• How to embed sparql in molgenis ?
  • ​SPARQL Engine for Java : http://sparql.sourceforge.net/
  • Basic Use of Engine : ​http://sparql.sourceforge.net/user-manual/manual.html#basics
    • not an RDF server of any sort, therefore it is not an end user semantic solution. If you want to store and access RDF data, see other projects like Sesame, Jena, etc ..VIRTUOSO.
      • Download (jar) sparql engine and try
        • Java Build Path --> Add external Jars
  • soap binding ?
  • Embed virtuoso in molgenis ..As external Jar .How to run ?
• Add peregrine in molgenis (references libraries) --> As Jar .How to run ?
  • Servlet in molgenis : (/molgenis_distro/handwritten/java/plugins/servlets/TestServlet.java)
    • ​http://sparql.sourceforge.net/user-manual/manual.html#basics *
• Meeting with Morris :
• See the presentation attached. Basically describes how the phenotypes should be constructed in a data source (database). I will have a talk with Eric who had done a similar work .
• TODO :
  • Term choose widget , try in simple ajax
  • Disease book:
    • Make a new application in molgenis ,
      • Import Marks' work inside?(not necesserily)
      • See from Eric about the fields how they are organized ..not as a lists (as Mark has implemented it)
        • About Phenotype See . ppt attache and data inserted in ​http://wwwdev.ebi.ac.uk/microarray-srv/pheno/
  • About the Ontocat on Concept Wiki --> ​Hackathonon 26/3/2010 --> Utrecht. about
  • RDF interface inside Molgenis
    • virtuoso, ​D2RQ(dowload and test how it works)
      • D2RQ Plattform - Treating Non-RDF Databases as Virtual RDF Graphs :
        • ​http://www4.wiwiss.fu-berlin.de/bizer/D2RQ/
        • ​http://www4.wiwiss.fu-berlin.de/bizer/D2RQ/spec/index.htm
        • ​http://sourceforge.net/projects/d2rq-map/
        • Example mapping file : ​http://www4.wiwiss.fu-berlin.de/bizer/D2RQ/example/mapping-iswc.n3
          • the corresponding database ​http://www4.wiwiss.fu-berlin.de/bizer/D2RQ/example/iswc-mysql.sql
          • and finally the ontology ​http://annotation.semanticweb.org/iswc/iswc.daml
          • Using a Semantic Web browser like ​Tabulator (​slides) or ​Disco, you can follow links from one resource to the next, surfing the Web of Data.
    • DONE : first mapping in molgenis db. through cygwin , browse to d2r directory and run
      • $ ./generate-mapping.bat -d com.mysql.jdbc.Driver -u molgenis -p molgenis jdbc:!mysql://127.0.0.1/molgenis
• DONe for Peregrine :
  • Created a new project
  • Drag and drop jar release of peregrine (rag and drop all jar files needed for peregrine --see ​wiki)
  • Import all those jar files from Properties--> Java Build Path --> (because we have drag and dropped the libraries , the can be found as internals)
  • Created a new java class RUNPeregrine whrere we need
    • * SingleFileOntologyImpl i = new SingleFileOntologyImpl("​file://myfile"); ..a file --> ask email from Dimitry
    • basically a way to make it run.
    • There is javadoc ..but no example in there C:\Documents and Settings\Morris Swertz\My Documents\Downloads\peregrine-api-0.2-javadoc
      • file:///C:/Documents%20and%20Settings/Morris%20Swertz/My%20Documents/Downloads/peregrine-api-0.2-javadoc/index.html

• HOW TO USE IndexingResult to highlight
  • (1) create html that highlights concepts
  • (2) get a list of concepts that are recognized.
• (Peregrine) send an email to Dimitry asking the above.
• DONE: PREP for Prep4Hackaton(in laptop) see attachment how2.txt:
  • installed d2rq, done mapping & rdf (from mysql) 
  • install jena (part of)