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: --relationships "Is a" "Maps to"
-o OUT_DIR, --out-dir OUT_DIR
Output directory. Defaults to current working directory.
-V, --vocab-outputs Create set of artefacts (CodeSystem, ConceptMap) for each vocabulary?
-C, --combined-outputs
Create set of artefacts (CodeSystem, ConceptMap) for all of OMOP vocabulary combined?
-e, --exclude-vocab-prefix
With this flag absent, the identifiers and file names for each vocabulary will be prefixed "OMOP".
-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} ...]
Warning: Option currently in development. Does not differentiate between different settings (particularly --vocabs
and --relationships). It considers all cached files relevant each time you run it using a given --out-dir. So if
you want to use caching and also want to change your settings, either (a) clear your --out-dir or (b) use a
different --out-dir. Caching options: `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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
omop2fhir-vocab-1.1.6.tar.gz
(9.6 kB
view hashes)
Built Distribution
Close
Hashes for omop2fhir_vocab-1.1.6-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1e45fa81962c7462b2ed4c8613c4a42a4869a3fb8329c1f38cbcda607c1a256b |
|
MD5 | e10b0d7904807ed821f2dbdaa60d20da |
|
BLAKE2b-256 | 6be5d175f2edb21da839c7eceeb88bc96574cc0e9854c703f38efa5daaf2c39c |