* gcc meeting & Molgenis scrum
 * skype about biobanking hackathon demo .
 * meeting with Morris about molgenis semantics

= Molgenis semantics =
 1. Create a new <field type = "ontology Term" . This will enable browsing like showing a dropdown menu or a wizard that could retreive term (connect to Ontocat)

 * Specification (manual)
 * code plan
 * Testing

 2. We need multiple molgenis systems using RDF , and connection between them.

 * How the data should look like ? (already n3 is available in molgenis by D2R )
 * We would like to define relationships
   * So we need an ontology file that described the data  o        Add an attribute in the molgenis xml file : rdf => rdf relatioship label....
   * If ontology references are available  --> reach RDF sources     o        (new data type in data model)

  e.g Let’s assume  "sample" in xgap two different entities but contains different synonyms for the same word.We would like to have a linkage between them like an owl file .  Fow example the id field in http://bioportal.bioontology.org/visualize/42838/?conceptid=Spectrometer&jump_to_nav=true      is  http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Spectrometer

  [[ /trac/molgenis/attachment/wiki/DespoinaLog/2010/10/1/Molsemantic.png Molsemantic.png] ]]
<p> 
<a style="padding:0; border:none" href="/trac/molgenis/attachment/wiki/DespoinaLog/2010/10/1/Molsemantic.png Molsemantic.png"><img src="/trac/molgenis/attachment/wiki/DespoinaLog/2010/10/1/Molsemantic.png Molsemantic.png" alt="RuG logo" title="RuG logo" /></a><a style="padding:0; border:none" href="/trac/animaldb/attachment/wiki/WikiStart/fmns_logo_en.png"><img src="/trac/animaldb/raw-attachment/wiki/WikiStart/fmns_logo_en.png" alt="FMNS log" title="FMNS log" /></a><a style="padding:0; border:none" href="/trac/animaldb/attachment/wiki/WikiStart/molgenis_logo.jpg"><img src="/trac/animaldb/raw-attachment/wiki/WikiStart/molgenis_logo.jpg" alt="molgenis logo" title="molgenis logo" /></a><br /> 
</p> 

 * XML  -→ OWL convert  XML ←? OWL

 3. RDF annotation
 3. <field rdf type=”Thesaurus.owl#Spectrometer”
 3. Generate into n3

 4. Pilot of RDF into 2 pheno systems

Could we query the two half phenos ?

 5. Can we use RDF to integrate different molgenis? (pheno & xgap )

== In semantic search (lucene indexing ) ==
Install in xgap & phenotype

 * Configure
 * Adjust
 * Test
 * Finish

  *