Stream: implementers
Topic: Synthea Patient Generator
Joel Francis (Jan 09 2019 at 15:03):
Hi,
Are there any guidelines on what/how to tweak Synthea to generate data for Canada? I am assuming one would have to supply customized .json and .csv files ?/
Thanks in advance for any help and advice.
Jason Walonoski (Jan 10 2019 at 13:48):
Joel, there is at least one other team that has successfully generated Synthea data for Canada. I believe they generated the province of Manitoba. They captured their lessons learned here: https://github.com/synthetichealth/synthea/wiki/Other-Areas---Canada
Jason Walonoski (Jan 10 2019 at 13:49):
Unfortunately, it seems like a lot of the input data that Synthea requires is not public in Canada, so they didn't feel like they were able to contribute it back to the main repository (sadly).
Joel Francis (Jan 10 2019 at 17:26):
Joel, there is at least one other team that has successfully generated Synthea data for Canada. I believe they generated the province of Manitoba. They captured their lessons learned here: https://github.com/synthetichealth/synthea/wiki/Other-Areas---Canada
@Jason Walonoski Thanks for the response. Another questions I have is, are the FHIR artifacts produced customizeable? Like can I change what artifacts I get out of the generator?
Jason Walonoski (Jan 11 2019 at 23:22):
In terms of FHIR, only a little. You can alter some FHIR export settings in the synthea.properties file:
exporter.fhir.export = false exporter.fhir_r4.export = true exporter.fhir_dstu2.export = false exporter.fhir.use_shr_extensions = false exporter.fhir.transaction_bundle = true exporter.fhir.bulk_data = false exporter.hospital.fhir.export = false exporter.hospital.fhir_r4.export = true exporter.hospital.fhir_dstu2.export = false exporter.practitioner.fhir.export = false exporter.practitioner.fhir_r4.export = true exporter.practitioner.fhir_dstu2.export = false
Jason Walonoski (Jan 11 2019 at 23:22):
You can also change how many years of data are exported:
exporter.years_of_history = 10
Jason Walonoski (Jan 11 2019 at 23:27):
Also, for anyone at the connectathon this weekend in San Antonio, I updated Synthea today for R4 (v4.0.0) in case anyone wants to generate and use synthetic records for the latest R4 version. I don't have sample data for download, but it is pretty easy to get started: https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running
Joel Francis (Jan 12 2019 at 14:29):
Thanks @Jason Walonoski . Lastly, is there anything in particular about the license for use of the generator?
Thanks again!
John Silva (Jan 12 2019 at 15:45):
@Jason Walonoski - I remember talking with you about this back at FHIR DevDays in Boston last summer. I had asked about datasets for neonates. Have you added any of those datasets to Synthea?
Michael O'Keefe (Jan 12 2019 at 16:42):
@Joel Francis The Synthea project is licensed under the Apache 2.0 License
Michael O'Keefe (Jan 12 2019 at 16:42):
Which means you can use it for any purpose, including commercial purposes
Michael O'Keefe (Jan 12 2019 at 16:44):
As long as it follows the requirements here: https://github.com/synthetichealth/synthea/blob/master/LICENSE
Michael O'Keefe (Jan 12 2019 at 16:45):
If you're at the Connectathon and have questions about Synthea, feel free to come find me--I'm at the Clinical Reasoning table
Joel Francis (Jan 12 2019 at 17:00):
Thanks @Michael O'Keefe. I will walk over and say hi.
Joel Francis (Jan 12 2019 at 17:28):
@Joel Francis The Synthea project is licensed under the Apache 2.0 License
@Michael O'Keefe , Json mentioned that a project from Canada contributed to the https://github.com/synthetichealth/synthea/wiki/Other-Areas---Canada, would you happen to know which project?
Michael O'Keefe (Jan 12 2019 at 17:33):
@Joel Francis Unfortunately I don't know which project that was.
Joel Francis (Jan 12 2019 at 21:01):
@Joel Francis Unfortunately I don't know which project that was.
thanks @Michael O'Keefe
Elano Machado (Jan 15 2019 at 13:12):
@Jason Walonoski , thanks for your tips on how to run/configure synthea. This software is spectacular!
Jon Lee (Mar 27 2019 at 18:34):
Hi,
Is it possible to generate data to support US CORE? This is great btw!!
Jason Walonoski (Mar 28 2019 at 17:48):
While it doesn't export resources with Resource.meta.profile filled with US Core or Argonaut profiles, the data that Synthea generates should be compliant/valid.
Eric Haas (Apr 05 2019 at 00:33):
The documentation for configuration does not mention R4 is that the new default?
Eric Haas (Apr 05 2019 at 03:08):
(deleted)
Jason Walonoski (Apr 05 2019 at 16:41):
Yes, Synthea now outputs R4 as default. I made that change a day or two ago.
Tien Thai (Aug 27 2020 at 13:59):
I have generated a number of synthetic patients using Synthea application but none of them meets the Inclusion criteria defined in my CDS artifact. I am looking for a way to customize synthetic patients to purposely make them meet the Inclusions, sub-populations, etc. criteria but not sure if that is possible. Can I just modify those synthetic patients?
Additionally, I am looking to see how MedicationStatement is being defined in those synthetic patients but could not find such patients. The only resourceType was used in those patients is MedicationRequest. Can you please provide a testing patient that uses MedicationStatement resourceType? Many thanks for your help.
Regards,
TT
Jason Walonoski (Aug 28 2020 at 14:44):
I have generated a number of synthetic patients using Synthea application but none of them meets the Inclusion criteria defined in my CDS artifact.
Synthea covers a lot of clinical concepts, but not everything. There is a fork of Synthea modified for certain eCQMs that might help. See https://github.com/projecttacoma/synthea.
I am looking for a way to customize synthetic patients to purposely make them meet the Inclusions, sub-populations, etc. criteria but not sure if that is possible.
You can make new modules that add the data you need using the Module Builder https://synthetichealth.github.io/module-builder/
Documentation is spread around the Synthea wiki, but you can start here https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework
Can I just modify those synthetic patients?
Absolutely!
Additionally, I am looking to see how MedicationStatement is being defined in those synthetic patients but could not find such patients.
The FHIR R4 exporter in Synthea only supports Medication, MedicationRequest, and MedicationAdministration.
Ming D. (Sep 23 2020 at 14:08):
I'm trying to add Ontario, Canada to patient location list. Is "resources/geography/zipcodes.csv" the only place I need to add to, as a minimal requirement?
Jason Walonoski (Sep 23 2020 at 15:48):
No, you need to also have an entry in demographics.csv. You'll also need provider locations otherwise you'll get NullPointerExceptions when there is nowhere for you patients to receive care. See https://github.com/synthetichealth/synthea/wiki/Other-Areas
Santosh Pai (Apr 21 2021 at 23:48):
Hi - trying to set up a developer portal with synthetic FHIR data.
Heard about synthea.. if anybody has tips how to use it would be appreciated.
Eg how to generate data, create relationships between resources , load into a FHIR server.
Thanks
Santosh
Lloyd McKenzie (Apr 22 2021 at 00:30):
@Jason Walonoski
Richard Stanley (Apr 22 2021 at 13:34):
Hi @Santosh Pai Definitely check out the Wiki. It helps a lot and answers many questions. https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running
Santosh Pai (Apr 26 2021 at 14:54):
Thanks Richard. Will do
Richard Stanley (Apr 27 2021 at 04:55):
Happy to help. Note that Synthea by default generates fake patients for the United States. This doesn't fit my particular use cases, so I'm looking into how to generate for 'Other Areas' which is also explained in the wiki and you can check out https://github.com/synthetichealth/synthea-international for European countries.
Jason Walonoski (May 12 2021 at 21:27):
For all of you Canadians, I finally got around to creating Synthea configurations files for Canada (still working on them). Here is a sample of the results: https://storage.googleapis.com/synthea-public/synthetic_canadians_fhir.12may2021.zip
Last updated: Apr 12 2022 at 19:14 UTC
