Use-case pregnancy journeys

[dkapitan]

Use-case pregnancy journeys: PharmAccess MomCare

Context

We take the MomCare project from PharmAccess Foundation as a use-case. Read more on it here and here. Objective of this use-case is to create standardized SQL-on-FHIR queries to monitor the journeys of pregnant mothers in low- and middle income countries using the WHO guidelines.

In essence, we want to query whether certain activities (encounter, procedure) have taken place at predefined times during the pregnancy. The care model aims to incentivise pregnant mothers and antenatal clinics to regular check-ups and visits, which have been shown to reduce infant and maternal mortality.

Synthetic pregnancy data

After installing Syntea we generate synthetic data of pregnancies in the bulk data format as follows:

touch ./synthea.properties
# set exporter.fhir.bulk_data = true with a text editor

java -jar synthea-with-dependencies.jar -c synthea.properties -p 1000 -g F -m Pregnancy

Queries with duckdb

We use duckdb and Python for demonstrating the type of queries we want to write for this use case. I have created a playground repo https://github.com/PharmAccess/hdc-sql-on-fhir

Here's the first query to create a flattened table of encounters/procedures as a first step of constructing the patient journey:
https://github.com/PharmAccess/hdc-sql-on-fhir/blob/main/test/test-synthea.ipynb