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ktym edited this page May 26, 2014 · 10 revisions 
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX faldo:<http://biohackathon.org/resource/faldo#>

SELECT ?gene ?transcript ?exon WHERE  {
  ?gene sio:SIO_010080 ?transcript . 
  ?transcript sio:SIO_000974 [ sio:SIO_000628 ?exon ] .
  ?exon faldo:location [ 
    faldo:begin [ faldo:position ?begin ]; faldo:end [ faldo:position ?end ] 
  ]
  FILTER ( ?begin >= 66119285 && ?end <= 66119659 )  
}

PREFIX dcterms: <http://purl.org/dc/terms/>
#PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>

SELECT ?gene ?transcript ?exon
WHERE {
  #?gene obo:so-part-of ?transcript .
  ?gene sio:SIO_010080 ?transcript .
  ?transcript sio:SIO_000974/sio:SIO_000628 ?exon .
  ?exon faldo:location [
    faldo:begin/faldo:position ?begin ;
    faldo:end/faldo:position ?end
  ]
  FILTER (?begin >= 66119285 && ?end <= 66119659)
}

store@ep1:~/rdf/hg19/human.gb% for i in 9606/**/*(.)
do
  echo $i
  dir=`dirname $i`
  mkdir -p ../human.ttl/$dir
  time ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.ttl
done
9606/PRJNA168/NC_000001
Features: {"assembly_gap":22,"misc_RNA":1135,"precursor_RNA":126,"ncRNA":224,"mRNA":6604,"CDS":6604,"exon":393,"tRNA":82,"rRNA":17}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  40.01s user 2.44s system 99% cpu 42.624 total
9606/PRJNA168/NC_000002
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":15,"mRNA":4380,"misc_RNA":915,"CDS":4463,"exon":232,"precursor_RNA":98,"ncRNA":149,"tRNA":8,"C_region":1,"J_segment":5,"V_segment":78}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  32.74s user 2.31s system 99% cpu 35.184 total
9606/PRJNA168/NC_000003
Features: {"assembly_gap":7,"misc_RNA":732,"mRNA":3902,"CDS":3901,"exon":202,"precursor_RNA":70,"ncRNA":115,"tRNA":4}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  28.43s user 1.82s system 99% cpu 30.416 total
9606/PRJNA168/NC_000004
Features: {"assembly_gap":12,"exon":199,"mRNA":2589,"CDS":2589,"misc_RNA":470,"precursor_RNA":56,"ncRNA":81,"tRNA":1}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  24.01s user 1.72s system 98% cpu 25.983 total
9606/PRJNA168/NC_000005
Features: {"assembly_gap":6,"mRNA":2666,"CDS":2666,"misc_RNA":541,"exon":197,"precursor_RNA":67,"ncRNA":94,"C_region":1,"tRNA":17}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  27.52s user 1.58s system 99% cpu 29.244 total
9606/PRJNA168/NC_000006
Features: {"assembly_gap":8,"exon":216,"misc_RNA":659,"mRNA":3150,"CDS":3150,"precursor_RNA":54,"ncRNA":83,"tRNA":153}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  21.73s user 1.43s system 99% cpu 23.220 total
9606/PRJNA168/NC_000007
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":8,"misc_RNA":678,"mRNA":2910,"CDS":2990,"precursor_RNA":67,"ncRNA":108,"exon":202,"C_region":3,"J_segment":13,"V_segment":63,"tRNA":22,"D_segment":1}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  21.22s user 1.32s system 99% cpu 22.587 total
9606/PRJNA168/NC_000008
Features: {"assembly_gap":9,"misc_RNA":452,"mRNA":2223,"CDS":2224,"precursor_RNA":67,"ncRNA":94,"exon":189,"V_segment":1,"tRNA":5}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  17.70s user 1.30s system 99% cpu 19.066 total
9606/PRJNA168/NC_000009
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":29,"misc_RNA":532,"mRNA":2607,"CDS":2616,"precursor_RNA":71,"ncRNA":117,"exon":157,"tRNA":3,"V_segment":9}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  17.75s user 1.32s system 99% cpu 19.109 total
9606/PRJNA168/NC_000010
Features: {"assembly_gap":12,"mRNA":2832,"CDS":2832,"precursor_RNA":60,"ncRNA":79,"misc_RNA":537,"exon":140,"tRNA":3}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  18.90s user 1.29s system 99% cpu 20.265 total
9606/PRJNA168/NC_000011
Features: {"assembly_gap":11,"exon":183,"misc_RNA":596,"mRNA":3891,"CDS":3891,"precursor_RNA":69,"ncRNA":133,"tRNA":13}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  26.53s user 1.38s system 99% cpu 27.966 total
9606/PRJNA168/NC_000012
Features: {"assembly_gap":8,"misc_RNA":603,"mRNA":3372,"CDS":3372,"precursor_RNA":56,"ncRNA":85,"exon":189,"tRNA":9}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  22.59s user 1.23s system 99% cpu 23.897 total
9606/PRJNA168/NC_000013
Features: {"assembly_gap":10,"exon":85,"misc_RNA":319,"ncRNA":79,"mRNA":1096,"CDS":1096,"precursor_RNA":37,"tRNA":4}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  9.54s user 0.96s system 99% cpu 10.556 total
9606/PRJNA168/NC_000014
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":5,"mRNA":2077,"CDS":2373,"exon":121,"misc_RNA":395,"ncRNA":172,"tRNA":19,"V_segment":180,"D_segment":30,"J_segment":74,"C_region":15,"precursor_RNA":83}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  15.79s user 1.04s system 99% cpu 16.874 total
9606/PRJNA168/NC_000015
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":10,"exon":146,"misc_RNA":454,"mRNA":2005,"CDS":2005,"precursor_RNA":56,"ncRNA":160,"tRNA":9}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  16.91s user 0.96s system 99% cpu 17.917 total
9606/PRJNA168/NC_000016
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":10,"exon":189,"misc_RNA":471,"mRNA":2720,"CDS":2723,"precursor_RNA":47,"ncRNA":77,"tRNA":27,"V_segment":3}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  22.72s user 0.84s system 99% cpu 23.620 total
9606/PRJNA168/NC_000017
Features: {"assembly_gap":5,"mRNA":3743,"CDS":3743,"misc_RNA":633,"exon":150,"precursor_RNA":82,"ncRNA":152,"tRNA":34}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  20.42s user 0.90s system 99% cpu 21.398 total
9606/PRJNA168/NC_000018
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":7,"exon":73,"misc_RNA":214,"mRNA":992,"CDS":992,"precursor_RNA":29,"ncRNA":43,"tRNA":1}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  7.28s user 0.65s system 99% cpu 7.971 total
9606/PRJNA168/NC_000019
Features: {"assembly_gap":8,"misc_RNA":523,"precursor_RNA":108,"ncRNA":206,"mRNA":4148,"CDS":4148,"exon":120,"tRNA":7}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  21.93s user 0.80s system 99% cpu 22.779 total
9606/PRJNA168/NC_000020
Features: {"assembly_gap":9,"mRNA":1720,"CDS":1720,"misc_RNA":339,"exon":51,"ncRNA":71,"precursor_RNA":40}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  9.73s user 0.65s system 98% cpu 10.549 total
9606/PRJNA168/NC_000021
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":14,"exon":47,"misc_RNA":210,"precursor_RNA":15,"ncRNA":22,"mRNA":712,"CDS":712,"tRNA":1}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  5.59s user 0.44s system 99% cpu 6.086 total
9606/PRJNA168/NC_000022
Error: New database 'IMGT/GENE-DB' found. Add it to the rs_id.json file and/or Identifiers.org.
Features: {"assembly_gap":9,"exon":64,"mRNA":1522,"CDS":1610,"misc_RNA":278,"V_segment":74,"precursor_RNA":35,"ncRNA":60,"J_segment":7,"C_region":7,"tRNA":1}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  8.81s user 0.55s system 98% cpu 9.457 total
9606/PRJNA168/NC_000023
Features: {"assembly_gap":21,"misc_RNA":311,"mRNA":2619,"CDS":2619,"exon":249,"precursor_RNA":107,"ncRNA":175,"tRNA":4}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  17.00s user 1.33s system 99% cpu 18.389 total
9606/PRJNA168/NC_000024
Features: {"assembly_gap":16,"misc_RNA":178,"mRNA":260,"CDS":260,"exon":60,"precursor_RNA":1,"ncRNA":1}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  3.87s user 0.49s system 98% cpu 4.428 total
9606/PRJNA30353/NC_012920
Features: {"D-loop":1,"tRNA":22,"rRNA":2,"STS":28,"misc_feature":1,"CDS":13}
ruby ~/rdf/rdfsummit/insdc2ttl/insdc2ttl.rb -d refseq $i > ../human.ttl/$i.tt  0.26s user 0.02s system 57% cpu 0.494 total

store@ep1:~/rdf/hg19/human.ttl% virtuoso.sh
Usage: /data/store/bin/virtuoso.sh {start|stop|status|watch|isql|port|path|list|log|edit|clear|loadrdf|loadttl|loaddir}
       /data/store/bin/virtuoso.sh loadrdf file.rdf graph_uri
       /data/store/bin/virtuoso.sh loadttl file.ttl graph_uri
       /data/store/bin/virtuoso.sh loaddir dir pattern graph_uri

store@ep1:~/rdf/hg19/human.ttl% virtuoso.sh loaddir /data/store/rdf/hg19/human.ttl '*.ttl' http://ep.dbcls.jp/hg19/refseq
Connected to OpenLink Virtuoso
Driver: 07.10.3207 OpenLink Virtuoso ODBC Driver
OpenLink Interactive SQL (Virtuoso), version 0.9849b.
Type HELP; for help and EXIT; to exit.
SQL> 
Done. -- 0 msec.
SQL> Connected to OpenLink Virtuoso
Driver: 07.10.3207 OpenLink Virtuoso ODBC Driver
OpenLink Interactive SQL (Virtuoso), version 0.9849b.
Type HELP; for help and EXIT; to exit.
SQL> 
Done. -- 4 msec.
SQL> Connected to OpenLink Virtuoso
Driver: 07.10.3207 OpenLink Virtuoso ODBC Driver
OpenLink Interactive SQL (Virtuoso), version 0.9849b.
Type HELP; for help and EXIT; to exit.
SQL> 
Done. -- 224419 msec.
SQL> Connected to OpenLink Virtuoso
Driver: 07.10.3207 OpenLink Virtuoso ODBC Driver
OpenLink Interactive SQL (Virtuoso), version 0.9849b.
Type HELP; for help and EXIT; to exit.
SQL> 
Done. -- 6909 msec.
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