• problem in molgenis rdf_test :
  • delete digital_identity entries in moglenis.n3
  • run again :
    • new errors:
      • * The import org.erasmusmc cannot be resolved
      • remove all references in Peregrine in /molgenis_rdf_test/handwritten/java/plugin/MainPage/MainPage.java
        • peregrine should run separately ! Needs a lot of memory !
        • run again , ok!
  • Now we got there : ​http://localhost:2020/ is actually showing molgenis data !
  • Now we need some real data : Form Joery : xgap_1_2_distro_15jan2010.sql
    1. Mysqlimport data into xgap_15_January:
       1. * mysql> create database xgap_15_January
       • grant all privileges on xgap_15_January.* to molgenis@localhost identified by 'molgenis'; flush privileges; *
       • * $ mysql5 -u root -p xgap_15_January < /Users/despoina/Documents/xgap_1_2_distro_15jan2010.sql
    2. Change database setting in molgenis.properties
    3. Run generate model
       1. copy model to file xgap_15_January_db.xml
       2. add :
          1. <?xml version="1.0" encoding="UTF-8"?>
          2. <molgenis name="xgap_15_January">
       • Field name was missing in some table in DB so error :

1. /molgenis/src/org/molgenis/model/jaxb/Model.java : add a check at if :
   1. * if (entity.getName().toLowerCase().equals(name.toLowerCase()))

• After the model is created we detect the missing field name :

1. mref field descriptionId
2. Material : added name="Material_id"
3. OntologyTerm? : added name="OntologyTerm?"
4. Strain: name="StrainId?"

• this could produce a lot of crap errors...import models form Joery (
  • fuge_db.xml, xgap_db_nochromosome.xml
  • these models work.
•  In order to see your data in ​http://localhost:2020/ first build the mapping .:
  • $ generate-mapping -d com.mysql.jdbc.Driver -u root -p ... jdbc:mysql://127.0.0.1/xgap_15_January > xgap_15_January.n3
  • In file : * /Users/despoina/Documents/workspace/molgenis_rdf_test/WebContent/WEB-INF/molgenis.n3
• TODO : the data showed in d2r browser are stack on address book . Where are they hiddenly cached?

• Misc : There are three different kinds of Web agents that can access data through simple HTTP-based interfaces:
  • RDF browsers, traditional HTML browsers, and SPARQL query clients.
  • ​http://www4.wiwiss.fu-berlin.de/bizer/d2r-server/publishing/ *
• ​http://www.mecheng.adelaide.edu.au/~will/texstart/ : Download this as a start : ​http://www.mecheng.adelaide.edu.au/~will/texstart/
• ​http://ii2.sourceforge.net/tex-index.html