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.
-I, --retain-intermediaries
Retain intermediary OWL files created during conversion process?
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