Static OWL content, pre and post converted to FHIR.
Another repository is set up to do this automaticaly. However, for reference, the steps to do so are here.
We are using https://github.com/incATools/ontology-access-kit/ to do the conversion.
$ pip install oaklib
$ runoak -i OWL_PATH dump -o OUTPATH -O fhirjson --include-all-predicates
# careful, that's not camel case. It's a lower case j in fhirjson.# `poetry` is a Python package manager that OAK uses
$ pip install poetry
$ git clone https://github.com/INCATools/ontology-access-kit.git; cd ontology-access-kit
# `poetry shell` creates a virtual environment if one does not exist, and activates it
$ poetry shell
$ poetry install
# As of 2022/12/06, `origin/fhir-updates` is a currently open development branch. It may be that `main` also has updates that haven't yet made it to release, so you could try running from that branch. If `origin/fhir-updates` is already closed/merged, you can look to see if there are any other open FHIR-related branches https://github.com/INCATools/ontology-access-kit/pulls
$ python src/oaklib/cli.py -i OWL_PATH dump -o OUTPATH -O fhirjson --include-all-predicates
# careful, that's not camel case. It's a lower case j in fhirjson.Latest releases can be found at the following locations.
- CompLOINC: https://github.com/loinc/comp-loinc/releases/latest/download/merged_reasoned_loinc.owl
- RxNorm: https://data.bioontology.org/ontologies/RXNORM/submissions/23/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
- HPO: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/hp-full.owl
- Mondo: https://github.com/monarch-initiative/mondo/releases/latest/download/mondo.owl
- SO: https://data.bioontology.org/ontologies/SO/submissions/304/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
- go-nucleus: