Run D2R server

• You will need :
  • jar files.
  • ...src\d2rq\generate_mapping.java as well as dump rdf class.
• "How to sparql molgenis "
  • D2R SERVER START working:
    • $ ./d2r-server.bat -p 2020 molgenis.n3
    • @ ​http://localhost:2020/snorql/ TADA!

Log

• molgenis_rdf_test from SVN. Problem running.
  • Updated molgenis version .
    • Just that Server Tomcat failed to Start
• Disease book from Mark , including :
  • Disease_book project
  • Molgenis3_3
  • ontologiedatabasetest *
• ​http://hackathon3.dbcls.jp/ - ​http://www.ustream.tv/channel/biohackathon2010 (!)
• Translate natural language to sparql :
  • "....Is there any way of translating a natural language query to a SPARQL one? or should we need to develop?
    Some "buffer" layer, which bridges the gap between highly structured language such as SPARQL and unstructured one (i.e., natural language), might be needed. ​Swoogle may be useful. Also, information extraction (IE) technology is crucial to identify a key concept in literature. Natural language processing (NLP) technology used for IE in life science such as ​MEDIE or ​Enju can be used......"
• next steps : how to map inheritance in the object model to the mapping file - if we can also add our descriptions from xml to the mapping
  (if it makes sense to embelish the model with more information). We need to generate this file automatically when the MOLGENIS generator runs.
  • The first step generate-mapping file from your source (here mysql database) and this is :
    • (outside molgenis)
      • Build d2r server (there should be a java class to create an instance)
      • (the above may need the appropriate jar includes)
      • log config
      • Class : d2rq.generate_mapping
        • [exec java -cp "$CP" -Xmx256M "-Dlog4j.configuration=${LOGCONFIG}" d2rq.generate_
          mapping "$@"]
        • D2RQ classes @ d2r-server-0.7/src/de/fuberlin/wiwiss/d2rs
    • ..So now we actually need the class to generate mapping and start Server
      • there is something missing .re-download d2rq server ..and TAD there it is in : .......src\d2rq\generate_mapping.java
      • So call this class!

• Links :

• semantic Web search : ​http://swoogle.umbc.edu/
• ​SparqlTutorial : http://hackathon3.dbcls.jp/wiki/SparqlTutorial
• RDF editor : ​http://www.cs.rpi.edu/~puninj/rdfeditor/ *