Stream: genomics
Topic: Connectathon 27
Jamie Jones (Mar 23 2021 at 18:15):
Hi folks--Have a look at the track page at https://confluence.hl7.org/display/FHIR/2021-05+Clinical+Genomics! So far we've got one scenario focused on $find-subject-variants mentioned on yesterday's call, and I've added another scenario for exploring different uses of Grouper -- should be a good introductory scenario as it involves generating reports and navigating results coming from different types of tests. As always, feedback is welcome!
Bret H (Apr 01 2021 at 13:24):
will 'derived from' and the other links be used to compare in querying with grouper? There's been some good questions on processing incoming reports. The 'derived from' and other reference links would still be used in organizing content with context, right?
Bret H (Apr 01 2021 at 13:27):
(deleted)
Jamie Jones (May 05 2021 at 22:24):
Reminder for Kickoff/orientation for this track tomorrow, 2-3p ET - details in WHOVA
Bob Dolin (May 14 2021 at 00:45):
@Jamie Jones I've placed the FHIR Genomics Operations resources on a google drive. Description of the files, etc, is here: https://docs.google.com/document/d/1kh0xtX0KrbobfFPO4d4rEJpbMqoB-RHCMggO95DnpCM/edit
Jamie Jones (May 14 2021 at 00:47):
Great, thanks!
Bob Dolin (May 14 2021 at 00:58):
oh, sorry @Jamie Jones forgot to mention that I revised the postman collection (to include more examples)
May Terry (May 17 2021 at 14:37):
@Jamie Jones - my Whova setting on local time shows the Clinical Genomics Touchpoint at 12p ET (4-5p GMT) rather than 2-3p ET. Can you confirm?
Jamie Jones said:
Reminder for Kickoff/orientation for this track tomorrow, 2-3p ET - details in WHOVA
Jamie Jones (May 17 2021 at 14:39):
Today we have one at 12p ET, that's correct. There was a separate live kickoff/preview session back on May 06. The recording should be available in Whova, but we will dig into the scenarios today as well so no worries :)
Bob Dolin (May 17 2021 at 17:10):
@Patrick Werner Here is an article on SPDI: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7523648/
May Terry (May 17 2021 at 17:26):
Duh...5 minutes after we had this discussion on preserving the FHIR Ids in examples, I figured out how to do this in the logica sandbox using Postman. PUT https://api.logicahealth.org/<sandbox id>/open/<FHIR resource of your example>/<the fhir id in your example>. :upside_down:
Bob Dolin (May 17 2021 at 20:55):
@Jamie Jones Hi Jamie, should we set up some time tomorrow to go over some of the Operations issues? (I
Bob Dolin (May 17 2021 at 20:55):
ve tried to summarize them on the google sheet)
Jamie Jones (May 17 2021 at 20:57):
Yes! I'll review and have a pass this afternoon checking the different logical cases
Patrick Werner (May 18 2021 at 16:59):
we fixed our genomic report viewer:
Here is the link to the MOLIT report viewer: https://molit.eu/genomics-reporting-viewer/
Patrick Werner (May 18 2021 at 16:59):
source code: https://github.com/molit-institute/genomics-reporting-viewer
Patrick Werner (May 18 2021 at 17:00):
some columns are not 100% compatible with the current IG
Patrick Werner (May 18 2021 at 17:00):
Will create a branch to fix these tomorrow.
Patrick Werner (May 18 2021 at 17:00):
You have to provide a FHIR Endpoint and a ID of a genomics report.
Jamie Jones (May 18 2021 at 17:04):
endpoint including resource type? or base url
Patrick Werner (May 18 2021 at 17:05):
left input: baseUrl of a FHIR Server, right input: id of the DiagnosticReport
Jamie Jones (May 19 2021 at 19:49):
Reminder for connectathon folks to add final items to the last 2 slides for the report out. Thanks all!
Bob Dolin (May 21 2021 at 21:44):
@Jamie Jones Thanks again for a very productive connectathon. I think you now have me convinced to move away from DiagnosticReport in Operations response :-)
Last updated: Apr 12 2022 at 19:14 UTC
