EHR-Int-Extract

The export functionality enables users to extract linked data from the FHIR server, providing a seamless interface for downstream applications. With this feature, Demographics, Measurements, Genomics, or all three of these entities can be exported as a data matrix. The exported data is formatted to ensure direct compatibility with other utilities, facilitating automated clinical outcome modelling.

1. Export Demographics

Help menu

To display the help menu of the EHR-Int-Extract demographic data extract utility.

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.ExtractDemographics -h

or

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.ExtractDemographics --help

Output

usage: ExtractDemographics.py [-h] [-n] [-lrs] [-hrs] [-fd] [-td] [-sp]

src.ehrgen.extract.ExtractDemographics

optional arguments:
-h, --help                  Show this help message and exit
-n, --name                  Patient name
-lrs, --lower_risk_score    Specify the lower risk score cutoff value. By default: [-lrs=0]
-hrs, --higher_risk_score   Specify the higher risk score cutoff value. By default: [-hrs=1]
-fd, --from_date            From Date in the format [YYYY-MM-DD]
-td, --to_date              To Date in the format [YYYY-MM-DD]
-sp, --save_path            Path of the file to store the outputs

2. Export Measurements

Help menu

To display the help menu of the EHR-Int-Extract measurements data extract utility.

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.ExtractMeasurements -h

or

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.ExtractMeasurements --help

Output

usage: ExtractMeasurements.py [-h] [-n] [-lrs] [-hrs] [-fd] [-td] [-sp]

src.ehrgen.extract.ExtractMeasurements

optional arguments:
-h, --help                  Show this help message and exit
-n, --name                  Patient name
-lrs, --lower_risk_score    Specify the lower risk score cutoff value. By default: [-lrs=0]
-hrs, --higher_risk_score   Specify the higher risk score cutoff value. By default: [-hrs=1]
-fd, --from_date            From Date in the format [YYYY-MM-DD]
-td, --to_date              To Date in the format [YYYY-MM-DD]
-sp, --save_path            Path of the file to store the outputs

3. Export Genomics

Help menu

To display the help menu of the EHR-Int-Extract genomics data extract utility.

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.ExtractGenomics -h

or

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.ExtractGenomics --help

Output

usage: ExtractGenomics.py [-h] [-n] [-lrs] [-hrs] [-fd] [-td] [-sp]

src.ehrgen.extract.ExtracGenomics

optional arguments:
-h, --help                  Show this help message and exit
-n, --name                  Patient name
-lrs, --lower_risk_score    Specify the lower risk score cutoff value. By default: [-lrs=0]
-hrs, --higher_risk_score   Specify the higher risk score cutoff value. By default: [-hrs=1]
-fd, --from_date            From Date in the format [YYYY-MM-DD]
-td, --to_date              To Date in the format [YYYY-MM-DD]
-sp, --save_path            Path of the file to store the outputs

4. Export Integrated Data

Help menu

To display the help menu of the EHR-Int-Extract integrated data extract utility.

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.Extract -h

or

(.venv) app_user@hostname:~$python -m src.ehrgen.extract.Extract --help

Output

usage: Extract.py [-h] [-n] [-lrs] [-hrs] [-fd] [-td] [-sp]

src.ehrgen.extract.Extrac

optional arguments:
-h, --help                  Show this help message and exit
-n, --name                  Patient name
-lrs, --lower_risk_score    Specify the lower risk score cutoff value. By default: [-lrs=0]
-hrs, --higher_risk_score   Specify the higher risk score cutoff value. By default: [-hrs=1]
-fd, --from_date            From Date in the format [YYYY-MM-DD]
-td, --to_date              To Date in the format [YYYY-MM-DD]
-sp, --save_path            Path of the file to store the outputs