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GEO

Transformation scripts for converting GEO to RDF.

#Raw data Download latest DB: http://gbnci.abcc.ncifcrf.gov/geo/ SQLite3 database Table descriptions: https://gbnci-abcc.ncifcrf.gov/geo/geo_help.php#description

#Tables:

  1. GSM
  2. GSE
  3. GPL
  4. GDS
  5. GSE_GPL
  6. GSE_GSM
  7. GDS_SUBSET

#Conversion using Sparqlify https://github.com/AKSW/Sparqlify git clone git://github.com/AKSW/Sparqlify.git cd Sparqlify/ git checkout devel

GSM - Channel 1 and Channel 2 java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSM1.sml -f gsmpart1.csv > gsmChannel1.nt java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSM2.sml -f gsmpart1.csv > gsmChannel2.nt

GSM Series java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSM_Series.sml -f gsm_series.csv > gsmseries.nt

GDS java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGDS.sml -f gds1.csv > gdsnew.nt

GDS_SUBSET java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGDS_Subset.sml -f gds_subset1.csv > gds_subset_new.nt

GSE java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSE.sml -f gsepart1.csv > GSE.nt GSE Summary java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSE1.sml -f gsepart2.csv > gseSummary.nt GSE Contributor java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSE1.sml -f gsepart3.csv > gseContributor.nt GSE Web link java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSE1.sml -f gsepart4.csv > gseWebLink.nt GSE Overall Design java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSE1.sml -f gsepart5.csv > gseOverallDesign.nt

GSE_GSM java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSE1.sml -f gse_gsm.csv > gse_gsm.nt

GSE_GPL java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGSE1.sml -f gse_gpl.csv > gse_gpl.nt

GPL java -Xmx20148m -cp sparqlify-cli-0.6.20-SNAPSHOT-jar-with-dependencies.jar org.aksw.sparqlify.csv.CsvMapperCliMain -c mappingGPL.sml -f gpl.csv > gplnew.nt