providers.yaml 4.95 KB
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- name: Enzyme
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  prefixes: ["EC"]
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  resources:
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      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:
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      type: 'internal'
      location: 'dbxref.retrieve.enzyme'
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- 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"
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- 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/"
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- name: Gene Identifier
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  prefixes: ["GI"]
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  resources:
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      html: ["https://www.ncbi.nlm.nih.gov/protein/GI:%i"]
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      xml: ["http://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&db=protein&dopt=xml&sort=&val=%i&retmode=file"]
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  # 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"
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- name: Conserved domain database
  prefixes: ["CDD"]
  resources:
      html: ["https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%i"]
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- name: Uniprot
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  prefixes: ["UniProtKB/TrEMBL", "UniProtKB/Swiss-Prot"]
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  resources:
      html: [ "http://www.uniprot.org/uniprot/%i"]
      xml: [ "http://www.uniprot.org/uniprot/%i.xml"]
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  check_existence: "http://www.uniprot.org/uniprot/%i.xml"
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  retriever:
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      type: 'internal'
      location: 'dbxref.retrieve.uniprot'
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- name: Taxonomy
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  prefixes: ["Taxon", "taxid"]
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  resources:
      html: ["http://www.uniprot.org/taxonomy/%i"]
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      json: ["https://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/tax-id/%i"]
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      xml: ["http://www.uniprot.org/taxonomy/%i.rdf"]
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      xml_ncbi: ["https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=%i"]
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  check_existence: "http://www.uniprot.org/taxonomy/%i"
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  retriever:
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      type: 'internal'
      location: 'dbxref.retrieve.taxonomy'
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- name: SequenceOntology
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  prefixes: ["SO"]
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  resources:
      html: ["http://www.sequenceontology.org/browser/current_svn/term/SO:%i"]
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      obo: ["http://www.sequenceontology.org/browser/current_svn/export/term_only/obo/SO:%i"]
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      tsv: ["http://www.sequenceontology.org/browser/current_svn/export/term_only/csv_text/SO:%i"]
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  # does not work
  # check_existence: "http://www.sequenceontology.org/browser/current_svn/term/SO:%i"
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  retriever:
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      type: 'internal'
      location: 'dbxref.retrieve.sequence_ontology'
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- name: RFAM
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  prefixes: ["RFAM"]
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  resources:
      html: ["http://rfam.xfam.org/family/%i"]
      xml: ["http://rfam.xfam.org/family/%i?content-type=text%2Fxml"]
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  # does not work
  # check_existence: "http://rfam.xfam.org/family/%i?content-type=text%2Fxml"
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- name: Pubmed
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  prefixes: ["Pubmed"]
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  resources:
      html: ["http://www.ncbi.nlm.nih.gov/pubmed/%i"]
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  check_existence: "http://www.ncbi.nlm.nih.gov/pubmed/%i"
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- name: Protein Families
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  prefixes: ["PFAM"]
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  resources:
      html: ["http://pfam.xfam.org/family/%i"]
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      xml: ["http://pfam.xfam.org/family/%i?output=xml"]
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  # does not work
  # check_existence: "http://pfam.xfam.org/family/%i?content-type=text%2Fxml"
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  retriever:
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      type: 'internal'
      location: 'dbxref.retrieve.pfam'
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- name: PDB
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  prefixes: ["PDB"]
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  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"]
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  check_existence: "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=xml&compression=NO&structureId=%i"
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- name: InterPro
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  prefixes: ["InterPro"]
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  resources:
      html: ["http://www.ebi.ac.uk/interpro/entry/%i"]
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  # does not work
  # check_existence: "http://www.ebi.ac.uk/interpro/entry/%i"
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- name: GeneID
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  prefixes: ["GeneID"]
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  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"]
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  # 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"
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- name: Gene Ontology
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  prefixes: ["GO"]
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  resources:
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      html: ["https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:%i"]
      xml: ["https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:%i&format=oboxml"]
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      json: ["https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:%i/complete"]
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  check_existence: "http://purl.obolibrary.org/obo/GO_%i"
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  retriever:
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      type: 'internal'
      location: 'dbxref.retrieve.gene_ontology'
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- name: KEGG
  prefixes: ["KO"]
  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'
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- name: HTTP
  prefixes: ["http", "https"]
  resources:
      html: ["%d:%i"]
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  check_existence: "%d:%i"
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