An experimental CQL execution engine for analyzing FHIR healthcare data at scale

CQL is a domain specific language designed for querying and executing logic on healthcare data. CQL excels at healthcare data analysis such as defining quality measures, clinical decision support, cohorts or preparing data for dashboards. CQL is designed for healthcare with first class support for terminologies, easy querying of FHIR via FHIRPath, graceful handling of mixed precision or missing data and built in clinical helper functions. You can find an intro to the CQL Language at https://cql.hl7.org.

Notable features of this engine include:

• Built in explainability - for each CQL expression definition we produce a tree that traces through the data and expressions involved in calculating the final result
• Built in custom CQL parser, reducing project dependencies and allowing optimizations between the parser and interpreter
• Benchmarked and optimized to be fast and memory efficient

In addition to the engine this repository has several tools that make it easy to launch and productionize CQL:

• A scalable Beam job for running CQL over large patient populations
• A CLI for easy configuration
• Integration into Google Cloud Storage

This CQL Engine is experimental and not an officially supported Google Product. The API to call the engine and the format of the results returned are subject to change. There is limited support of certain parts of the CQL Language:

• Only the FHIR version 4.0.1 data model is supported
• Only the Patient Context is supported
• Not all system operators are supported
• No support for Quantities with UCUM units
• No support for Interval/List Promotion and Demotion
• No support for related context retrieves
• No support for uncertainties
• No support for importing or exporting ELM

There are several different ways to use this engine. For quick experimentation we have a Command Line Interface and REPL. For executing CQL over a large patient population there is a Beam job. Finally, the CQL Golang Module allows you to execute CQL by implementing your own connector to a database and terminology server.

⚠️⚠️ Warning ⚠️⚠️

When using these tools with protected health information (PHI), please be sure to follow your organization's policies with respect to PHI.

When intending to run the CQL engine locally over small populations or for quick experimentation use the CLI located at cmd/cli. For documentation and examples see cmd/cli/README.md.

The Beam pipeline is recommended when running CQL over large patient populations. More information and usage examples are documented at beam/README.md.

The engine can be used via the CQL golang module documented in the godoc. The Retriever interface can be implemented to connect to a custom database or FHIR server. The Terminology Provider interface can be implemented to connect to a custom Terminology server.

For quick experiments with our CQL Engine we have a REPL. More information and usage examples are documented at cmd/repl/README.md.

If you are interested in how this engine was implemented see docs/implementation.md for an overview of the codebase.