Pathling is a set of tools that make it easier to use clinical terminology and FHIR® within health data analytics. It is built on Apache Spark, and includes both language libraries and a server implementation.
What can it do?
Health data often contains codes from systems such as SNOMED CT, LOINC or ICD. These codes contain a great deal of information about diagnoses, procedures, observations and many other aspects of a patient's clinical record.
It is common to group these codes based upon their properties, relationships to other codes, or membership within a pre-defined set. Pathling can automate the task of calling out to a FHIR terminology server to ask questions about the codes within your data.
Examples of the types of questions that can be answered include:
- Is this SNOMED CT procedure code a type of endoscopy?
- Does this LOINC test result code have an analyte of bilirubin?
- Is this ICD-10 code within the pre-defined list of codes within my cohort definition?
See Terminology functions for more information.
Query and transformation of FHIR data
FHIR R4 is the dominant standard for exchanging health data. It comes in both JSON or XML formats, and can contain over 140 different types of resources, such as Patient, Observation, Condition, Procedure, and many more.
Pathling is capable of reading all the different types of FHIR resources into a format suitable for data analysis tasks. This makes the following things possible:
- Querying FHIR data using SQL and FHIRPath
- Transforming data into other formats, such as CSV or Parquet
- Performing terminology queries against coded fields within the FHIR data
See Encoders for more information.
FHIR analytics API
Pathling also provides a FHIR server implementation, providing a REST API that can be used to perform analytic queries over FHIR data. This is useful for powering interactive web and mobile applications that need to be able to aggregate, group and transform FHIR data.
See Server for more information.
Licensing and attribution
Pathling is copyright © 2018-2023, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230. Licensed under the Apache License, version 2.0.
This means that you are free to use, modify and redistribute the software as you wish, even for commercial purposes.
If you use this software in your research, please consider citing our paper, Pathling: analytics on FHIR.
Pathling is experimental software, use it at your own risk! You can get a full description of the current set of known issues here.