• 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

[http://gbic.target.rug.nl/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
4. <field rdf type=”Thesaurus.owl#Spectrometer”
5. 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

*