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#>
8 select distinct ?name ?cell ?antibody ?sex ?control ?strain ?controlId ?library_id ?treatment ?protocol ?readType ?insertLength ?replicate, ?mapAlgorithm ?species_name ?taxon_id ?extractMolecule ?growthProtocol ?extractProtocol ?dataProtocol ?experiment_type ?library_selection ?library_source
10 <{{submission}}> a submissionOntology:submission ;
11 submissionOntology:library ?library ;
12 submissionOntology:name ?name .
14 OPTIONAL { <{{submission}}> ucscDaf:control ?control }
15 OPTIONAL { <{{submission}}> ucscDaf:controlId ?controlId }
16 OPTIONAL { ?library libraryOntology:antibody ?antibody }
17 OPTIONAL { ?library libraryOntology:cell_line ?cell .
18 OPTIONAL { ?cell_line cells:cell ?cell ;
19 cells:documents ?growthProtocol . }}
20 OPTIONAL { ?library ucscDaf:sex ?sex }
21 OPTIONAL { ?library libraryOntology:library_id ?library_id }
22 OPTIONAL { ?library libraryOntology:replicate ?replicate }
23 OPTIONAL { ?library libraryOntology:species ?species_name .
24 ?species libraryOntology:species ?species_name ;
25 libraryOntology:taxon_id ?taxon_id . }
26 OPTIONAL { ?library libraryOntology:condition_term ?treatment }
27 OPTIONAL { ?library libraryOntology:experiment_type ?experiment_type }
28 OPTIONAL { ?library libraryOntology:librarySelection ?library_selection }
29 OPTIONAL { ?library libraryOntology:librarySource ?library_source }
30 OPTIONAL { <{{submissionSet}}> geoSoft:data_processing ?dataProtocol }
31 OPTIONAL { ?library libraryOntology:extractMolecule ?extractMolecule }
32 OPTIONAL { ?library libraryOntology:extractProtocol ?extractProtocol }
33 OPTIONAL { ?library ucscDaf:protocol ?protocol }
34 OPTIONAL { ?library ucscDaf:readType ?readType }
35 OPTIONAL { ?library ucscDaf:strain ?strain }
36 OPTIONAL { ?library libraryOntology:insert_size ?insertLength }
37 OPTIONAL { ?library ucscDaf:mapAlgorithm ?mapAlgorithm }
39 ?species libraryOntology:species ?species_name ;
40 libraryOntology:taxon_id ?taxon_id .