wiki:DespoinaLog/2010/10/1

Version 3 (modified by antonak, 14 years ago) (diff)

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  • 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
  1. 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

  • XML -→ OWL convert XML ←? OWL
  1. RDF annotation
  2. <field rdf type=”Thesaurus.owl#Spectrometer”
  3. Generate into n3
  1. Pilot of RDF into 2 pheno systems

Could we query the two half phenos ?

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

In semantic search (lucene indexing )

Install in xgap & phenotype • Configure • Adjust • Test • Finish

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