KNOX-OMOP2KG

Converts data from the OMOP CDM, to a KG based on a general purpose ontology. Made for the AAU KNOX Superproject.

Dependencies

• rdflib
  • To install use: pip install rdflib

Relevant files:

• "Main.py"
• "IO.py"
• "TripleGenerator.py"
• All CSV files used to test are included in the repo under "Dataset/mimic-iv-demo-data-in-the-omop-common-data-model-0.9/1_omop_data_csv". These files are the MIMIC-IV demo converted to OMOP form.
• The relevant ontology files are in the Ontology folder. "Ont.ttl" is the full ontology we created, and "Ont_Linked.tll" is a linked version, containing references to class definitions
• "Triples.txt" contains information regarding what data is loaded into the program
• "Mapping.txt" contains information regarding names of csv column and which ontology class that corresponds to

Running the program

python Main.py ONTOLOGY_LOCATION python Main.py .\Ontology\Ont_Linked.ttl