omop2fhir-vocab 1.1.1

Convert OMOP vocab to FHIR.

OMOP2FHIR-vocab

Convert OMOP vocab to FHIR.

Prerequisites

• Python 3.9+
• Java 11+

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.