Stream: genomics
Topic: January 2021 Virtual WGM thread
Jamie Jones (Jan 25 2021 at 17:33):
Hi folks, here are some links for the WGM this week:
Confluence Agenda: https://confluence.hl7.org/display/CGW/2021-01+CG+WGM+Agenda+-+Virtual
Attendance sign-in (please "check-in" once then update for later sessions) : https://confluence.hl7.org/display/CGW/2021-01+CG+WGM+Attendance
Minutes (updated live during sessions) : https://confluence.hl7.org/display/CGW/2021-01+CG+WGM+Minutes
Whova links -- Filter by tracks for "Clin Gen" on the top left of agenda page after you've signed in to https://whova.com/portal/webapp/jwgm_202101/Agenda. Note that times default to PST.
As always, feel free to reach out here or on the listserv if there are any questions. Hope to see you all soon!
Kevin Power (Jan 25 2021 at 19:03):
If you encounter any issues, please email WGMHelpDesk@HL7.org
Kevin Power (Jan 25 2021 at 19:03):
Or, ask here and we can try to help.
Bret H (Jan 25 2021 at 19:39):
nice comment from @Nephi Walton Two different workflows. Population based approach to genomics. Patient based approach to genomics.
Bret H (Jan 25 2021 at 19:43):
@Kevin Power with work presented. I wonder about the data representation within Cerner? is each field a separate variable in an unlinked model? Or would it be conceptually like a table for each test type described?
Kevin Power (Jan 25 2021 at 19:51):
@Bret H -- Current implementation in the Cerner API has distinct attributes. But not a ‘table by test type’, more a ‘variant’ and ‘implication’ table (not really, but conceptually).
Bret H (Jan 25 2021 at 19:51):
Thanks. seems like a good approach.
Bret H (Jan 25 2021 at 19:57):
@Rachel Kutner with error handling - or rather looking for completion. There is a mechanism in FHIR where conformance to a profile is used for error checking. any thoughts on that?
May Terry (Jan 25 2021 at 23:00):
quick question - which CG Reporting IG profile/element represents clinical significance?
Jamie Jones (Jan 25 2021 at 23:04):
Clinsig is on diagnostic implication so folks can point to a relatedArtifact
Bret H (Jan 26 2021 at 13:08):
is the Q0 on?
Kevin Power (Jan 26 2021 at 13:09):
In one hour :smile:
Kevin Power (Jan 26 2021 at 13:09):
sorry, 'TWO' hours
Bret H (Jan 26 2021 at 13:11):
Tuesday Jan 26 7:00 AM - 8:30 AM (PDT) (UTC-8)
Q0
S4G (short update): Bob F and Tracy Okubo
mCode (May T) (may not need full hour, derive from CG)
may need supplemental genomics guide for mCode
work through process of git, branch, edit FSH, develop examples - demo? Best practices of workflow (May T)
How to best summarize what was changed?
Bret H (Jan 26 2021 at 13:11):
Got it!
Bret H (Jan 26 2021 at 15:50):
in an oncology tumor genetic test would a change that is not cancer causing be considered pathogenic? what if the variant causes a truncation in a copy of a gene but the gene has other intact copies that resolve into a molecular phenotype which is 'normal'? Clearly the terms pathogenic and benign need more context to understand at what level the term applies. some use the term classification for the base level (genetic variant in the abstract sense - not associated with disease or patient) call...
Kevin Power (Jan 26 2021 at 15:52):
@Bret H -- Did you mean to ask this question on a different thread, or maybe in the chat of the current session?
Kevin Power (Jan 26 2021 at 18:55):
Hey to everyone in #genomics -- For our Tuesday Q2 joint with O&O, please join via the O&O session link.
Arthur Hermann (Jan 26 2021 at 19:06):
Can you please provide link to O&O session? i don't see it anywhere
Kevin Power (Jan 26 2021 at 19:06):
There is currently some mix-ups. Please hold :smile:
Patrick Werner (Jan 26 2021 at 19:09):
https://hl7-org.zoom.us/j/2371347432?pwd=T1BLOG4zQWxzVFdROUdqNGs2VHpjZz09#success
Patrick Werner (Jan 26 2021 at 19:09):
Its live again
Patrick Werner (Jan 26 2021 at 19:09):
this is the direct zoom link
Jamie Jones (Jan 26 2021 at 19:10):
that is not the link i have
Kevin Power (Jan 26 2021 at 19:10):
This seemed to work for me :smile:
Patrick Werner (Jan 26 2021 at 19:11):
its the link that works... :smile:
Kim Peifer (Jan 26 2021 at 19:11):
ditto
Kevin Power (Jan 26 2021 at 19:12):
I still don't see the Clin Gen for Q2 in Whova, but that Zoom link got me to the right place. Seemingly.
Patrick Werner (Jan 26 2021 at 19:12):
its listed as O&O call
Jamie Jones (Jan 26 2021 at 19:13):
link is good, starting in now
Arthur Hermann (Jan 26 2021 at 20:36):
Are we able to find and listen to the recordings of the WGMs? I don't see links in notes.. can cany tell me where they might be?
Jamie Jones (Jan 26 2021 at 20:55):
I think information will be provided afterwards, likely with info in an email to participants. We will update here with any extra info if it seems needed.
Kevin Power (Jan 26 2021 at 21:15):
The recordings from yesterday are linked in Whova. I think the ones from today will be linked by tomorrow.
May Terry (Jan 27 2021 at 15:17):
Attached is the mCODE genomics update from Tuesday's Q0 session: mCODE-Genomics-Update_HL7WGM_20210126.pptx
Kevin Power (Jan 27 2021 at 20:58):
For anyone attending the joint with FHIR-I, please join via the FHIR-I session (NOT the Clin Gen session)
Arthur Hermann (Jan 27 2021 at 21:05):
do you have link for this meeting?
Kevin Power (Jan 27 2021 at 21:06):
https://hl7-org.zoom.us/j/7400566890?pwd=VVJUOHVUczc3L3FWUlBsMm1hMTQvZz09
Kevin Power (Jan 27 2021 at 22:26):
May Terry said:
Attached is the mCODE genomics update from Tuesday's Q0 session: mCODE-Genomics-Update_HL7WGM_20210126.pptx
@May Terry - I know you didn't really cover it fully, but would you mind sharing your PPT for the FSH / Authoring Tools discussion?
May Terry (Jan 28 2021 at 00:48):
if it's all well-and-good @Kevin Power , I'd rather present the slides before sharing. I didn't get very far since the last preso went significantly overtime and I'd have to convert a number of them to "slideument" material. Happy to reschedule to when I can present this again at a future meeting.
Kevin Power (Jan 28 2021 at 01:06):
Fine by me - if you don't mind, could you close the task in the notes, and add that text to the notes?
Rachel Kutner (Jan 28 2021 at 14:54):
@Bret H (from a coworker who knows more about this:) Conformance to the profile is necessary but not sufficient for semantic interoperability. Patient, specimen, and order IDs, catalog IDs, references to knowledgebases -- all things thing point to entities outside of the payload itself. In the results interface ecosystem that's been built up over decades around v2, there are mechanisms for queuing errors, acknowledgements in both directions, resubmission capabilities, etc. This is all to some extent being rebuilt around FHIR and there's no FHIR-inherent way of doing it.
Bret H (Jan 28 2021 at 14:59):
You do not get a guarantee of semantic interoperability with V2 either. FHIR has more potential than V2. @Rachel Kutner my point was around structure and use. And yes, one can argue that the possibility is there to check the syntax of the message in FHIR as well as it is done in V2. It is a sunken cost argument, if you argue that V2 is a choice because it is. There's no technical limitation to building tools to check FHIR syntax. Conformance is a nice in-built feature. Consider an IG. If I send a system a FHIR payload that conforms to an IG, then the system which knows the IG can handle the data and structure appropriately. A well done CapabilityStatement (with associated IGs) includes rules around the values for each element and presence/absence as well as logic. The CapabilityStatement is the future. The CapabilityStatement sits inside a server as part of the conformance module. It can/should be a computable statement of what the server 'knows' and expects. An IG is a set of rules that can be computed. Folks are still getting into FHIR for sure. But it has better opportunity for explicit, computable interoperability than V2 - only because the lessons of V2 have been learned (as well as CDAs).
Bret H (Jan 28 2021 at 15:06):
but don't take my word for it, start here: https://www.hl7.org/fhir/conformance-module.html.
Bret H (Jan 28 2021 at 15:16):
A lot of the accessories built around V2 are not a product of the spec but a product of use. No denying they exist. My comments are intended to stimulate investigation into how the conformance module (statement and use of IGs) enable a FHIR server to accomplish some pretty neat features. The FHIR spec does tell a system what to expect as a response if a FHIR Server is unhappy with the payload, the spec also tells a FHIR server what it can send to tell a system about the status of a payload. Take a deep look into the spec, it has a lot of great goodies in it.
Bret H (Jan 28 2021 at 15:22):
If your development team is developing a FHIR server I hope they are familiar with the capabilityStatement, terminology servers etc...
Last updated: Apr 12 2022 at 19:14 UTC
