Welcome to ML on FHIR’s documentation!¶
Installation¶
TODO
Getting Started¶
Connecting to a FHIR Server¶
To connect to a FHIR server, create a FHIRClient object and provide its BaseURL:
1 2 | from fhir_client import FHIRClient client = FHIRClient(service_base_url='https://r3.smarthealthit.org') |
The server’s compatibility statement is queried to determine whether the connection was sucessful established.
Get an Overview of your Data¶
Before querying patients that belong to a specific cohort, we can get an overview of available procedures and via:
1 2 3 | import pandas as pd procedures = client.get_all_procedures() pd.DataFrame([prod.code['coding'][0] for prod in procedures]).drop_duplicates().sort_values(by=['display']).head() |
This might take a while but will give you an overview of available procedures. E.g.
| ID | code | display | system |
|---|---|---|---|
| 893 | 183450002 | Admission to burn unit | http://snomed.info/sct |
| 83 | 305428000 | Admission to orthopedic department | http://snomed.info/sct |
| 13687 | 35637008 | Alcohol rehabilitation | http://snomed.info/sct |
Similarily, we can receive a list of available conditions via:
1 2 | conditions = client.get_all_conditions() pd.DataFrame([cond.code['coding'][0] for cond in conditions]).drop_duplicates(subset=['display']).sort_values(by='display', ascending=True).head() |
| ID | code | display | system |
|---|---|---|---|
| 488 | 30473006 | Abdominal pain | http://snomed.info/sct |
| 140 | 102594003 | Abnormal ECG | http://snomed.info/sct |
| 6801 | 26079004 | Abnormal involuntary movement | http://snomed.info/sct |
Query Patients¶
With a list of available conditions we can query patients for which a certain condition was diagnosed. To do so we can either use the code of a coding nomenclature (e.g. SNOMED) or its readable name:
1 2 | patients_by_condition_text = client.get_patients_by_condition_text("Abdominal pain") patients_by_procedure_code = client.get_patients_by_procedure_code("http://snomed.info/sct","73761001") |