Convert OMOP vocab to FHIR.
Project description
OMOP2FHIR-vocab
Convert OMOP vocab to FHIR.
Prerequisites
Installation
pip install omop2fhir-vocab
Running
Run: omop2fhir-vocab OPTIONS
CLI
omop2fhir-vocab --help
usage: omop2fhir-vocab [-h] -c CONCEPT_CSV_PATH -r CONCEPT_RELATIONSHIP_CSV_PATH [-v VOCABS [VOCABS ...]] [-R RELATIONSHIPS [RELATIONSHIPS ...]] [-o OUT_DIR]
[-I]
Convert OMOP vocab to FHIR.
options:
-h, --help show this help message and exit
-c CONCEPT_CSV_PATH, --concept-csv-path CONCEPT_CSV_PATH
Path to CSV of OMOP concept table.
-r CONCEPT_RELATIONSHIP_CSV_PATH, --concept-relationship-csv-path CONCEPT_RELATIONSHIP_CSV_PATH
Path to CSV of OMOP concept_relationship table.
-v VOCABS [VOCABS ...], --vocabs VOCABS [VOCABS ...]
Which vocabularies to include in the output? Usage: --vocabs "Procedure Type" "Device Type"
-R RELATIONSHIPS [RELATIONSHIPS ...], --relationships RELATIONSHIPS [RELATIONSHIPS ...]
Which relationship types from the concept_relationship table's relationship_id field to include? Default is "Is a" only. Passing "ALL"
includes everything. Usage: --realationships "Is a" "Maps to"
-o OUT_DIR, --out-dir OUT_DIR
Output directory. Defaults to current working directory.
-S, --exclude-code-system
Exclude CodeSystem outputs.
-M, --exclude-concept-map
Exclude ConceptMap outputs.
-H {all,omop2fhir,omop2owl,owl2fhir} [{all,omop2fhir,omop2owl,owl2fhir} ...], --caching {all,omop2fhir,omop2owl,owl2fhir} [{all,omop2fhir,omop2owl,owl2fhir} ...]
Caching options. Warning: Developer option. Use at your own risk. Currently this option is in development and it
will only work if you don't change your options after running it for the first time. If you use this and then want
to change your options, particularly --vocabs and --relationships, you will have to (a) not use caching for
subsequent runs, or (b) uninstall and reinstall the program. `all`: Turns on all cache options. `omop2fhir`: Saves
any intermediate files at the top level of this pipeline, which basically entails caching of output from omop2owl
which is used by owl2fhir. `omop2owl`: Intermediates used by that package, such as robot templates. `owl2fhir`:
Intermediates used by that package, such as Obographs JSON.
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