201705 Data Analytics
Return to September 2017 Proposals
FHIR Data Analytics Track
Submitting WG/Project/Implementer Group
FHIR Management Group (FMG)
Justification
FHIR connectathons have been limited to developers to participate, or at least, for people who have tooled up development environments. But there are many people who come to HL7 who are interested in FHIR and need to learn more about it who are not in that position. This stream leverages the work done to prepare for the AMIA FHIR based datathon - uses the same set of tools to provide a data analytics platform that anyone who attends HL7 and is interested in informatics (most of us) can take part in.
The tools/platform provided, along with the test data, will allow participanst to explore FHIR in practical ways.
Links:
Proposed Track Lead
Coordinator: Corey Spears . also see Zulip topic
Expected participants
- Health Intersections - terminology server
- - Synthetic data
- Chris Grenz - data analytics platform
Roles
In this track, users perform directed and undirected queries against the FHIR servers and data
Scenarios
These scenarios are just a starting point to stimulate your thinking at the outset, but participants are entirely free to explore others. The initial scenarios will explore searching for potential subjects for clinical trials who meet stated eligibility criteria (inclusion & exclusion). Example conditions to explore include asthma and dyslipidemia. Where you go beyond this will be up to you.
Scenario 1: Asthma Eligibility
Demographics
Age: 18-70 Gender: Both Race: All
Clinical Condition
Asthma History:
- Has the subject had sinusitis? Yes or No
- Has the subject had atopic dermatitis? Yes or No
- Has the subject had eczema? Yes or No
- Has the subject had seasonal allergic rhinitis? Yes or No
- Has the subject had bronchitis? Yes or No
- Has the subject had pneumonia? Yes or No
Diagnostic results of FEV1/FVC tests
Possible exclusion or inclusion:
- Current or Prior use of corticosteroids.
- Current or recent (last 2 years) use of an NSAID.
- Has had a nasal sinus endoscopy procedure performed.
TestScripts
N/A
Background, Tools & Methods
The Data
SyntheticMass – A “Realistic” Synthetic Patient Clinical Data Set SyntheticMass (https://syntheticmass.mitre.org) is an open-source, simulated Health Information Exchange (HIE) populated with one million realistic “synthetic residents” of Massachusetts. The data is free from cost, privacy, and security restrictions. It can be used without restriction for a variety of secondary uses in academia, research, industry, and government.
SyntheticMass provides:
- Realistic population health and demographic data at the city and town level
- The ability to drill down to individual synthetic patient data covering numerous common medical conditions
- APIs such as HL7 FHIR STU3 (https://syntheticmass.mitre.org/fhir) and HL7 CCDA
In SyntheticMass, you can use the dashboard (https://syntheticmass.mitre.org/dashboard) to drill down to individual synthetic patient data covering numerous common medical conditions.
The FHIR Server you can use to query is at: https://syntheticmass.mitre.org/fhir (In the [clinFHIR.org clinFHIR.org]tool the server name is GoFHIR)
The conditions covered can be found here: [https://github.com/synthetichealth/synthea/wiki#currently-supported-diseases https://github.com/synthetichealth/synthea/wiki#currently-supported-diseases ] The list of all the concepts you may find in SyntheticMass can be found here: https://goo.gl/VeQ9Bq
The Tools
Below are a few tools we will be using for this track. They are provided to help you explore the data using FHIR.
clinFHIR – A Tool to Get Started on FHIR
clinFHIR is an educational tool that allows people to create or search for FHIR based resources and link them to tell a clinical story. clinFHIR is meant to help those not currently familiar with FHIR to start to understand what it is and how it can be used. clinFHIR is a front end tool that can be used to connect to any number of FHIR servers to explore and even store new data.
clinFHIR consists of a number of models that provide several capabilities that are beyond what we will be looking at for this track. For most of our work, the Query Tool (http://clinfhir.com/query.html) and Patient Viewer Tool (http://clinfhir.com/patientViewer.html) will be of most interest, however, you are welcome to explore the other modules (http://clinfhir.com). A description of those modules can be found here: (https://fhirblog.com/2017/02/20/new-ui-for-clinfhir/). Be sure to configure the FHIR server at the http://clinFHIR.org (SyntheticMass server name is GoFHIR).
Apache Drill – Direct Clinical BI on FHIR
This track introduces using the NoSQL to SQL engine Apache Drill to directly query FHIR formatted resources stored in NoSQL data stores. This track will:
- Introduce the technique: https://www.linkedin.com/pulse/mining-fhir-clinical-bi-chris-grenz
- Introduce practical considerations for accessing FHIR via Drill SQL
- Provide a demonstration environment loaded with MITRE’s SyntheticMass patient set
We will be using the same methodology and tools that were introduced in the recent AMIA Datathon more information about this approach can be found at the AMIA Datathon SQL Resources Site: http://amia.analystseim.com/
This site includes information about installing Drill related tools and the AMIA Datathon Drill environment.
