- name: Enzyme
  prefixes: ["EC"]
  resources:
      html: ["https://enzyme.expasy.org/EC/%i"]
      text: ["https://enzyme.expasy.org/EC/%i.txt"]
  check_existence: "https://enzyme.expasy.org/EC/%i.txt"
  retriever:
      type: 'internal'
      location: 'dbxref.retrieve.enzyme'
- name: HAMAP
  prefixes: ["HAMAP"]
  resources:
      html: ["https://hamap.expasy.org/signature/%i"]
      text: ["https://hamap.expasy.org/signature/%i.txt"]
  check_existence: "https://hamap.expasy.org/signature/%i.txt"
- name: OMA - Orthologous MAtrix
  prefixes: ["OMA"]
  resources:
      html: ["https://omabrowser.org/oma/omagroup/%i/"]
      json: ["https://omabrowser.org/api/group/%i/"]
  check_existence: "https://omabrowser.org/api/group/%i/"
- name: Gene Identifier
  prefixes: ["GI"]
  resources:
      html: ["https://www.ncbi.nlm.nih.gov/protein/GI:%i"]
      xml: ["http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=protein&dopt=xml&sort=&val=%i&retmode=file"]
  # does not work
  # check_existence: "http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=protein&dopt=xml&sort=&val=%i&retmode=file"
- name: Conserved domain database
  prefixes: ["CDD"]
  resources:
      html: ["https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%i"]
- name: Uniprot
  prefixes: ["UniProtKB/TrEMBL", "UniProtKB/Swiss-Prot"]
  resources:
      html: [ "http://www.uniprot.org/uniprot/%i"]
      xml: [ "http://www.uniprot.org/uniprot/%i.xml"]
  check_existence: "http://www.uniprot.org/uniprot/%i.xml"
  retriever:
      type: 'internal'
      location: 'dbxref.retrieve.uniprot'
- name: Taxonomy
  prefixes: ["Taxon", "taxid"]
  resources:
      html: ["http://www.uniprot.org/taxonomy/%i"]
      json: ["https://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/tax-id/%i"]
      xml: ["http://www.uniprot.org/taxonomy/%i.rdf"]
      xml_ncbi: ["https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=%i"]
  check_existence: "http://www.uniprot.org/taxonomy/%i"
  retriever:
      type: 'internal'
      location: 'dbxref.retrieve.taxonomy'
- name: SequenceOntology
  prefixes: ["SO"]
  resources:
      html: ["http://www.sequenceontology.org/browser/current_svn/term/SO:%i"]
      obo: ["http://www.sequenceontology.org/browser/current_svn/export/term_only/obo/SO:%i"]
      tsv: ["http://www.sequenceontology.org/browser/current_svn/export/term_only/csv_text/SO:%i"]
  # does not work
  # check_existence: "http://www.sequenceontology.org/browser/current_svn/term/SO:%i"
  retriever:
      type: 'internal'
      location: 'dbxref.retrieve.sequence_ontology'
- name: RFAM
  prefixes: ["RFAM"]
  resources:
      html: ["http://rfam.xfam.org/family/%i"]
      xml: ["http://rfam.xfam.org/family/%i?content-type=text%2Fxml"]
  # does not work
  # check_existence: "http://rfam.xfam.org/family/%i?content-type=text%2Fxml"
- name: Pubmed
  prefixes: ["Pubmed"]
  resources:
      html: ["http://www.ncbi.nlm.nih.gov/pubmed/%i"]
  check_existence: "http://www.ncbi.nlm.nih.gov/pubmed/%i"
- name: Protein Families
  prefixes: ["PFAM"]
  resources:
      html: ["http://pfam.xfam.org/family/%i"]
      xml: ["http://pfam.xfam.org/family/%i?output=xml"]
  # does not work
  # check_existence: "http://pfam.xfam.org/family/%i?content-type=text%2Fxml"
  retriever:
      type: 'internal'
      location: 'dbxref.retrieve.pfam'
- name: PDB
  prefixes: ["PDB"]
  resources:
      html: ["http://www.rcsb.org/pdb/explore/explore.do?structureId=%i"]
      xml: ["http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=xml&compression=NO&structureId=%i"]
  check_existence: "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=xml&compression=NO&structureId=%i"
- name: InterPro
  prefixes: ["InterPro"]
  resources:
      html: ["http://www.ebi.ac.uk/interpro/entry/%i"]
  # does not work
  # check_existence: "http://www.ebi.ac.uk/interpro/entry/%i"
- name: GeneID
  prefixes: ["GeneID"]
  resources:
      html: ["http://www.ncbi.nlm.nih.gov/gene/%i"]
      xml: ["http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=gene&dopt=xml&sort=&val=%i&retmode=file"]
  # does not work
  #  check_existence: "http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=gene&dopt=xml&sort=&val=%i&retmode=file"
- name: Gene Ontology
  prefixes: ["GO"]
  resources:
      html: ["https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:%i"]
      xml: ["https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:%i&format=oboxml"]
      json: ["https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:%i/complete"]
  check_existence: "http://purl.obolibrary.org/obo/GO_%i"
  retriever:
      type: 'internal'
      location: 'dbxref.retrieve.gene_ontology'
- name: KEGG
  prefixes: ["KO", "KEGG"]
  resources:
      html: ["https://www.genome.jp/dbget-bin/www_bget?%i"]
      text: ["http://rest.kegg.jp/get/%i"]
  check_existence: "http://rest.kegg.jsdjkaap/get/%i"
  # not implemented yet
  # retriever:
  #    type: 'internal'
  #    location: 'dbxref.retrieve.kegg'
- name: HTTP
  prefixes: ["http", "https"]
  resources:
      html: ["%d:%i"]
  check_existence: "%d:%i"
- name: EggNOG
  prefixes: ['eggnog']
  resources:
    html: ["http://eggnogdb.embl.de/#/app/results?target_nogs=%i"]