htsworkflow/templates/geo_files.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
   7 select distinct ?filename, ?md5sum, ?file_type ?file_type_label ?flowcell_id ?read_length ?flowcell_type ?image_software ?image_version ?basecall_software ?basecall_version ?sequencer_model
   8 WHERE {
   9   <{{submission}}> ucscDaf:has_file ?file ;
  10                    a submissionOntology:submission .
  11
  12   ?file ucscDaf:filename ?filename ;
  13         ucscDaf:md5sum ?md5sum ;
  14         libraryOntology:has_lane ?lane ;
  15         a ?file_type .
  16   ?file_type a <{{file_class}}> ;
  17              geoSoft:fileTypeLabel ?file_type_label .
  18
  19   OPTIONAL { ?lane libraryOntology:flowcell ?flowcell .
  20              ?flowcell libraryOntology:flowcell_id ?flowcell_id ;
  21                        libraryOntology:read_length ?read_length ;
  22                        libraryOntology:flowcell_type ?flowcell_type ;
  23                        libraryOntology:image_software ?image_software ;
  24                        libraryOntology:image_version ?image_version ;
  25                        libraryOntology:basecall_software ?basecall_software ;
  26                        libraryOntology:basecall_version ?basecall_version ;
  27                        libraryOntology:sequenced_by ?sequencer .
  28              ?sequencer libraryOntology:sequencer_model ?sequencer_model
  29   }
  30 }