| 2 | | * meeting with Morris about molgenis semantics |
| 3 | | * skype about biobanking hackathon demo . |
| | 2 | * meeting with Morris about molgenis semantics |
| | 3 | |
| | 4 | = Molgenis semantics = |
| | 5 | 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) |
| | 6 | |
| | 7 | * Specification (manual) |
| | 8 | * code plan |
| | 9 | * Testing |
| | 10 | |
| | 11 | |
| | 12 | |
| | 13 | 2. We need multiple molgenis systems using RDF , and connection between them. |
| | 14 | |
| | 15 | * How the data should look like ? (already n3 is available in molgenis by D2R ) |
| | 16 | * We would like to define relationships |
| | 17 | * So we need an ontology file that described the data o Add an attribute in the molgenis xml file : rdf => rdf relatioship label.... |
| | 18 | * If ontology references are available --> reach RDF sources o (new data type in data model) |
| | 19 | |
| | 20 | 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 |
| | 21 | |
| | 22 | * XML -→ OWL convert XML ←? OWL |
| | 23 | |
| | 24 | |
| | 25 | |
| | 26 | 3. RDF annotation |
| | 27 | 3. <field rdf type=”Thesaurus.owl#Spectrometer” |
| | 28 | 3. Generate into n3 |
| | 29 | |
| | 30 | 4. Pilot of RDF into 2 pheno systems |
| | 31 | |
| | 32 | Could we query the two half phenos ? |
| | 33 | |
| | 34 | 5. Can we use RDF to integrate different molgenis? (pheno & xgap ) |
| | 35 | |
| | 36 | In semantic search (lucene indexing ) |
| | 37 | |
| | 38 | Install in xgap & phenotype • Configure • Adjust • Test • Finish |
| | 39 | |
| | 40 | * skype about biobanking hackathon demo . |
