HL7 FHIR to schema.org conversion tool
See: https://github.com/crDDI/docs/wiki/FHIRToSDO for implementation details
- python3 (ideally >= 3.5, but any 3.x version will do). You can determine whether you have python on your machine and its version by:
python -v-- if 3.x you are ready to go, otherwise...
python3 -v-- if this works you are also ready to go
- virtualenv -- if this isn't on your machine, see http://pythoncentral.io/how-to-install-virtualenv-python/
- java -- we need version 1.7 or greater
Set up a python3 virtual environment:
> virtualenv fhirtosdo -p python3 > . fhirtosdo/bin/activate (fhirtosdo) > pip install fhir-to-sdo
Downloading the FHIR specification
To download the latest copy of the FHIR spec and unzip it:
(fhirtosdo) > download_fhir_spec --striptext
Note that the above function can take considerable time, as the zipped image of the fhir spec is quite large. Note that the "-u" option can be used to download different fhir builds as needed
Downloading the FHIR metadata specification
Currently it is possible to get a copy of the FHIR 'ontology' from the FHIR svn repository as
./build/publish/fhir.ttl An image of a recent fhir.ttl is also available in
./data/ttl/fhir.ttl in this distribution.
Run the w5tosdo transformation
(fhirtosdo) > w5tosdo -i ../data/ttl/fhir.ttl -o w5.rdfa --loglevel INFO
Run the fhirtosdo transformation
(fhirtosdo) > fhirtosdo -id data/site -o fhir.rdfa --loglevel INFO
The results of these two transformation
Note that the above transformation may generate a number of error messages of the form "ValueSet access error: http://hl7.org/fhir/ValueSet/measure-population (Not Found)". This is because not all of the value sets referenced in the FHIR structure definitions are currently available on the official fhir website.
The outputs (w5.rdfa, fhir.rdfa) can then be transferred to the schema.org environment.