htsworkflow/templates/geo_run_details.sparql

   1 PREFIX libraryOntology: <http://jumpgate.caltech.edu/wiki/LibraryOntology#>
   2 PREFIX submissionOntology: <http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#>
   3 PREFIX ucscDaf: <http://jumpgate.caltech.edu/wiki/UcscDaf#>
   4 PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
   5 PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
   6 PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
   7
   8 # right now we're just grabbing the sequencer model
   9 # it might make sense to report each of the flowcell/image software.
  10 select ?flowcell ?read_length ?image_software ?image_version ?basecall_software ?basecall_version
  11 where {
  12   <{{submission}}> submissionOntology:library ?library ;
  13                    a submissionOntology:submission .
  14
  15   ?library libraryOntology:library_id ?library_id ;
  16            libraryOntology:has_lane ?lane ;
  17            a libraryOntology:library .
  18   OPTIONAL { ?flowcell libraryOntology:has_lane ?lane .
  19              ?flowcell libraryOntology:read_length ?read_length ;
  20                        libraryOntology:image_software ?image_software ;
  21                        libraryOntology:image_version ?image_version ;
  22                        libraryOntology:basecall_software ?basecall_software ;
  23                        libraryOntology:basecall_version ?basecall_version ;
  24                        libraryOntology:sequenced_by ?sequencer .
  25              ?sequencer libraryOntology:sequencer_model ?sequencer_model
  26   }
  27 }