Stream: omop + fhir
Topic: FHIR + OMOP Oncology
May Terry (Nov 12 2021 at 15:27):
Hi all,
Based on the Doodle Poll, our next FHIR to OMOP Oncology meeting will be this coming Thursday, November 18, from 12-1p ET. The meeting invite is below:
https://teams.microsoft.com/l/meetup-join/19%3ameeting_ZjAwZjQ4NGYtZTljZC00NzM5LTk3NTMtMGQxYzI0MzZhZWMz%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
For our call, we will be continuing the structural and semantic gap analysis for CancerPatient and PrimaryCancerCondition and next steps for creating a simple prototype to convert CancerPatient and PrimaryCancerCondition mCODE FHIR instances to OMOP elements to demonstrate capability.
Please join us if you can!
May Terry said:
Hi all - We have setup a Doodle Poll for our next meeting re: FHIR to OMOP Oncology alignment. If interested, please fill out this Doodle Poll and add your preference for a date/time by Thursday, Nov 11: https://doodle.com/poll/d577kwwtk3wyapxs/
I will then choose what the majority decides and post the invite and Teams details to this thread by the end of this week. Thanks!
May Terry (Nov 18 2021 at 20:59):
Thanks all who attended today's FHIR to OMOP Oncology WG work session.
Meeting minutes and presented slides are available here: https://confluence.hl7.org/display/OOF/2021-11-18+-+Oncology+Use+Case+WG
We have established a recurring Thursday bi-weekly meeting at 12p ET.
Our next meeting is on December 2, 2021 at 12p ET.
Join us as we further push the envelope in standardizing the exchange cancer data between our communities! :smile:
May Terry (Dec 01 2021 at 19:45):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is on December 2, 2021 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Join us as we further push the envelope in standardizing the exchange cancer data between our communities! :smile:
May Terry (Dec 16 2021 at 14:41):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is today, December 16, 2021 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Join us as we further push the envelope in standardizing the exchange cancer data between our communities! :smile:
May Terry (Dec 16 2021 at 19:02):
Thanks all who attended today's FHIR+OMOP Oncology meeting on December 16 at 12p.
It was a very productive discussion on example mappings for core FHIR value sets (condition-clinical, verificationStatus) and the implications for the other FHIR-OMOP use case sub-groups.
Meeting minutes are here: https://confluence.hl7.org/display/OOF/2021-12-16+-+Oncology+Use+Case+WG
Our next meeting is on January 6th, 2022 at 12p ET.
May Terry (Jan 05 2022 at 18:48):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, January 6, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Join us as we further push the envelope in standardizing the exchange cancer data between our communities! :smile:
May Terry (Jan 07 2022 at 05:01):
Thanks all who attended today's FHIR-to-OMOP Oncology meeting. @Qi Yang created a first pass mapping from mCODE to OMOP CDM (spreadsheet), presenting a walkthrough of the approach. The team then did a closer review of the mCODE CancerPatient to OMOP. Meeting minutes are here: https://confluence.hl7.org/display/OOF/2022-01-06+-+Oncology+Use+Case+WG
Our next meeting is on Thursday, January 13, 2022 at 12p ET where we plan on continuing the detailed review of the mCODE to OMOP first pass mapping.
May Terry (Jan 13 2022 at 02:29):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, January 13, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
For our agenda, we plan on continuing the detailed review of @Qi Yang 's mCODE to OMOP first pass mapping.
May Terry (Jan 13 2022 at 18:33):
Thanks all who attended today's FHIR-to-OMOP Oncology meeting where we are now doing a deeper dive analysis of @Qi Yang's first pass mapping from mCODE to OMOP CDM spreadsheet. We're working through identifying and triaging structural and semantic gaps as well as determining a process for tracking these gaps and escalating them to the appropriate groups as needed.
Meeting minutes are here: https://confluence.hl7.org/display/OOF/2022-01-13+-+Oncology+Use+Case+WG.
Because our meetings are getting deeper into element/vocab analysis, we are moving back to a weekly meeting cadence for now.
Our next FHIR+OMOP Oncology meeting is on Thursday, January 20, 2022 at 12p ET.
May Terry (Jan 20 2022 at 04:36):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, January 20, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
For our agenda, we plan on continuing the detailed review of comorbid conditions in @Qi Yang 's mCODE to OMOP first pass mapping spreadsheet.
May Terry (Jan 20 2022 at 18:34):
Thanks all who attended today's FHIR-to-OMOP Oncology meeting where we are continuing with our deeper dive analysis of @Qi Yang's first pass mapping from mCODE to OMOP CDM spreadsheet. We're working through identifying and triaging structural and semantic gaps as well as determining a process for tracking these gaps and escalating them to the appropriate groups as needed.
Meeting minutes are here: https://confluence.hl7.org/display/OOF/2022-01-20+-+Oncology+Use+Case+Sub-group.
Our next FHIR+OMOP Oncology meeting is on Thursday, January 27, 2022 at 12p ET.
Davera Gabriel (Jan 21 2022 at 23:27):
May Terry said:
Thanks all who attended today's FHIR-to-OMOP Oncology meeting where we are continuing with our deeper dive analysis of @Qi Yang's first pass mapping from mCODE to OMOP CDM spreadsheet. We're working through identifying and triaging structural and semantic gaps as well as determining a process for tracking these gaps and escalating them to the appropriate groups as needed.
Meeting minutes are here: https://confluence.hl7.org/display/OOF/2022-01-20+-+Oncology+Use+Case+Sub-group.
Our next FHIR+OMOP Oncology meeting is on Thursday, January 27, 2022 at 12p ET.
Hello @May Terry
What version of the OMOP CDM are you using to support this work? I looked at your working artifacts and must have missed it
Many thanks!
Davera
May Terry (Jan 26 2022 at 16:40):
Originally it was going to be 5.4 but we went back to 5.3 since most of the OHDSI tooling and implementations today support that version.
Davera Gabriel said:
Hello @**May Terry|192302**
What version of the OMOP CDM are you using to support this work? I looked at your working artifacts and must have missed it
Many thanks!
Davera
````
May Terry (Jan 26 2022 at 16:44):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, January 27, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
For our agenda, we plan on continuing the detailed review of @Qi Yang 's mCODE to OMOP first pass mapping spreadsheet. We'll also be revisiting timelines and potential sandbox environments and GitHub repos for creating and sharing prototype ETLs.
Davera Gabriel (Jan 28 2022 at 21:42):
May Terry said:
Originally it was going to be 5.4 but we went back to 5.3 since most of the OHDSI tooling and implementations today support that version.
Davera Gabriel said:
Hello @**May Terry|192302** What version of the OMOP CDM are you using to support this work? I looked at your working artifacts and must have missed it Many thanks! Davera ```` ````` Great news / good thinking! It was a revelation when we started N3C to learn why 5.3.1 was the best choice... because most of the OHDSI community persisted on this version due to the Atlas stack alignment there.
May Terry (Jan 31 2022 at 16:11):
Thanks all who attended last Thursday's FHIR-to-OMOP Oncology meeting.
Meeting minutes are here: https://confluence.hl7.org/display/OOF/2022-01-27+-+Oncology+Use+Case+Sub-Group.
Our next FHIR+OMOP Oncology meeting is on Thursday, February 3, 2022 at 12p ET.
May Terry (Feb 03 2022 at 15:43):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is today, February 3, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- continuing the detailed review of mCODE to OMOP first pass mapping and some updates migrating these mappings to the recently published mCODE STU2 FHIR IG.
- developing sandbox environments and GitHub repos for creating and sharing prototype ETLs
May Terry (Feb 10 2022 at 15:53):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is today, February 10, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- continuing the detailed review of mCODE to OMOP first pass mappings - completion of how to handle PrimaryCancerCondition to OMOP CDM Oncology
- developing sandbox environments and GitHub repos for creating and sharing prototype ETLs
Mike Hamidi (Feb 10 2022 at 17:17):
Apologies, I will miss this meeting. I'm also OOO next week.
May Terry (Feb 10 2022 at 19:22):
Thanks to all who attended and participated in today's engaging discussion on mapping PrimaryCancerCondition, preliminary considerations in genomics element mappings, and approaches to specifying terminology mappings in different ways (FHIR ConceptMap, flat-crosswalks, by reference).
Meeting minutes are here. Our next meeting will be on Thursday, February 17, 2022 at 12p ET.
May Terry (Feb 17 2022 at 15:10):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is today, February 17, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- reviewing different mapping options for PrimaryCancerCondition topology and morphology
- reviewing terminology binding example that shows "map by reference" to CaDSR
- planning for May 2022 FHIR Connectathon
May Terry (Feb 18 2022 at 16:49):
Thanks to all who attended and participated in a great discussion and achieving consensus on PrimaryCancerCondition mapping options as well as the interest in participating in a FHIR-OMOP Oncology Use Case track at the upcoming May 2022 FHIR Connectathon.
Meeting minutes are here.
Our next meeting will be on Thursday, February 24, 2022 at 12p ET where we will be going over Connectathon Track Use Case Scenarios, connectathon environment, and the scope of mCODE profiles that will be tested in its conversion to OMOP CDM.
May Terry (Feb 23 2022 at 18:40):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, February 24, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- reviewing terminology binding example that shows "map by reference" to CaDSR
- May 2022 FHIR Connectathon planning
- Review mapping of TumorMarkerTest, CancerRelatedMedicationAdministration.
May Terry (Feb 24 2022 at 20:05):
Thanks to all who attended and participated today's meeting. We had great and enlightening discussion on mapping the GenomicVariant gene-studied component to OMOP and identified several changes that need to be addressed with the OMOP Genomics Sub-group. Many thanks to @Qi Yang who provided a great introduction to the design of the OMOP genomic concept hierarchy so we can better understand the alignment with the HL7 Genomics Working Group design. We also reviewed the FHIR-OMOP Oncology Use Case track proposal scenarios for the upcoming May 2022 FHIR Connectathon.
Meeting minutes are here: https://confluence.hl7.org/display/OOF/2022-02-24+-+Oncology+Use+Case+Sub-Group?flashId=834486629
Our next meeting will be on Thursday, March 3, 2022 at 12p ET where we will be continuing our mapping review of GenomicVariant to OMOP as well as FHIR Connectathon planning.
May Terry (Mar 02 2022 at 21:22):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, March 3, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- continuing our mapping review of GenomicVariant to OMOP CDM
- FHIR Connectathon planning
May Terry (Mar 03 2022 at 19:37):
Thanks to all who attended and participated today's meeting where we had a really great discussion on Connectathon Planning details as well as a Python ETL demo of mCODE CancerPatient to OMOP CDM PERSON.
Meeting minutes and action items are here: https://confluence.hl7.org/display/OOF/2022-03-03+-+Oncology+Use+Case+Sub-Group
Our next meeting will be on Thursday, March 10, 2022 at 12p ET where we will be reviewing the first-pass scope of profiles and elements for the FHIR Connectathon as well as continuing our mapping review of GenomicVariant to OMOP.
May Terry (Mar 09 2022 at 18:18):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, March 10, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- FHIR Connectathon planning - review of scoped profiles/elements
- mapping review of GenomicVariant to OMOP CDM
May Terry (Mar 16 2022 at 19:08):
Quick note that our regularly scheduled FHIR to OMOP Oncology meeting scheduled for March 17, 2022 is cancelled because I am at HIMSS 22. Our next meeting is Thursday, March 24, 2022 at 12p ET where we will be discussing FHIR Connectathon Planning (including some great updates on the test environment and securing an OMOP CDM database environment) and the mapping of mCODE genomics variant to OMOP.
May Terry (Mar 23 2022 at 13:26):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, March 24, 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- FHIR Connectathon planning - update on the track test environment and timelines for availability prior to the Connectathon event.
- mapping review of GenomicVariant to OMOP CDM - I did a first pass mapping for some of the variant components with considerations and potential issues with how some of the genomic codes are handled in OMOP.
May Terry (Mar 30 2022 at 17:26):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, March 31, 2022 at 12p ET where we will be focusing first on the mCODE GenomicVariant and CancerRelatedMedicationAdministration mappings to OMOP CDM.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- mapping review of GenomicVariant to OMOP CDM - I did a first pass mapping for some of the variant components with considerations and potential issues with how some of the genomic codes are handled in OMOP.
- mapping review of CancerRelatedMedicationAdministration to OMOP CDM.
- (if time remaining) FHIR Connectathon planning - test environment setup.
May Terry (Apr 06 2022 at 15:09):
Just a quick reminder that our next FHIR+OMOP Oncology meeting is tomorrow, April 7 2022 at 12p ET.
The meeting invite is here: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MGVhOTJkNTctMWNkMS00MDQ1LTg5YzItNmMyZWMzYTAwZTIy%40thread.v2/0?context=%7b%22Tid%22%3a%22c620dc48-1d50-4952-8b39-df4d54d74d82%22%2c%22Oid%22%3a%22912e5167-1db2-4628-b366-47b76d2062f8%22%7d
Agenda items include:
- FHIR Connectathon planning - test environment update.
- mapping review of CancerRelatedMedicationAdministration to OMOP CDM.
- (if time remaining) follow-up discussion GenomicVariant to OMOP CDM.
Last updated: Apr 12 2022 at 19:14 UTC
