Link

Documentation

Pathling is a server based on the HL7® FHIR® standard, implementing special functionality designed to ease the delivery of analytics-enabled apps and augment tasks related to health data analytics.

Pathling is licensed under the CSIRO Open Source Software Licence Agreement, which is a permissive licence based upon the BSD and MIT licences. This means that you are free to use, modify and redistribute the software as you wish, even for commercial purposes.

Pathling is experimental software, use it at your own risk! You can get a full description of the current set of known issues over on our GitHub page.

Motivation

Health care is a complex domain, and health care information models reflect this complexity. Linking data with clinical terminology adds a further degree of complexity, often requiring expert knowledge of coding systems and skill in the correct use of them within the analytic context.

Generalized tools for data analytics and business intelligence do little to insulate their users from this complexity, as it is often impractical for them to cater for requirements unique to specialist areas such as health care. Users often deal with this complexity by writing large volumes of code to cover the domain-specific functionality missing from their tools. This code is sometimes shared in the form of libraries and packages, but is more often written and maintained in isolation from other users.

Pathling is an attempt to encapsulate a set of functionality useful for health data analytics application development and workflow into a server implementation that natively understands FHIR on the way in, and on the way out. This functionality is designed to service the following use cases:

  1. Exploratory data analysis – Exploration of hypotheses, assessment of assumptions, and selection of appropriate statistical tools and techniques.
  2. Patient cohort selection – Selection and retrieval of patient records based upon complex inclusion and exclusion criteria.
  3. Data preparation – Processing and re-shaping data in preparation for use with statistical and machine learning tools.

Functionality

The diagram below shows the functionality that we are working towards within Pathling.

FHIR Analytics API

In summary, the operations available within Pathling are:

  1. import - An operation for importing FHIR data in bulk into the server, making it available for query using the other operations.
  2. search - A way of retrieving a set of individual FHIR resources that match a set of criteria, described using expressions.
  3. aggregate - A “pivot table as an API”, able to take in a set of expressions that describe aggregations, groupings and filters and return grouped aggregate data.
  4. summarize (currently under development) - An operation that allows a client to describe a custom tabular extract of FHIR data, and retrieve it in bulk.

You can find some examples of how to interact with Pathling in our Postman collection:

Run in Postman

See the Roadmap for more information about the features that are currently under development.

FHIRPath

Pathling uses a language called FHIRPath to facilitate the description of expressions within requests to these operations. FHIRPath is a language that is capable of navigating and extracting data from within the graph of resources and data types that FHIR uses as its data model. It provides a convenient way for us to abstract away the complexity of navigating FHIR data structures that we ecounter when using more general query languages such as SQL.

You can get further information about supported syntax and functions within FHIRPath here.

Cluster execution

Pathling has the ability to integrate with Apache Spark in order to enable the execution of queries and other operations with the help of a distributed computing cluster. This is useful when the volume of data is large enough to warrant the use of compute and memory resources from more than a single server.

You can get further information about this functionality here.


Table of contents