FHIR Chat · Covid19 Test Server

Stream: Covid-19 Response

Topic: Covid19 Test Server

Abbie Watson (Mar 24 2020 at 17:22):

Hey,
We're making some great progress over in the Synthea project with developing a COVID19 module.
https://github.com/synthetichealth/synthea/issues/679

@Jason Walonoski and I have managed to generate a synthetic population of COVID19 patients (using the ValueSets that @Grahame Grieve created in the #terminology stream). I subsequently loaded them into a local HAPI server, and have validate the FHIR queries and quality of data.

Long story short, it looks like we're ready to load some synthetic COVID19 data into a public server. Any recommendations for where to point our tag-loader utility towards?

@Lloyd McKenzie - is the Canadian public HAPI server still available? Anybody else with a public FHIR server?

Lloyd McKenzie (Mar 24 2020 at 17:33):

@James Agnew

James Agnew (Mar 24 2020 at 17:43):

Feel free to upload to hapi.fhir.org - Would this merit a dedicated endpoint (I'm not clear on what people would do with this data..)? If so I'm happy to set one up

Abbie Watson (Mar 24 2020 at 17:47):

Well, for instance, I just validated that the following endpoints return actual data:

# DSTU2 - Search for all testing encounters "Encounter for symptom (procedure)" ???
http://localhost:3100/baseDstu2/Encounter?type=185345009

# DSTU2 - Search for all conditions with "Cough (finding)"
http://localhost:3100/baseDstu2/Condition?code=49727002

# DSTU2 - Search for all conditions with "Dyspnea (finding)"
http://localhost:3100/baseDstu2/Condition?code=267036007

# DSTU2 - Search for all conditions with "Fever (finding)"
http://localhost:3100/baseDstu2/Condition?code=386661006

# DSTU2 - Search for all conditions with "Suspected COVID-19"
http://localhost:3100/baseDstu2/Condition?code=840544004

# DSTU2 - Search for all conditions with "Suspected COVID-19" in the month of March 2020
http://localhost:3100/baseDstu2/Condition?code=840544004&onset=ge2020-03-01&onset=le2020-03-31

# DSTU2 - Search for all conditions with "COVID-19"
http://localhost:3100/baseDstu2/Condition?code=840539006

# DSTU2 - Search for all conditions with "Pneumonia"
http://localhost:3100/baseDstu2/Condition?code=233604007

# DSTU2 - Search for medication admininstrations of "Hydroxychloroquine Sulfate 200 MG Oral Tablet"
http://localhost:3100/baseDstu2/MedicationAdministration?code=979092

# DSTU2 - Search for all procedures of type "Oxygen administration by mask (procedure)"
http://localhost:3100/baseDstu2/Procedure?code=371908008

#==================================================

# R4 - Search for all testing encounters "Encounter for symptom (procedure)" ???
http://localhost:3100/baseR4/Encounter?type=185345009

# R4 - Search for all conditions with "Cough (finding)"
http://localhost:3100/baseR4/Condition?code=49727002

# R4 - Search for all conditions with "Dyspnea (finding)"
http://localhost:3100/baseR4/Condition?code=267036007

# R4 - Search for all conditions with "Fever (finding)"
http://localhost:3100/baseR4/Condition?code=386661006

# R4 - Search for all conditions with "Suspected COVID-19"
http://localhost:3100/baseR4/Condition?code=840544004

# R4 - Search for all conditions with "Suspected COVID-19" in the month of March 2020
http://localhost:3100/baseR4/Condition?code=840544004&onset-date=ge2020-03-01&onset-date=le2020-03-31

# R4 - Search for all conditions with "COVID-19"
http://localhost:3100/baseR4/Condition?code=840539006

# R4 - Search for all conditions with "Pneumonia"
http://localhost:3100/baseR4/Condition?code=233604007

# R4 - Search for medication admininstrations of "Hydroxychloroquine Sulfate 200 MG Oral Tablet"
http://localhost:3100/baseR4/MedicationAdministration?code=979092

# R4 - Search for all procedures of type "Oxygen administration by mask (procedure)"
http://localhost:3100/baseR4/Procedure?code=371908008

Abbie Watson (Mar 24 2020 at 17:48):

Which allows us to begin writing COVID19 specific applications. If we need to count capacity of oxygen administration, send food deliveries or follow up social workto home addresses of people who are "Suspected COVID19", etc.

A sample test data set allows us to begin addressing adhoc workflows specific to this outbreak.

James Agnew (Mar 24 2020 at 17:55):

Makes sense to me. :) @Abigail Watson I'll set up a dedicated server this afternoon and post the details here.

Josh Mandel (Mar 24 2020 at 18:10):

Super cool -- are there instructions or a script for how we can run this to generate data (so we can load independently)?

James Agnew (Mar 24 2020 at 18:12):

oh, one question- is this data DSTU2? or R4?

Abbie Watson (Mar 24 2020 at 18:12):

@Josh Mandel - The steps are documented in this github repo:
https://github.com/symptomatic/covid19-hackathon#generating-a-synthetic-dataset-of-covid19-patients

Abbie Watson (Mar 24 2020 at 18:13):

@James Agnew - The Synthea utility outputs in both formats. I've validated both. Will be doing STU3 shortly.

James Agnew (Mar 24 2020 at 18:47):

is an R4 endpoint ok for the dedicated one?

Abbie Watson (Mar 24 2020 at 18:49):

Mmmm... it's a tough call. Most of the currently deployed Epic and Cerner servers are DSTU2, but ONC says R4 going forward; and that's just for the US.

How about we do R4 for the dedicated server, and we can use that as proof-of-concept to push Epic and Cerner and Allscripts and others to do their own load into their own sandboxes, which might still be as DSTU2.

So... yeah, let's go with R4. (But anybody seriously developing solutions will probably need to focusing on both or do mix-mode support.)

Keith Boone (Mar 24 2020 at 20:06):

Mixed mode support isn't terribly difficult. Took me about a day and a half to build: https://motorcycleguy.blogspot.com/2019/04/juggling-fhir-versions-in-hapi.html

Jason Walonoski (Mar 24 2020 at 20:17):

Also, the covid19 Synthea module is a work in progress, and I expect there to be many updates over the next week or two.

James Agnew (Mar 25 2020 at 01:23):

@Abigail Watson : Went ahead and provisioned two:

https://covid19-under-fhir.smilecdr.com/baseR4
https://covid19-under-fhir.smilecdr.com/baseDstu2

Abbie Watson (Mar 25 2020 at 01:25):

Sending 1000 COVID19 patients to https://covid19-under-fhir.smilecdr.com/baseR4

Abbie Watson (Mar 25 2020 at 21:35):

@James Agnew
Hey, upload to the new servers doesn't seem to be working. I was able to upload successfully to hapi.fhir.org, but am getting ETIMEDOUT and Request Entity Too Large errors when sending to https://covid19-under-fhir.smilecdr.com/baseR4

Screen-Shot-2020-03-25-at-4.33.19-PM.png