alexanderpico/wp2lod

Java source for conversion of WikiPathways GPML to triples

wp2lod

This repo is a collection of all the files needed to run the wp2lod pipeline. Follow the steps below to clone and run this code.

##Command line git clone <paste wp2lod repo url>

##Set config properties

• Rename config.properties.default to config.properties
• Edit the config.properties with relevant file locations

##In Eclipse

• Create a new project and point to cloned code
• Add lib jars to Build Path
• Specify (create?) src folder
• Check BridgeDb file path in WP2RDFConversion.java:91 (should point to derby files on local or server)
• RunConfiguration: main=Pathway2RDFv2
• File>Export>Runnable JAR file (to tmp/WP2Rdf.jar; expect warnings)

##Command line sh scripts/masterScript.sh (references runnable jars)

##Ragamuffin

• output files from pipeline:
• wpContent_…_ttl
• void.ttl
• These files get copied to: /home/virtuoso/andra/wp/db
• Other ontologies files go into this same dir, e.g., *.owl and *.obo files

#Check new files in test instance

cd /home/virtuoso/andra/

sudo cp -R wp wpcache ##takes a while!

cd wpcache/db/

vi wp.ini

• change [paramerter] ServerPort to 5556 ##any free port numbers will do: netstat -aunt
• change [HTTPServer] ServerPort to 5557

virtuoso-t +conf ##launch test instance

• Open virtuoso command line and load new ttl and owl files (see below)

• Run benchmark queries and compare to live sparql endpoint

  • Need to tunnel to reach alt HTTPServer port (e.g., 5557):
  • Open new terminal and run this from localhost:
  • ssh -T -N -L 5557:localhost:1234 <username>@ragamuffin.bigcat.unimaas.nl
  • In browser, navigate to localhost:1234/sparql
  • Close tunnel by:
  • ps aux | grep localhost (note )
  • sudo kill -9 <pid>

• Should include Raptor validation step

• If ready then shutdown:

SQL> DELETE FROM DB.DBA.RDF_QUAD;

SQL> shutdown();

cd ..

sudo rm -rf wpcache/*

• Then go to live dir: cd ../../wp/db and load new files into

• Open command line for virtuoso: isql-vt -S 1973 #port specified in wp.ini file

• Load new ttl file:

SQL> DELETE FROM DB.DBA.RDF_QUAD; #warning: this deletes everything! This is useful during dev periods and for major db reconstruction; should NOT be used during normal production updates.

SQL> DB.DBA.TTLP_MT (file_to_string_output ('wpContent_v0.0.69675_20130710.ttl'), '', 'http:/opsv13.wikipathways.org');

SQL> DB.DBA.RDF_LOAD_RDFXML (...); for all .owl files ## .obo files should be converted to .owl files prior to loading with this same syntax (http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page).

• need to look into batch loading script

• Now, the sparql is live and ready for queries.

• Note: sparql.wikipathways.org is proxy to 1974 port via apache.