Ontolia

Ontolia is an ONTology LInking Application. The software connects to EMBL-EBI's Ontology Lookup Service to gather regimens and treatments specified in NCIT. Not all branches are loaded by the application, see the branch definitions for more info. Once the regimens and treatments are loaded, the application tries to link regimen terms to their corresponding set of treatment terms, then Ontolia will export this knowledge into an output file. To do this the user has to specify a valid output directory, using the --dir= program argument.

Running the application

java -jar ontolia.jar --dir=/Users/csaba/Ontolia

This command will run the application and creates the ontolia output file at: /Users/csaba/Ontolia/ontolia_output.txt

Ontolia output file format

RegimenId=TreatmentTermId1,TreatmentTermId2,TreatmentTermIdX*

Example output:

NCIT_C37600=NCIT_C1282,NCIT_C405,NCIT_C456,NCIT_C491

NCIT_C37600 = Carboplatin/Cyclophosphamide/Doxorubicin/Etoposide