sequence record | fasta-html | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query    Sequence record | genbank-html | dbEST accession | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query    Sequence record | genbank-html | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Query    Sequence record | HTML {est} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Query    Sequence record | HTML {docsum} | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Query    Sequence record | fasta-html | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Query    Sequence record | genbank-html | GI number | http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Example dbEST accession | f12345


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 0000719 | Protein-protein interaction
EDAMdat 0002359 | Domain-domain interaction
EDAMid  0001138 | Pfam accession number
EDAMfmt 0002331 | HTML
Query    Domain-domain interaction | HTML | Pfam accession number | http://webclu.bio.wzw.tum.de/dima/DomQuery?domain=%s
Example DomQuery domain | PF00419


ID      dip
Acc     DB-0016
Name    Database of interacting proteins (DIP)
Desc    The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
URL     http://dip.doe-mbi.ucla.edu/
Cat     Protein-protein interaction databases
Taxon   1 | all
EDAMtpc 0000719 | Protein-protein interaction
EDAMdat 0001565 | Protein-protein interaction
EDAMid  0002616 | DIP ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein-protein interaction {DIP entry} | HTML | DIP ID | http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?PK=84
Example DIP ID | 84


ID      disprot
Acc     DB-0017
Name    Database of protein disorder (DisProt)
Desc    A curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
URL     http://www.disprot.org/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0000698 | Protein tertiary structure
EDAMdat 0002722 | Disordered protein annotation
EDAMid  0002723 | Protein ID (DisProt)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    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 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation | HTML | UniProt accession number | http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=O43818
Example UniProt accession number | 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 0000719 | Protein-protein interaction
EDAMdat 0000896 | Protein annotation
EDAMdat 0001565 | Protein-protein interaction
EDAMdat 0002093 | Data reference
EDAMid  0001026 | Gene symbol
EDAMid  0000989 | Protein identifier
EDAMid  0002802 | Protein ID (EcID)
EDAMfmt 0002331 | HTML
Query    Data reference {Protein sequence ID table} | HTML | Protein identifier | http://ecid.bioinfo.cnio.es/Php/PreQuery.php?busca=%s
Query    Protein-protein interaction {Predictions Mode} | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/Summary.php?view=pred&ID=%s1&seq=%s2&gn=%s3
Query    Protein-protein interaction {Experimental Mode} | HTML | Protein identifier;Protein ID (EcID);Gene symbol | http://ecid.bioinfo.cnio.es/Php/Summary.php?ID=%s1&seq=%s2&gn=%s3&view=exp
Query    Protein annotation | 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    This Database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on varios functional categories enabling quick and subsequent analysis.
URL     http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi
Cat     2D gel databases
Taxon   562 | Escherichia coli
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation {ECO2DBASE entry} | HTML | UniProt accession number | http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?%s
Example UniProt accession number | P02930
Example UniProt accession number | P52697


ID      elm
Name    Eukaryotic linear motif resource (ELM)
Desc    A resource for predicting functional sites in eukaryotic proteins. Putative functional sites are identified by patterns (regular expressions). To improve the predictive power, context-based rules and logical filters are applied to reduce the amount of false positives.
URL     http://elm.eu.org/
Taxon   1 | all
EDAMtpc 0000158 | Sequence motifs
EDAMtpc 0000748 | Protein functional sites
EDAMtpc 0000158 | Sequence motifs
EDAMdat 0001298 | Sequence motif report
EDAMid  0002705 | GO term ID (cellular compartment)
EDAMid  0002291 | UniProt ID
EDAMid  0000848 | Sequence
EDAMid  0001868 | Taxon
EDAMfmt 0002331 | HTML
Query    Sequence motif report {ELM report} | HTML | UniProt ID | http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s
Query    Sequence motif report {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    ELM report | HTML | 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 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 0000643 | Genome
EDAMtpc 0002818 | Eukaryote
EDAMtpc 0000643 | Genome
EDAMdat 0000849 | Sequence record
EDAMdat 0000916 | Gene annotation
EDAMid  0001033 | Gene ID (Ensembl)
EDAMid  0002725 | Transcript ID (Ensembl)
EDAMfmt 0001929 | fasta
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
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 | 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
Acc     DB-0024
Name    Enzyme nomenclature database (ENZYME)
Desc    A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
URL     http://www.expasy.org/enzyme/
Cat     Enzyme and pathway databases
Taxon   1 | all
EDAMtpc 0000821 | Enzymes
EDAMtpc 0002811 | Nomenclature
EDAMdat 0001509 | Enzyme annotation
EDAMid  0001011 | EC number
EDAMfmt 0002331 | HTML
Xref    SP_implicit None
Query    Enzyme annotation | Text | EC number | http://www.expasy.ch/enzyme/%s.txt
Query    Enzyme annotation | 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 0001811 | Prokaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
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 0000630 | Gene structure


ID      gene3d
Acc     DB-0029
Name    Gene3D structural and functional annotation of protein families
Desc    Gene3D structural and functional annotation of protein families incorporates several different sources including CATH, DRUGBANK, PFAM etc.
URL     http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
URLlink http://gene3d.biochem.ucl.ac.uk/Gene3D/linking
URLsoap http://funcnet.eu/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0000724 | Protein families
EDAMdat 0000907 | Protein family annotation
EDAMid  0001040 | CATH domain ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
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
Example CATH node ID (family) | 2.10.10.10
Example CATH domain ID | 1cukA00


ID      genecards
Acc     DB-0030
Name    GeneCards database of human genes, protein and diseases
Desc    GeneCards is a searchable, integrated database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs & compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.
URL     http://www.genecards.org/
Cat     Human genes and diseases database
Taxon   9606 | Homo sapiens
EDAMtpc 0000803 | Genes
EDAMtpc 0000586 | Proteins
EDAMtpc 0000803 | Human disease
EDAMtpc 0000719 | Protein-protein interaction
EDAMtpc 0000602 | Pathways, networks and models
EDAMtpc 0000199 | Mutation and polymorphism
EDAMtpc 0000643 | Genome
EDAMdat 0000916 | Gene annotation
EDAMid  0001099 | UniProt accession number
EDAMid  0001026 | Gene symbol
EDAMid  0002298 | Gene ID (HGNC)
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_explicit None
Query    Gene annotation | HTML | Gene symbol | http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s
Query    Gene annotation | HTML | UniProt accesion number | http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Query    Gene annotation | HTML | EntrezGene id | 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
Example Gene symbol | CASP3
Example Gene ID (HGNC) | 2041


ID      genedb
Name    GeneDB database from Sanger Institute Pathogen Sequencing Units
Desc    Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units).
URL     http://www.genedb.org/
Taxon   1 | all
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMdat 0000916 | Gene annotation
EDAMid  0001026 | Gene symbol
EDAMfmt 0002331 | 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 0000724 | Protein families
EDAMtpc 0000780 | Plant
EDAMtpc 0000621 | Organism
EDAMdat 0000916 | Gene annotation
EDAMdat 0000907 | Protein family annotation
EDAMid  0002295 | Gene ID
EDAMid  0002731 | Protein family ID (GeneFarm)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Gene annotation | HTML | Gene ID | http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s
Query    Protein family annotation | HTML | Protein family ID (GeneFarm) | http://urgi.versailles.inra.fr/Genefarm/Family/display_family.htpl?FAM_ID=%s
Example Protein family ID (GeneFarm) | 59
Example Gene ID | 907


ID      geneid
Acc     DB-0118
Name    GeneID database of genes from NCBI RefSeq genomes
Desc    Database of genes from NCBI RefSeq genomes
URL     http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
Cat     Genome annotation databases
Taxon   1 | all
EDAMtpc 0000623 | Gene family or system
EDAMtpc 0000643 | Genome
EDAMdat 0001025 | Gene identifier
EDAMid  0002581 | GO term name
EDAMid  0001176 | GO term ID
EDAMid  0001026 | Gene symbol
EDAMid  0001045 | Species name
EDAMid  0001011 | EC number
EDAMid  0000987 | Chromosome name
EDAMid  0001097 | Sequence accession number (nucleic acid)
EDAMid  0000968 | Keyword
EDAMid  0001187 | PubMed unique identifier
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Xref    SP_FT None
Query    Gene identifier {GeneID gene list} | HTML | Keyword | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=%s
Query    Gene identifier {GeneID gene list} | HTML | Sequence accession number (nucleic acid) | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[accn]
Query    Gene identifier {GeneID gene list} | HTML | Gene symbol | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[sym]
Query    Gene identifier {GeneID gene list} | HTML | PubMed unique identifier | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[PMID]
Query    Gene identifier {GeneID gene list} | HTML | GO term name | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="%s"[GO]
Query    Gene identifier {GeneID gene list} | HTML | GO term ID | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="%s"[GO]
Query    Gene identifier {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 identifier {GeneID gene list} | HTML | EC number | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[EC]
Example Keyword | haem
Example Sequence accession number (nucleic acid) | M11313
Example Gene symbol | BRCA1
Example PubMed unique identifier | 11331580
Example GO term name | cell+adhesion
Example Chromosome name | Y
Example Species name | human
Example EC number | 1.9.3.1


ID      glycosuitedb
Acc     DB-0036
Name    GlycoSuiteDB glycan database
Desc    An annotated and curated relational database of glycan structures.
URL     http://glycosuitedb.expasy.org/
Cat     PTM databases
Taxon   1 | all
EDAMtpc 0000152 | Carbohydrates
EDAMdat 0002313 | Carbohydrate structure annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Carbohydrate structure annotation {GlycoSuiteDB entry} | HTML | Uniprot accession number | http://glycosuitedb.expasy.org/glycosuite/results?prot_swissprot=%s;results_index=protein;ig_hist=1
Example Uniprot accession number | P02763


ID      goa
IDalt   GOA-UniProt
Name    Gene ontology annotation database for UniProt (GOA-UniProt)
Desc    Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI).
URL     http://www.ebi.ac.uk/goa
Taxon   1 | all
EDAMtpc 0000644 | Proteome
EDAMtpc 0000219 | Annotation
EDAMdat 0001716 | GO term
EDAMdat 0002093 | Data reference
EDAMid  0001009 | Protein name
EDAMid  0000989 | Protein identifier
EDAMid  0001176 | GO term ID
EDAMid  0002582 | GO term name (biological process)
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Xref    EMBL_explicit None
Query    Data reference {GOA-UniProt protein entry} | HTML | Protein name | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein
Query    Data reference {GOA-UniProt protein entry} | HTML | Protein identifier | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein
Query    GO term | HTML | GO term ID | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO
Query    GO term | HTML | GO term name (biological process) | http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO
Example GO term name (biological process) | apoptosis
Example GO term ID | GO:0006915
Example Protein name | tropomyosin
Example Protein identifier | 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 0000820 | Membrane
EDAMtpc 0000717 | Protein-ligand interaction
EDAMdat 0002401 | Membrane protein annotation
EDAMid  0001131 | Protein family name
EDAMfmt 0002331 | HTML
Xref    SP_implicit None
Query    Membrane protein annotation {GPCRDB entry} | HTML | Protein family name | http://www.gpcr.org/7tm/proteins/%s
Example Protein family name | a1kyp5_petma
CCxref  All Swiss-Prot entries that contains a CC line of the type "-!- SIMILARITY: Belongs to the G-protein coupled receptor ..."


ID      gramene
Acc     DB-0039
Name    Gramene database for comparative grass genomics
Desc    Gramene adds value to public data sets of grass genomes and helps to compare, identify and understand genes, pathways and phenotypes from different grass species.
URL     http://www.gramene.org/
Cat     Organism-specific databases
Taxon   4479 | Poaceae
EDAMtpc 0000797 | Comparative genomics
EDAMtpc 0000625 | Genotype and phenotype
EDAMtpc 0000621 | Organism
EDAMtpc 0000602 | Pathways, networks and models
EDAMdat 0000896 | Protein annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein annotation {Gramene entry} | HTML | Sequence accession number (protein) | http://www.gramene.org//db/protein/protein_search?acc=%s
Example Sequence accession number (protein) | P93436


ID      hamap
Acc     DB-004
Name    High-quality automated and manual annotation of microbial proteomes (HAMAP)
Desc    A system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.
URL     http://www.expasy.org/sprot/hamap/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0000644 | Proteome
EDAMtpc 0000644 | Proteome
EDAMtpc 0000724 | Protein families
EDAMdat 0000896 | Protein annotation
EDAMdat 0000849 | Sequence record
EDAMid  0002291 | UniProt ID
EDAMid  0002766 | HAMAP ID
EDAMfmt 0002331 | HTML
EDAMfmt 0002188 | uniprot
Xref    SP_explicit None
Query    UniProt ID {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 annotation {HAMAP family rules} | HTML | HAMAP ID | http://www.expasy.org/unirule/MF_%s
Query    Protein annotation {HAMAP family rules} | Text | HAMAP ID | http://www.expasy.org/unirule/MF_%s.txt
Example HAMAP ID | 00314
Status  Referenced

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 0000719 | Protein-protein interaction
EDAMdat 0000906 | Protein interaction annotation
EDAMid  0001130 | IntAct accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein interaction annotation {IntAct entry} | HTML | IntAct accession number | http://www.ebi.ac.uk/intact/binary-search/faces/search.xhtml?query=%s
Example IntAct accession number | None


ID      interpro
Acc     DB-0052
Name    InterPro integrated database of protein families, domains, regions, repeats and functional sites
Desc    Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.
URL     http://www.ebi.ac.uk/interpro/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0000724 | Protein families
EDAMtpc 0000748 | Protein functional sites
EDAMtpc 0000641 | Repeat sequences
EDAMdat 0001355 | Protein signature data
EDAMid  0001133 | InterPro accession
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Xref    SP_FT None
Xref    EMBL_explicit None
Query    Protein signature data | 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 0000644 | Proteome
EDAMdat 0000849 | Sequence record
EDAMid  0002384 | IPI protein ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
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
Status  Referenced

ID      lgicdb
Name    Ligand-gated ion channel database (LGICdb)
Desc    Nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.
URL     http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
Taxon   1 | all
EDAMtpc 0000182 | Sequence alignment
EDAMtpc 0000084 | Phylogenetics
EDAMdat 0002401 | Membrane protein annotation
EDAMid  0002797 | Protein ID (LGICdb)
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Query    Membrane protein annotation {Ligand-Gated Ion Channel database entry} | HTML | Protein ID (LGICdb) | http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/%s.php
Query    Membrane protein annotation {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 0000821 | Enzymes
EDAMtpc 0002811 | Nomenclature
EDAMdat 0000896 | Protein annotation
EDAMid  0002629 | Enzyme ID (MEROPS)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein annotation {MEROPS page} | HTML | Clan | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Query    Protein annotation {MEROPS page} | HTML | Family | http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Query    Protein annotation {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 0000719 | Protein-protein interaction
EDAMdat 0001565 | Protein-protein interaction
EDAMid  0002615 | MINT ID
EDAMfmt 0002331 | HTML
Query    Protein-protein interaction {MINT interaction} | HTML | MINT ID | http://mint.bio.uniroma2.it/mint/search/interaction.do?ac=MINT-%s
Example MINT ID | 3979570
Status  Not referenced

ID      nmpdr
Acc     DB-0125
Name    National microbial pathogen
Desc    Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.
URL     http://www.nmpdr.org
URLlink http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/LinkingToTheGenomeViewer
Cat     Genome annotation databases
Taxon   2 | Bacteria
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
EDAMtpc 0000797 | Comparative genomics
EDAMdat 0000916 | Gene annotation
EDAMid  0001179 | NCBI taxonomy ID
EDAMid  0002737 | FIG ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Xref    SP_FT None
Query    Genome 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 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation {OGP entry} | HTML | UniProt accession number | http://proteomewww.glycob.ox.ac.uk/cgi-bin/2d-search-ac?%s
Example UniProt accession number | P04406


ID      oma
Acc     DB-0137
Name    Identification of orthologs from complete genome data (OMA database)
Desc    Identification of orthologs from complete genome data.
URL     http://www.omabrowser.org
Cat     Phylogenomic databases
Taxon   1 | all
EDAMtpc 0000722 | Nucleic acid classification
EDAMtpc 0000084 | Phylogenetics
EDAMtpc 0000194 | Phylogenomics
EDAMdat 0002093 | Data reference
EDAMid  0000989 | Protein identifier
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Data reference | HTML | Protein identifier | http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=%s
Example SERC3_HUMAN | Protein identifier


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
Cat     Protein sequence classification database
Taxon   1 | all
EDAMtpc 0000602 | Pathways, networks and models
EDAMtpc 0000724 | Protein families
EDAMtpc 0000623 | Gene family or system
EDAMtpc 0000084 | Phylogenetics
EDAMdat 0000946 | Pathway or network annotation
EDAMdat 0000907 | Protein family annotation
EDAMid  0001161 | Pathway ID (Panther)
EDAMid  0002783 | Protein family ID (PANTHER)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein family annotation {PANTHER Family} | HTML | Protein family ID (PANTHER) | http://www.pantherdb.org/panther/family.do?clsAccession=%s
Query    Biological pathway | 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 0001811 | Prokaryote
EDAMtpc 0000643 | Genome
EDAMtpc 0000783 | Pathogen
Xref    SP_FT None

ID      pathoplant
Name    PathoPlant database of plant-pathogen interactions and Arabidopsis expression
Desc    Plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. Also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.
URL     http://www.pathoplant.de
Taxon   1 | all
EDAMtpc 0000197 | Gene expression and regulation
EDAMtpc 0000780 | Plant
EDAMtpc 0000754 | Signalling pathways
EDAMtpc 0000780 | Plant
EDAMtpc 0000783 | Pathogen


ID      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
Cat     Peptide identification database
Cat     Mass spectrometry database
Taxon   1 | all
EDAMtpc 0000613 | Peptides (general)
EDAMtpc 0000767 | Peptide identification
EDAMdat 0000896 | Protein annotation
EDAMdat 0000767 | Peptide identification
EDAMdat 0002536 | Mass spectrometry experimental data
EDAMid  0002291 | UniProt ID
EDAMid  0002384 | IPI protein ID
EDAMid  0002398 | Protein ID (Ensembl)
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_explicit None
Query    Peptide identification | HTML | Protein ID (Ensembl) | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000 <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=ENSP00000374576&QUERY_NAME=AT_GetPep tides&apply_action=QUERY>&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) | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000 <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=ENSP00000374576&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=xml>&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) | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000 <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=ENSP00000374576&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=xml>&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 experimental data {Recommended transitions for human protein} | HTML | Protein ID (Ensembl) | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ViewMRMList?protein_name_constraint=%s&atlas_build_id=182&consensus_library_id=9&action=QUERY> &atlas_build_id=182&consensus_library_id=9&action=QUERY
Query    Protein annotation {ptideAtlas entry} | HTML | IPI protein ID | https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?atlas_build_id=242&protein_name=%s&action=QUERY
Example Protein ID (Ensembl) | ENSP00000374576
Example IPI protein ID | IPI00795032


ID      peroxibase
Acc     DB-0072
Name    PeroxiBase peroxidase family database
Desc    Sequences from peroxidase superfamilies with annotation on putative functions and transcription regulation.
URL     http://peroxibase.isb-sib.ch/index.php
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0000635 | Specific protein
EDAMdat 0000896 | Protein annotation
EDAMid  0002792 | Protein ID (PeroxiBase)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein annotation {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 0000741 | Protein sequence alignment
EDAMtpc 0000188 | Sequence profiles and HMMs
EDAMtpc 0000724 | Protein families
EDAMtpc 0000736 | Protein domains
EDAMdat 0000907 | Protein family annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMid  0001138 | Pfam accession number
EDAMid  0001179 | NCBI taxonomy ID
EDAMid  0002758 | Pfam clan ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Xref    SP_FT None
Query    Protein family annotation {Pfam entry} | HTML | Sequence accession number (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 number (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 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation | HTML | UniProt accession number | http://www.gram.au.dk/cgi-bin/get-2d-entry?%s
Example UniProt accession number | P17821

ID      phi_base
Name    PHI-base pathogen host interactions database
Desc    Curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries.
URL     http://www.phibase.org
Taxon   1 | all
EDAMtpc 0000623 | Gene family or system
EDAMtpc 0000783 | Pathogen
Status  Not referenced

ID      phosphoelm
Name    PhosphoELM database of S/T/Y phosphorylation sites
Desc    Experimentally verified phosphorylation sites in eukaryotic proteins.
URL     http://phospho.elm.eu.org/
Taxon   1 | all
EDAMtpc 0000751 | Phosphorylation
EDAMdat 0002762 ! Sequence motif annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMid  0002775 | Kinase name
EDAMid  0001009 | Protein name
EDAMfmt 0002331 | HTML
Query    Sequence motif annotation {Phospho-ELM report} | HTML | Protein name {Substrate} | http://phospho.elm.eu.org/cgimodel.py?fun=Search&substrate=%s
Query    Sequence motif annotation {Phospho-ELM report} | HTML | Sequence accession number (protein) | http://phospho.elm.eu.org/cgimodel.py?fun=Search&accession=%s
Query    Sequence motif annotation {Phospho-ELM report} | HTML | Kinase name | http://phospho.elm.eu.org/cgimodel.py?fun=Search&kinase=%s
Example Kinase | Abl2
Example Sequence accession number (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 0000751 | Phosphorylation
EDAMdat 0002762 ! Sequence motif annotation
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Sequence motif annotation {PhosphoSite entry} | HTML | UniProt accession number | http://www.phosphosite.org/uniprotAccAction.do?id=%s
Example UniProt accession number | 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 0000639 | Protein sequences
EDAMdat 0002201 | Sequence record full
EDAMid  0000989 | Protein identifier
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Xref    SP_FT None
Query    Sequence record full | HTML | Protein identifier | http://pir.georgetown.edu/cgi-bin/nbrfget?uid=%s
Example Protein identifier | S12345

ID      pirsf
Acc     DB-0079
Name    PIRSF whole-protein classification database
Desc    Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains.
URL     http://pir.georgetown.edu/pirsf/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0000164 | Sequence clustering
EDAMtpc 0000724 | Protein families
EDAMdat 0000907 | Protein family annotation
EDAMid  0001136 | PIRSF ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
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 0000602 | Pathways, networks and models
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Unknown | HTML | UniProt accession number | http://substrate.burnham.org/lookup/uniprot/%s


ID      pptasedb
Acc     DB-0081
Name    Prokaryotic protein phosphatase database (PptaseDB)
Desc    Prokaryotic protein phosphatases.
URL     http://vigen.biochem.vt.edu/p3d/p3d.htm
Cat     Protein family/group databases
Taxon   2 | Bacteria
EDAMtpc 0000635 | Specific protein
EDAMdat 0000896 | Protein annotation
EDAMid  0000842 | Identifier
EDAMid  0000989 | Protein identifier
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein annotation {PptaseDB entry} | HTML | Protein identifier | http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=accession&extref=%s
Example Protein identifier | None


ID      pride
Acc     DB-0130
Name    PRIDE proteomics identifications database
Desc    Standards compliant, public data repository for proteomics data, protein and peptide identifications together with the evidence supporting these identifications.
URL     http://www.ebi.ac.uk/pride
URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do
Cat     Proteomic databases
Taxon   1 | all
EDAMtpc 0000767 | Peptide identification
EDAMtpc 0000121 | Proteomics
EDAMdat 0002536 | Experimental data (proteomics)
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Experimental data (proteomics) {PRIDE entry} | HTML | Sequence accession number (protein) | http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=%s
Example Sequence accession number (protein) | P29375


ID      prints
Acc     DB-0082
Name    PRINTS protein motif fingerprint database
Desc    A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family.
URL     http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0000724 | Protein families
EDAMtpc 0000748 | Protein functional sites
EDAMtpc 0000158 | Sequence motifs
EDAMdat 0001355 | Protein signature data
EDAMid  0001137 | PRINTS code
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein signature data {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 0000724 | Protein families
EDAMtpc 0000736 | Protein domains
EDAMdat 0000872 | Phylogenetic tree
EDAMdat 0001281 | Sequence signature map
EDAMdat 0000907 | Protein family annotation
EDAMdat 0001382 | Sequence alignment (multiple)
EDAMid  0001142 | ProDom accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
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 (multiple) {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 signature map {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 (multiple) {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 0000724 | Protein families
EDAMdat 0000907 | Protein family annotation
EDAMid  0002291 | UniProt ID
EDAMfmt 0001978 | dasgff
EDAMfmt 0002331 | HTML
Xref    SP_implicit None
Query    Protein family annotation {ProtoNet entry} | HTML | UniProt ID | http://www.protonet.cs.huji.ac.il/sp.php?prot=%s
Query    Protein family annotation {ProtoNet entry} | dasgff | UniProt ID | http://www.protonet.cs.huji.ac.il/das/protonet/features?segment=%s
Example UniProt ID | P01011
CCxref  All UniProtKB entries


ID      reactome
Acc     DB-0088
Name    Reactome knowledgebase of biological pathways
Desc    Curated knowledgebase of biological pathways and processes.
URL     http://www.reactome.org/
URLlink http://www.reactome.org/referring2GK.html
URLsoap http://www.reactome.org/download/index.html
Cat     Enzyme and pathway databases
Taxon   1 | all
EDAMtpc 0000602 | Pathways, networks and models
EDAMdat 0000946 | Pathway or network annotation
EDAMdat 0000896 | Protein annotation
EDAMid  0000989 | Protein identifier
EDAMid  0001099 | UniProt accession number
EDAMid  0001027 | Gene ID (NCBI)
EDAMid  0001011 | EC number
EDAMid  0001174 | ChEBI ID
EDAMid  0001056 | Database name
EDAMid  0000990 | Compound ID (KEGG)
EDAMid  0001155 | Pathway ID (reactome)
EDAMid  0001176 | GO term ID
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_explicit None
Query    Pathway or network annotation | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%s&ZOOM=2
Query    Pathway or network annotation | XML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/sbml_export?DB=gk_current&ID=%s
Query    Protein annotation {Reactome entry} | HTML | Database name;Protein identifier | http://www.reactome.org/cgi-bin/link?SOURCE=%s1&ID=%s2
Query    Protein annotation {Reactome entry} | HTML | UniProt accession number | http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=%s
Query    Protein annotation {Reactome entry] | HTML | ChEBI ID | http://www.reactome.org/cgi-bin/link?SOURCE=CHEBI&ID=%s
Query    Protein annotation {Reactome entry} | HTML | Compound ID (KEGG) | http://www.reactome.org/cgi-bin/link?SOURCE=COMPOUND&ID=%s
Query    Protein annotation {Reactome entry} | HTML | GO term ID | http://www.reactome.org/cgi-bin/link?SOURCE=GO&ID=%s
Query    Protein annotation {Reactome entry} | HTML | EC number | http://www.reactome.org/cgi-bin/link?SOURCE=EC&ID=%s
Query    Protein annotation {Reactome entry} | HTML | Gene ID (NCBI) | http://www.reactome.org/cgi-bin/link?SOURCE=Entrez+Gene&ID=%s
Query    Protein annotation {Reactome entry} | HTML | Pathway ID (reactome) | http://www.reactome.org/cgi-bin/link?SOURCE=Reactome&ID=%s
Example UniProt accession number | P30304
Example ChEBI ID | 15422
Example Compound ID (KEGG) | C00002
Example GO term ID | 0030060
Example EC number | 1.1.1.37
Example Gene ID (NCBI) | 4171
Example Pathway ID (reactome) | REACT_1


ID      rebase
Acc     DB-0089
Name    REBASE restriction enzymes and methylases database
Desc    Restriction enzymes and methylases database.
URL     http://rebase.neb.com/
Cat     Protein family/group databases
Taxon   1 | all
EDAMtpc 0000821 | Enzymes
EDAMdat 0001509 | Enzyme annotation
EDAMid  0001012 | Enzyme name
EDAMid  0002325 | REBASE enzyme number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Enzyme annotation | HTML | Enzyme name | http://rebase.neb.com/rebase/enz/%s.html
Query    Enzyme annotation | HTML | REBASE enzyme number | http://rebase.neb.com/rebase/enz/%s.html
Example Enzyme name | EcoRI
Example REBASE enzyme number | 993


ID      redidb
Name    RNA editing database (REDIdb)
Desc    Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored.
URL     http://biologia.unical.it/py_script/overview.html
Taxon   1 | all
EDAMtpc 0000630 | Gene structure
EDAMdat 0002043 | Sequence record lite
EDAMdat 0000596 | Sequence alignment
EDAMid  0002781 | REDIdb ID
EDAMfmt 0002310 | fasta-html
EDAMfmt 0002331 | HTML
Query    Sequence record lite {REDIdb entry} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s
Query    Sequence record lite {REDIdb fasta} | fasta-html | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s
Query    Sequence alignment {REDIdb overview} | HTML | REDIdb ID | http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s
Query    Sequence alignment {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 0000584 | Sequence analysis
EDAMtpc 0000797 | Comparative genomics
EDAMdat 0000849 | Sequence record
EDAMid  0000989 | Protein identifier
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Sequence record {RefSeq entry} | HTML | Protein identifier | http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=%s
Example Protein identifier | S12345


ID      reproduction_2dpage
IDalt   REPRODUCTION2DPAGE
Acc     DB-0090
Name    REPRODUCTION-2DPAGE database
Desc    REPRODUCTION-2DPAGE 2D gel protein database.
URL     http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation | HTML | Sequence accession number (protein) | http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s&format=text
Query    2D PAGE annotation | Text | Sequence accession number (protein) | http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s
Example Sequence accession number (protein) | P00352


ID      resid
Name    RESID database of protein modifications
Desc    A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
URL     http://www.ebi.ac.uk/RESID/
Taxon   1 | all
EDAMtpc 0000601 | Protein modifications
EDAMdat 0002191 | Protein modification annotation
EDAMid  0002619 | RESID ID
EDAMfmt 0002331 | HTML
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 0000740 | Nucleic acid sequence alignment
EDAMtpc 0000697 | RNA structure and alignment
EDAMdat 0002354 | RNA family annotation
EDAMid  0002356 | RFAM accession
EDAMid  0002357 | RFAM name
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_FT None
Xref    EMBL_explicit None
Query    RNA family | HTML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s
Query    RNA family | HTML | RFAM name | http://rfam.sanger.ac.uk/family?acc=%s
Query    RNA family | XML | RFAM accession | http://rfam.sanger.ac.uk/family?acc=%s&output=xml
Query    RNA family | 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 0000602 | Pathways, networks and models
EDAMdat 0002093 | Data reference
EDAMdat 0002024 | Enzyme kinetics data
EDAMdat 0000908 | Reaction annotation
EDAMid  0002309 | Reaction ID (SABIO-RK)
EDAMid  0002648 | Reaction kinetics ID (SABIO-RK)
EDAMid  0001011 | EC number
EDAMfmt 0002331 | HTML
Query    Reaction annotation {SABIO-RK reaction} | HTML | SABIO-RK reaction ID | 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 SABIO-RK reaction ID | 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 0000736 | Protein domains
EDAMdat 0001554 | SCOP node
EDAMdat 0002093 | Data reference
EDAMid  0001042 | SCOP sunid
EDAMid  0001127 | PDB ID
EDAMid  0000968 | Keyword
EDAMfmt 0002331 | HTML
Query    SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Query    Data reference {PDB Entry search} | HTML | PDB ID | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?pdb=%s
Query    Data reference | HTML | Keyword | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s
Example SCOP sunid | 47718
Example PDB ID | 1djh
Example 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 0000587 | Protein interaction
EDAMdat 0002359 | Domain-domain interaction
EDAMid  0001127 | PDB ID
EDAMid  0001042 | SCOP sunid
EDAMfmt 0002331 | HTML
Query    Domain-domain interaction | HTML | PDB ID | http://www.scowlp.org/scowlp/Pdb.action?show=&pdbId=%s
Query    Domain-domain interaction | HTML | SCOP sunid {SCOP family id} | http://www.scowlp.org/scowlp/Search.action?childs=&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 0000084 | Phylogenetics
EDAMtpc 0000623 | Gene family or system
EDAMdat 0000872 | Phylogenetic tree
EDAMdat 0002093 | Data reference
EDAMid  0001131 | Protein family name
EDAMid  0000968 | Keyword
EDAMid  0000989 | Protein identifier
EDAMid  0001127 | PDB ID
EDAMfmt 0002331 | HTML
Query    Phylogenetic tree {Selectome entry} | HTML | Selectome identifier;Protein family name;Taxon | http://bioinfo.unil.ch/cgi-bin/selectome/subfamily.cgi?ac=%s1&sub=%s2&taxon=%s3
Query    Selectome family | HTML | 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 | Keyword | http://bioinfo.unil.ch/cgi-bin/selectome/getGene.cgi?query=%s
Query    Data reference {Selectome gene family} | HTML | Keyword | http://bioinfo.unil.ch/cgi-bin/selectome/getGeneFamily.cgi?query=%s
Example Selectome identifier | TF105041
Example Selectome identifier;Protein family name;Taxon | TF105041;1;v
Example PDB ID | 1HCL
Example Protein identifier | P24941
Example Keyword | kidney
Example Keyword | Ascc3_F2
Example 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 0000724 | Protein families
EDAMtpc 0000736 | Protein domains
EDAMdat 0002377 | Domain annotation
EDAMid  0001139 | SMART accession number
EDAMid  0002782 | SMART domain name
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Domain annotation {SMART entry} | HTML | SMART domain name | http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY
Query    Domain annotation {SMART entry} | HTML | SMART accession number | http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY
Example SMART domain name | KISc
Example SMART accession number | SM00129


ID      smr
Acc     DB-0098
Name    A database of annotated 3D protein structure models
Desc    Annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
URL     http://swissmodel.expasy.org/repository/
Cat     3D structure databases
Taxon   1 | all
EDAMtpc 0000698 | Protein tertiary structure
EDAMdat 0001460 | Protein tertiary structure
EDAMid  0001099 | UniProt accession number
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Protein tertiary structure {SMR entry} | HTML | UniProt accession number | http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s
Example UniProt accession number | 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 0000630 | Gene structure
EDAMtpc 0000747 | Nucleic acid functional sites
EDAMtpc 0000114 | RNA splicing
EDAMtpc 0000748 | Protein functional sites
EDAMtpc 0000158 | Sequence motifs
EDAMdat 0000896 | Protein annotation
EDAMid  0001009 | Protein name
EDAMfmt 0002331 | HTML
Query    Protein annotation | 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 0000719 | Protein-protein interaction
EDAMdat 0001663 | Protein-protein interaction network annotation
EDAMid  0002302 | STRING ID
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Query    Protein-protein interaction network map | 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    Protein-protein interaction network map | 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 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMdat 0002372 | 2D PAGE spot annotation
EDAMid  0000989 | Protein identifier
EDAMid  0002374 | Spot serial number
EDAMid  0001099 | UniProt accession number
EDAMid  0002791 | Reference map name (SWISS-2DPAGE)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    2D PAGE annotation | HTML | Protein identifier | http://www.expasy.org/swiss-2dpage/%s
Query    2D PAGE annotation | HTML | UniProt accession number | http://www.expasy.org/swiss-2dpage/%s
Query    2D PAGE annotation | Text | UniProt accession number | 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    2D PAGE annotation {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 ULAD_HUMAN
Example UniProt accession number | 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 0000643 | Genome
EDAMtpc 0000780 | Plant
Xref    SP_explicit None


ID      tigrfam
Acc     DB-0104
Name    A protein family database
Desc    Protein families based on hidden Markov models (HMMs).
URL     http://www.tigr.org/TIGRFAMs/
Cat     Family and domain databases
Taxon   1 | all
EDAMtpc 0000724 | Protein families
EDAMtpc 0000188 | Sequence profiles and HMMs
EDAMdat 0002788 | Sequence profile annotation
EDAMid  0001141 | TIGRFam ID
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Sequence profile annotation {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 0000820 | Membrane protein
EDAMdat 0002401 | Membrane protein annotation
EDAMid  0002789 | Protein ID (TopDB)
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Query    Membrane protein annotation {TOPDB entry} | HTML | Protein ID (TopDB) | http://topdb.enzim.hu/?m=show&tab=HTML&id=%s
Query    Membrane protein annotation {TOPDB entry} | HTML {graphic} | Protein ID (TopDB) | http://topdb.enzim.hu/?m=show&tab=Graph&id=%s
Query    Membrane protein annotation {TOPDB entry} | HTML {flash} | Protein ID (TopDB) | http://topdb.enzim.hu/?m=show&tab=Flash&id=%s
Query    Membrane protein annotation {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 0000635 | Specific protein
EDAMdat 0000896 | Protein annotation
EDAMid  0001009 | Protein name
EDAMfmt 0002331 | HTML
Query    Protein annotation | 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 0000639 | Protein sequences
EDAMdat 0000849 | Sequence record
EDAMid  0002392 | UniParc accession
EDAMfmt 0002331 | HTML
Xref    SP_FT None
Query    Sequence record {UniParc entry} | HTML | UniParc accession | http://www.uniprot.org/uniparc/%s
Example UniParc accession | UPI0000000001


ID      uniprot
IDalt   UniProtKB
Name    Universal protein resource
Desc    A comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
URL     http://www.uniprot.org/
Taxon   1 | all
EDAMtpc 0000639 | Protein sequences
EDAMdat 0002201 | Sequence record full
EDAMid  0001099 | UniProt accession number
EDAMfmt 0001929 | fasta
EDAMfmt 0002376 | RDF
EDAMfmt 0002188 | uniprot
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_FT None
Query    Sequence record full | HTML | UniProt accession number | http://www.uniprot.org/uniprot/%s
Query    Sequence record full | uniprot | UniProt accession number | http://www.uniprot.org/uniprot/%s.txt
Query    Sequence record full | XML | UniProt accession number | http://www.uniprot.org/uniprot/%s.xml
Query    Sequence record full | RDF | UniProt accession number | http://www.uniprot.org/uniprot/%s.rdf
Query    Sequence record full | fasta | UniProt accession number | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession number | 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
EDAMtpc 0000639 | Protein sequences
EDAMdat 0001230 | UniProt protein sequence record
EDAMid  0001099 | UniProt accession number
EDAMfmt 0001929 | fasta
EDAMfmt 0002376 | RDF
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_FT None
Xref    EMBL_explicit None
Query    UniProt protein sequence record | HTML | UniProt accession number | http://www.uniprot.org/uniprot/%s
Query    UniProt protein sequence record | Text | UniProt accession number | http://www.uniprot.org/uniprot/%s.txt
Query    UniProt protein sequence record | XML | UniProt accession number | http://www.uniprot.org/uniprot/%s.xml
Query    UniProt protein sequence record | RDF | UniProt accession number | http://www.uniprot.org/uniprot/%s.rdf
Query    UniProt protein sequence record | fasta | UniProt accession number | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession number | 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
EDAMtpc 0000639 | Protein sequences
EDAMdat 0001230 | UniProt protein sequence record
EDAMid  0001099 | UniProt accession number
EDAMfmt 0001929 | fasta
EDAMfmt 0002376 | RDF
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_FT None
Query    UniProt protein sequence record | HTML | UniProt accession number | http://www.uniprot.org/uniprot/%s
Query    UniProt protein sequence record | Text | UniProt accession number | http://www.uniprot.org/uniprot/%s.txt
Query    UniProt protein sequence record | XML | UniProt accession number | http://www.uniprot.org/uniprot/%s.xml
Query    UniProt protein sequence record | RDF | UniProt accession number | http://www.uniprot.org/uniprot/%s.rdf
Query    UniProt protein sequence record | fasta | UniProt accession number | http://www.uniprot.org/uniprot/%s.fasta
Example UniProt accession number | Q00177


ID      uniref
Name    Non-redundant reference (UniRef) databases
Desc    Clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
URL     http://www.uniprot.org/help/uniref
Cat     Other
Taxon   1 | all
EDAMtpc 0000164 | Sequence clustering
EDAMdat 0001245 | Sequence cluster (protein)
EDAMid  0002347 | Sequence cluster ID (UniRef100)
EDAMid  0002348 | Sequence cluster ID (UniRef90)
EDAMid  0002349 | Sequence cluster ID (UniRef50)
EDAMfmt 0001929 | fasta
EDAMfmt 0002376 | RDF
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | XML
Xref    SP_implicit None
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 | 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 | 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 | 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
CCxref  All Swiss-Prot and TrEMBL (UniProt knowledgebase) entries


ID      vectorbase
Acc     DB-0120
Name    Invertebrate vectors of human pathogens
Desc    Invertebrate vectors of human pathogens.
URL     http://www.vectorbase.org/
URLlink http://neuron.cse.nd.edu/vectorbase/index.php/Website_redirects
Cat     Genome annotation databases
Taxon   1 | all
EDAMtpc 0000783 | Pathogen
EDAMdat 0002399 | Transcript annotation
EDAMdat 0000895 | Peptide annotation
EDAMdat 0000916 | Gene annotation
EDAMid  0002759 | Gene ID (VectorBase)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
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    Transcript annotation | 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 0000133 | Two-dimensional gel electrophoresis
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
Query    Unknown | HTML | Sequence accession number (protein) | world-2dpage.expasy.org/repository/%s
Status  Referenced

ID      world_2dpage_0003_
IDalt   0003
Name    World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome
Desc    World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome.
URL     http://www.expasy.org/world-2dpage/
Taxon   3702 | Arabidopsis thaliana
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMtpc 0000780 | Plant
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Query    2D PAGE annotation | HTML | Sequence accession number (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0003
Example Sequence accession number (protein) | O65719


ID      world_2dpage_0004_
IDalt   0004
Name    World-wide gel-based proteomics database (0004) for mature rat olfactory bulb
Desc    World-wide gel-based proteomics database (0004) for mature rat olfactory bulb.
URL     http://www.expasy.org/world-2dpage/
Taxon   10114 | Rattus
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Query    2D PAGE annotation | HTML | Sequence accession number (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0004
Example Sequence accession number (protein) | A7VJC3
Status  Not referenced

ID      world_2dpage_0005_
IDalt   0005
Name    World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose
Desc    World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose.
URL     http://www.expasy.org/world-2dpage/
Taxon   33196 | Botrytis
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Query    2D PAGE annotation | HTML | Sequence accession number (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0005
Example Sequence accession number (protein) | A6RHV6


ID      world_2dpage_0006_
IDalt   0006
Name    World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee
Desc    World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee.
URL     http://www.expasy.org/world-2dpage/
Taxon   7460 | Apis mellifera
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Query    2D PAGE annotation | HTML | Sequence accession number (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=0006
Example Sequence accession number (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 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Query    2D PAGE annotation | HTML | Sequence accession number (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=cgl14067-2dpage
Example Sequence accession number (protein) | O31139


ID      world_2dpage_nibr_2d_page_
IDalt   NIBR 2D-PAGE
Name    World-wide gel-based proteomics database (NIBR 2D-PAGE)
Desc    World-wide gel-based proteomics database (NIBR 2D-PAGE)
URL     http://www.expasy.org/world-2dpage/
Taxon   1 | all
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | 2D PAGE annotation
EDAMid  0001096 | Sequence accession number (protein)
EDAMfmt 0002331 | HTML
Query    2D PAGE annotation | HTML | Sequence accession number (protein) | http://world-2dpage.expasy.org/repository/ac=%s&database=nibr_2d-page
Example Sequence accession number (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 0002819 | Invertebrate
EDAMtpc 0000643 | Genome
EDAMtpc 0000621 | Organism
EDAMdat 0000916 | Gene annotation
EDAMid  0001026 | Gene symbol
EDAMid  0002295 | Gene ID
EDAMid  0000989 | Protein identifier
EDAMfmt 0002331 | HTML
Xref    SP_explicit None
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 0002846 | Gene regulatory networks
EDAMtpc 0000747 | Nucleic acid functional sites
EDAMtpc 0000110 | Transcription and translation
EDAMtpc 0000811 | Transcription factor and binding site
EDAMtpc 0000782 | Fungal
EDAMdat 0000896 | Protein annotation
EDAMdat 0002147 | Transcription factor annotation
EDAMdat 0000916 | Gene annotation
EDAMdat 0002765 | Ontological annotation
EDAMdat 0000929 | Gene expression annotation
EDAMid  0002755 | Transcription factor name
EDAMid  0001009 | Protein name
EDAMid  0001807 | ORF name
EDAMid  0002299 | Gene name
EDAMid  0001209 | Consensus sequence
EDAMfmt 0002331 | HTML
Query    Gene annotation | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query    Protein annotation | HTML | ORF name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query    Ontological annotation {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 annotation | HTML | Gene name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query    Ontological annotation {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 annotation | HTML | Protein name | http://www.yeastract.com/view.php?existing=locus&orfname=%s
Query    Ontological annotation {GO information} | HTML | Protein name | http://www.yeastract.com/view.php?existing=go&orfname=%s
Query    Gene expression annotation {Regulation reference} | HTML | Transcription factor name;Gene name {target gene} | http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Query    Gene expression annotation {Regulation reference} | HTML | Transcription factor name;ORF name {target ORF} | http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Query    Transcription factor annotation {TF binding site reference} | HTML | Transcription factor name;Consensus sequence | http://www.yeastract.com/view.php?existing=consensus&proteinname=%s1&consensus=%s2
Query    Transcription factor annotation {Documented regulators of a given set of genes} | HTML | Genes | 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 6.4.0-2 / usr / share / EMBOSS / test / data / DRCAT.dat
