Stream: genomics/committers
Topic: Planning - Week of Nov 12-16 - LAST WEEK BEFORE CUTOFF
Kevin Power (Nov 09 2018 at 22:50):
Well, we are down to one week left before the cutoff. From my query now, I still see 26 pending changes. I will have some time next week, but likely not near enough to get all of these done, plus ensuring we get the ballot reconcillation spreadsheet done. How about others? @James Jones @Patrick Werner @ Bob Milius (who still has some trackers assigned to generate new and enhance some current examples).
Bob Milius (Nov 12 2018 at 18:45):
I'll have the HLA examples and narrative up soon. What's the status of IG publisher? I understand the build happens okay locally but there are errors on the server with examples. Is that still occurring?
Kevin Power (Nov 12 2018 at 18:55):
It is still failing, but Grahame put up another fix (I think), so I will try again soon.
Kevin Power (Nov 12 2018 at 18:56):
But you are still free to push up changes after building and ensuring it looks good locally.
Kevin Power (Nov 12 2018 at 19:12):
FYI - Still getting errors during the cloud build, but the local build is fine. And to be clear, it is no longer about the examples. Follow along in the #IG creation stream to see more detail.
Patrick Werner (Nov 13 2018 at 11:36):
I'm back from vacation, on my way to the FHIR DevDays Amsterdam
Patrick Werner (Nov 13 2018 at 11:37):
i can work on open trackers, how can i support with the reconcilliation spreadsheet?
Kevin Power (Nov 13 2018 at 12:23):
Thanks Patrick. I will take care of the spreadsheet
Kevin Power (Nov 13 2018 at 12:30):
The IG is building again!
Jamie Jones (Nov 13 2018 at 15:37):
There was confusion on call last week about what the final proposal for GF#16175 and GF#16177 (levels of evidence) are, has there been further discussion on these since then?
Kevin Power (Nov 13 2018 at 15:38):
I think I responded to @Bret H on those, but I haven't gotten a response from him yet?
Kevin Power (Nov 13 2018 at 15:41):
But it is possible I didn't.
Bret H (Nov 13 2018 at 16:10):
But it is possible I didn't.
I think we are good. I am waiting to hear from Clem. However, for the value sets, for the IG we can create FHIR value set profiles. This would be faster than waiting for a change in LOINC. I have built value set FHIR profiles in the past.
Jamie Jones (Nov 13 2018 at 20:08):
I applied changes for 6 of those trackers from today, but 2 are using the "todo" LOINC code.
For GF#16467 I am not sure what we are supposed to do as it is flagged for FHIR IG Tooling/Pubs work group.
Kevin Power (Nov 13 2018 at 20:59):
For GF#16467 I am not sure what we are supposed to do as it is flagged for FHIR IG Tooling/Pubs work group.
I think we can ignore this one? If we can? This turns out to be a tooling fix, so ultimately up to Grahame.
Kevin Power (Nov 15 2018 at 03:13):
Current state of changes that still need to be made (note, the ones assigned to @Bret H are actually being driven by Clem (the LOINC requests):
ID Summary Assignee
16239 Need an Observation.code for DescribedVariant Bret Heale
16272 Revise answer list for Genotype Medication Efficacy Impact profile (LOINC 51961-1) Bret Heale
16180 Inherited Disease Pathogenicity - Must have mode-of-inheritance value set Bret Heale
16244 Need a LOINC for Coordinate System Bret Heale
16264 Modify dna-chg-type answer list Bret Heale
16513 need glossary James Jones
14319 define "VariantChange" ComponentGroup in the spec James Jones
14320 define "GenomicLocation" ComponentGroup in the spec James Jones
14322 define "AllelicState" ComponentGroup in the spec James Jones
14323 define "AminoAcidChange" ComponentGroup in the spec James Jones
16509 Tranplantation/HLA needs more complete narative Bob Milius
16194 revise example usage of HLA nomenclature code system Bob Milius
16508 deconstruct HLA example bundle Bob Milius
16876 Use of publically available external coding systems and autocomplete lookup tables - 2018-May Genomics #58 Nobody
16510 Need more examples Nobody
So @James Jones , @ Bob Milius , can @Patrick Werner or I help out with any of these? I will have some time Thursday and some time Friday.
Jamie Jones (Nov 15 2018 at 03:20):
Thanks for this, I had lost track of those component groups, can address that no problem. For the glossary, is there more we need to do for now than the definitions we put in the background section? If so we will probably have to defer it, I believe Bob Milius logged the tracker so would love his input.
Kevin Power (Nov 15 2018 at 03:31):
@ Bob Milius - Thoughts on the Glossary tracker?
Bob Milius (Nov 15 2018 at 15:33):
re Glossary Tracker: (GF#16513) The resolution says we agree, but need a formal proposal, which we don't have yet. I suggest we defer it. We have definitions for each element in the SDs, but they need to be more robust and unambiguous. Each SD should have a paragraph describing what it is and how it's used. eg. http://build.fhir.org/ig/HL7/genomics-reporting/obs-haplotype.html doesn't have anything describing haplotype. I think the CG group should have a glossary that's agnostic to the standard, so perhaps should be separate from IG but pointed to by the IG? Maybe developed by IM? Each term could be pointing to SO, or VMC, or some external definition when appropriate, with added considerations for CG, and the IG would describe considerations for FHIR . Maybe it starts out as part the IG, eg a separate artifact/static page, just labeled 'glossary', and later de-couple it from FHIR. But at this stage, maybe we can create a page with some of these comments on it and looking for input.
Kevin Power (Nov 15 2018 at 15:48):
To be honest, I am less interested in a formal definition, but agree that it is more likely to come out of the IM work. In the shorter term, I am much more interested in a computable definition, and guidance on how to use it. In general, the additional implementer guidance of "how and when to use what and where" needs some work.
Jamie Jones (Nov 15 2018 at 16:17):
What is the official procedure for deferring them at this point? I know on call we decided to defer a couple as well.
Kevin Power (Nov 15 2018 at 16:19):
I have already updated two from the Tuesday call. Since they were already approved, I copy/pasted the previous resolution and vote details into a comment, then updated with the new details from Tuesday, and marked the status as Deferred. For anything we won't get done by Sunday, we likely will want to do the same thing, perhaps tomorrow?
Kevin Power (Nov 15 2018 at 16:28):
So maybe we have a cutoff for work to be done on Trackers by EOD Friday. I can then generate/post the ballot reconciliation over the weekend?
Jamie Jones (Nov 16 2018 at 17:40):
For the component groups on described variant, there's also a spot down there that just says: "TODO: gene-studied, cytogenetic-location, dna-region-name" ... is this now covered by the region-studied profile? I guess the guidance for that could go here in the "Location" component group or on http://build.fhir.org/ig/HL7/genomics-reporting/sequencing.html. Thoughts?
Kevin Power (Nov 16 2018 at 17:42):
Actually, I think the "Location" component group is more about the location of the variant
Jamie Jones (Nov 16 2018 at 17:48):
okay I'm seeing the trackers have specific components they wanted listed in each section. Will ask about any that may need updating from when these were logged, thanks
Patrick Werner (Nov 16 2018 at 18:04):
i'm now on my way back from the FHIR DevDays. I only had time for one issue this week :unamused:
Jamie Jones (Nov 16 2018 at 19:38):
Alrighty, I am seeing 10 left with the "change required" status and only 1 (GF#16876) left unassigned
Patrick Werner (Nov 16 2018 at 22:38):
Alrighty, I am seeing 10 left with the "change required" status and only 1 (GF#16876) left unassigned
As the amount of work needed for this tracker is higher than estimated i tend to defer it. Only adding a HTML File of the LRI CodeSystems without defining the CodeSystem URIs for all of them isn't useful and probably misleading. I assigned the tracker to myself and will continue to work on it together with @Julian Sass .
Kevin Power (Nov 16 2018 at 22:41):
Thanks for the update Patrick.
Bret H (Nov 17 2018 at 00:30):
@Kevin Power you and Clem met. Yesterday. I'm waiting on Liz for changes to make. all set to put them into the FHIR spreadsheets and build. Should I wait for Liz or put in changes now?
Kevin Power (Nov 17 2018 at 00:54):
If you have made changes feel free to push them up. I have a feeling all Liz was going to tell you was to put something like change the TBD on the LOINC changes we are gonna request to TBD-REQUESTED
Bret H (Nov 17 2018 at 03:02):
and what about the component for coordinate system? I can put in a component with an exemplar set of values. it will be non-binding. I'll put it in the next couple of hours. It can always be removed.
Kevin Power (Nov 17 2018 at 03:27):
Yea you can put it in while we are waiting on the LOINC code
Bret H (Nov 17 2018 at 04:09):
wow , there's lots in them spreadsheets. two down. I'll be done soon and leave a note here after I've pushed.
Bret H (Nov 17 2018 at 04:56):
done locally...building....local build failed
Bret H (Nov 17 2018 at 05:18):
think I have the problem, one sec
Bret H (Nov 17 2018 at 06:33):
build locally successful - problem with github repo authentication. Sent email to @Kevin Power @Patrick Werner with FHIR build spreadsheet that had successful build. Can you guys push my changes in? Thanks.
Kevin Power (Nov 17 2018 at 13:07):
I will see if I can push it up in a little bit
Kevin Power (Nov 17 2018 at 13:47):
It has been pushed and built. Bret, do you want to QA the changes http://build.fhir.org/ig/HL7/genomics-reporting/index.html ?
Bret H (Nov 17 2018 at 15:08):
looking now
Bret H (Nov 17 2018 at 15:29):
looks good. Many thanks. Also, #16081 on PGx Transporter profile was put in by @James Jones
Bret H (Nov 17 2018 at 15:32):
note: I set coordinate system value set as extensible. I believe all variations that are used are represented but extensible leaves room for additional. note: I interpreted add guidance for #16272 Med Impact profile values to mean add guidance in the profile. I hope @Bob Dolin will review during the balloting process. THANK YOU ALL FOR YOUR HARD WORK!
Kevin Power (Nov 17 2018 at 16:02):
So everything looks good?
Last updated: Apr 12 2022 at 19:14 UTC
