Stream: genomics
Topic: Sep 2020 WGM Topics
Bob Milius (Aug 11 2020 at 15:28):
Placeholder for WGM topics
Kevin Power (Aug 11 2020 at 18:56):
Hope this is OK, but wanted to start this conversation by posting what was discussed on today's call (I missed the call, but this is from the notes)
May - continue discussion with Swapna with LOINC - need to contact for availability
Bob - look up old minutes to prioritize topics, summarize and email or post to zulip
Arthur - look at whole IG, examples, identify what needs to be updated
Patrick - interested in order entry, what does it mean to order a panel. Need examples. Need guidance.
Bob - need to provide specific guidance around ServiceRequst codes and DR codes.
Anand (Clinical Architecture) - wholehearted agreement in need for examples
focusing on variant right now
standard genetic test data
interested in retrospective reports
will provide examples of their needs
Arthur - need a session on IM at WGM and implications on the IG
May - revisit tooling, delve into IG authoring tool options
right now we're editing SDs
Kevin (from zulip) - I know the meeting is going on, but while I am on my conflict call, but for WGM topics, don't forget we can/should do a review of pending JIRAs. Discuss resolution, and perhaps even vote on some
Jamie - finish work on implication (current Jira tickets)
Arthur - be clear on which zulip stream to discuss this
Please add your ideas about WGM topics to this zulip stream
https://chat.fhir.org/#narrow/stream/179197-genomics/topic/Sep.202020.20WGM.20Topics
Bret - can we work through an example during one session?
Jamie - can put through an example of something that has been figured out
Bret - can we record the intro session?
Jamie - can create more slides for intro/teaching. We created some for DevDays
Patrick - need to update those slides
Jamie - have a session on mCode or another external effort?
Arthur - update on eMerge?
Jamie - Sync 4 Genes?
Arthur - review v2 LRI genetics examples - can we convert each to FHIR without losing information?
Jamie Jones (Aug 11 2020 at 19:31):
Adding to one point that came up further in the notes--we could go through intro slides covering the IG and some major use cases and examples for newcomers. We could build it out from materials we've presented at DevDays in the past and may even want to add a link to a slidedeck to the IG itself--the bulk data IG does this, though we may want to host it on confluence rather than somebody's google account
Jamie Jones (Aug 11 2020 at 19:33):
Also we still need to cover how our joint with O&O and FHIR-I are structured - who is hosting, is anything else happening in 'our room' during, and talking points
Arthur Hermann (Aug 27 2020 at 15:57):
This has been captured to some extent in previous notes, but I wanted to create a clear statement for an area that I feel is critical to prepare for the WGM and then discuss (BTW - sorry to have missed the last few Tuesday Meetings -I have had unavoidable conflicts - suddenly 8am my time - has become a very active time for important meetings).
I feel very strongly that we need to provide clear guidance on how to use the IG. One way to do this (and I would like to discuss others with the team if possible) is to ( Note: I am using the Patient resource as the example for all of these)
-
Within Content Pages; http://hl7.org/fhir/patient.html#maternity
-
Detailed Descriptions Pages http://hl7.org/fhir/patient-definitions.html
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An examples page where we should show the most common Lab Tests (Here are examples for Patient) http://hl7.org/fhir/patient-examples.html
Including --- Panel, ACMG Genes,PGx,Targeted gene such as Cystic Fibrosis, Carrier Screening, CDC-1, Somatic testing (Oncology Reports, Exome, WGS etc... --- of course, everyone should add to this list so that we get a complete set of what we feel are the most common use cases for your organization or what you know of the field.
Arthur Hermann (Sep 03 2020 at 19:08):
I created a Jira tracker for the item above - sorry, but don't have the # handy and I am not good at using Jira. Just noting that there is now a tracker items associated with above request/suggestion.
Kevin Power (Sep 03 2020 at 20:14):
@Arthur Hermann -- There is some help for JIRA here: https://confluence.hl7.org/pages/viewpage.action?pageId=11501600#c4472ec9-1ffa-4734-835d-ea12286e013e-31686915 (can't vouch for them, but might be worth a review)
Arthur Hermann (Sep 16 2020 at 16:01):
It appears that the first session we have scheduled overlaps with a portion of the plenary. Can someone verify if what I am seeing in my calendar is correct? Plenary is 6:45 to 9:30 PT and our session is 9:00 to 10:30 PT...
Kevin Power (Sep 16 2020 at 16:08):
You are correct @Arthur Hermann , I just noticed that this morning as well. Not sure where the disconnect was to be honest, but I don't think we are the only WG in this situation - there are many groups that have sessions with the same 30 minute overlap.
On the Plenary agenda the overlapped session is listed as "Closing Comments" - I would say I am OK with dropping off the Plenary and getting started with our CG session. What do others think?
Arthur Hermann (Sep 16 2020 at 16:47):
If it is only closing comments - then likely not a problem -- personally I have to be there if Walter Suarez (HL7 Chair) is giving those comments since he is now my manager :grinning_face_with_smiling_eyes:
Arthur Hermann (Sep 16 2020 at 16:49):
Sorry for second comment - all the more reason we will likely want to allow for "spill over" of the focus of this session (examples for IG) into the next WG session
Jamie Jones (Sep 17 2020 at 21:18):
I volunteered for chairing that first session, and think we can do some less formal introductions and WGM-procedural discussions based on whoever is in attendance at the 9am PT start time, expecting that some folks may be joining late as they review the schedules.
May Terry (Sep 21 2020 at 14:04):
Hi all! Sorry to request this again, but would it be possible to swap our mCODE update/Tooling discussion (Session 6) with the JIRA review (Session 5). i.e.: move this to Tuesday afternoon.
Reason is that the CIC scheduled a joint working session with the CIMI group on Wednesday morning to provide an mCODE update and review/block vote for mCODE STU1 JIRA issues. Because it's a joint session, it's harder to change on their side. Also, @Mark Kramer would like to be present for the Tooling discussion so he can address any questions regarding FHIR Shorthand/SUSHI.
Kevin Power (Sep 21 2020 at 14:11):
That is probably OK, but the WG can discuss in our first session (in about 2 hours from now)
Liz Amos (Sep 21 2020 at 14:22):
This is a dumb question... are we supposed to use the Whoova this to participate in the WGM? Or is there some special Zoom?
Jamie Jones (Sep 21 2020 at 14:23):
Both! We'll use Whova to access the special zoom :)
Arthur Hermann (Sep 21 2020 at 23:40):
Per our discussion today re: examples - I had forgotten - but I believe this example is showing a series of errors (unless I am misunderstanding it). Can we put this on the priority list of exmples to review? http://build.fhir.org/ig/HL7/genomics-reporting/DiagnosticReport-report-CYP2C19.json.html
May Terry (Sep 21 2020 at 23:46):
If you're referring to the "This Observation could not be resolved" error in <text /> then I think it could be because the IG publisher might not be supporting the rendering of contained resources in the generated narrative. That might not be necessarily be a problem with the actual coded part of the example but related to a limitation in the IG publisher.
Dora Walter (Sep 22 2020 at 12:31):
Is it possible to show a walk through via screensharing during WGM?
Kevin Power (Sep 22 2020 at 12:33):
A walk through of what exactly @Dora Walter ?
Kevin Power (Sep 22 2020 at 12:34):
And I will take a closer look at that example
Dora Walter (Sep 22 2020 at 12:36):
maybe it is me, but it is harder to understand someone problems without pictures oder screenshots of a problem.
Kevin Power (Sep 22 2020 at 12:45):
Ahh got ya. So you just mean see the example and look at the problems with it?
Arthur Hermann (Sep 22 2020 at 15:39):
Is there a section during our WGM during the Plenary where we can confirm that all of the Emerge issues have been responded to? If not, can we prioritize those issues? Perhaps this is work to do off-line then bring back to the working group. Emerge has an excellent list of these issues which can be found here: https://emerge-fhir-spec.readthedocs.io/en/latest/issues_and_resolutions.html
Kevin Power (Sep 22 2020 at 15:51):
We invited EMERGE to give an update at the WGM but they didn't take us up on the invite.
Kevin Power (Sep 22 2020 at 15:51):
There are still a few JIRAs pending from Mullai and Larry from EMERGE?
Kevin Power (Sep 23 2020 at 13:37):
@May Terry - Can we have the slides you presented yesterday?
Kevin Power (Sep 23 2020 at 13:37):
Would like to add them to the notes.
Kevin Power (Sep 23 2020 at 13:38):
@Bob Freimuth - Can we have the S4G slides you presented?
Kevin Power (Sep 23 2020 at 13:39):
@Grant Wood - Can we have a link the Pedigree mapping document you presented?
Patrick Werner (Sep 23 2020 at 13:42):
Liz already added her slides to the minutest. thanks @Liz Amos ! :thank_you:
Bob Freimuth (Sep 23 2020 at 13:45):
@Kevin Power Yup. I confirmed with ONC they are able to be shared. I'll upload somewhere.
May Terry (Sep 23 2020 at 15:28):
@Kevin Power - mCODE update and tooling slides posted to the Q6 minutes: https://confluence.hl7.org/pages/viewpage.action?pageId=90899714#CG202009WGMMinutes-Quarter3:14:00-15:30ET(Q6).
May Terry (Sep 23 2020 at 20:49):
@Kevin Power - follow-up to our knowledgebase discussion, here is the URL to the mCODE Knowledge base which we had created with support from Josh Procious, who initially created the space for us. https://confluence.hl7.org/display/COD/Knowledge+Base+-+mCODE
Grant Wood (Sep 23 2020 at 22:02):
https://docs.google.com/document/d/1UAtSLBEQ_7ePRLvDPRpoFpiXnl6VQEJXL2eQByEmfGY/edit?usp=sharing
Just a reminder to all that this is a GA4GH working document comments and
feedback ar welcome.
Grant
Kevin Power (Sep 23 2020 at 22:18):
@May Terry -- Here is the link to our IG in GitHub (in case you didn't already find it): https://github.com/HL7/genomics-reporting
Arthur Hermann (Sep 24 2020 at 21:50):
@Bob Freimuth did you post your slides? If so, can you clarify where?? Thanks so much.. it was a great presentation....
Kevin Power (Sep 24 2020 at 22:16):
@Bob Freimuth - In your case, we are looking for slides for both S4G and IM updates.
Bob Freimuth (Sep 25 2020 at 02:03):
Thanks for the reminder and your patience. Slides uploaded, links added to the minutes.
Last updated: Apr 12 2022 at 19:14 UTC
