Stream: genomics/committers
Topic: FHIR-32715 - Drug class should be supported
Kevin Power (Feb 01 2022 at 23:55):
I have applied the last of the approved JIRAs! I wanted to have other review this last one however, especially @Bret H and probably @Bob Dolin
http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-medication-assessed.html (new extension)
http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-therapeutic-implication.html (see the additional guidance under Figure 1).
http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-therapeutic-implication-definitions.html#Observation.extension:medication-assessed (review the details of using the extension)
http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-therapeutic-implication-definitions.html#Observation.component:medication-assessed (review the changes to the component)
Bret H (Feb 03 2022 at 03:24):
@Kevin Power I'll comment by end of day tomorrow
Bret H (Feb 03 2022 at 03:42):
In http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-therapeutic-implication.html
There's a typo I think. Should it be specific not specifics? Also, the word is highlighted is it supposed to be a link?
Also suggest altering:
It is important to note that the therapy-assessed component is not intended for medications. This component should be used to deliver non-medication therapy whose implication on the outcome is being predicted (e.g. altered diet, radiation therapy, surgery, etc.)
TO: It is important to note that the therapy-assessed component is not intended for medications. This component should be used for non-medication therapy/ies which is/are the subject of the implication prediction (e.g. altered diet, radiation therapy, surgery, etc.)
Bret H (Feb 03 2022 at 03:43):
No comments on the rest. (I'm done)
Kevin Power (Feb 03 2022 at 14:07):
Thanks @Bret H !
Bob Dolin (Feb 03 2022 at 15:28):
@Kevin Power This looks great. Thanks! Do we have or should we have another Jira, to update the Figures?
Kevin Power (Feb 03 2022 at 15:29):
I am about to push up changes to address @Bret H 's findings. For the figures, I think we can consider syncing up the figures with the changes as part of QA (meaning we don't need an additional JIRA).
Bret H (Feb 03 2022 at 15:31):
Do we have lucid chart versions of the figures?
Kevin Power (Feb 03 2022 at 15:31):
Nope :frown: -- but we need them.
Bret H (Feb 03 2022 at 15:32):
Hmm...I think I could take the figs for groupers as a starting place and create them (to keep the look consistent). Want me to update the figures on Theraputic Implication?
Kevin Power (Feb 03 2022 at 15:34):
That would be FANTASTIC @Bret H :smile:
Bret H (Feb 03 2022 at 15:34):
on it.
Kevin Power (Feb 03 2022 at 15:38):
@Bret H @Bob Dolin - I pushed some changes, do you all mind re-reading the section about medication and therapy assessed details under the first figure?
http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-therapeutic-implication.html
Bob Dolin (Feb 03 2022 at 15:40):
@Kevin Power Looks good to me
Bret H (Feb 03 2022 at 15:56):
is there more than figure 1 (http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-therapeutic-implication.html#pharmacogenomic-specific-genomic-implications) that should be changed?
Bret H (Feb 05 2022 at 17:34):
I'm working on figure 1 only then if there are no other figures.
Kevin Power (Feb 05 2022 at 18:46):
I will try to do a review and look for others but welcome anyone to review during the QA period to identify other images that need to change
Bret H (Feb 07 2022 at 04:45):
I will be modifying: http://build.fhir.org/ig/HL7/genomics-reporting/somatics.html figure 1 as well (similar modifications). Also, I will update the text to match the figure. I can do a branch or @Kevin Power let me know when to coordinate adding my changes.
Bret H (Feb 07 2022 at 04:46):
it's pretty minor, except we'll have lucid chart images backing up the figs for future maintenance.
Kevin Power (Feb 07 2022 at 13:36):
@Bret H - feel free to create your own branch anytime. Or if you feel lucky just apply the change directly to master :grinning_face_with_smiling_eyes:
Bret H (Feb 08 2022 at 19:59):
So, what name is the Recommendation going by? Medication Usage Task or Medication Recommendation? The profile is Medication Recommendation but it's being referred to as either one in the text, in multiple pages ( incl Emerge example)
Kevin Power (Feb 08 2022 at 21:39):
If you can point out the specific locations where the text is out of sync, feel free to log a technical correction JIRA and we can get it synced up.
Bret H (Feb 09 2022 at 16:04):
Ok. but which name is right? Medication Recommendation, correct? it is the name of the profile. To be clear, we want to use that name.
Bret H (Feb 09 2022 at 16:08):
TEXT
C:....GitHub\genomics-reporting\input\fsh\CGExamples.fsh (8 hits)
Line 149: Description: "Example of a Genotype, Medication Usage Task, and MedicationStatement"
Line 162: Description: "Example of a Medication Usage Task"
Line 173: Description: "Example of a Report carrying a Genotype, Therapeutic Implication, and Medication Usage Task"
Line 800: Description: "Example of a Medication Usage Task for alternatives to clopidogrel"
Line 809: Description: "Example of a Medication Usage Task for alternatives to voriconazole"
Line 818: Description: "Example of a Medication Usage Task for decreasing dosage for citalopram"
Line 827: Description: "Example of a Medication Usage Task for decreasing dosage for escitalopram"
Line 836: Description: "Example of a Medication Usage Task for decreasing dosage for amitriptyline"
And in
C:...GitHub\genomics-reporting\input\pages\pharmacogenomics.md (4 hits)
Line 55: To associate a Therapeutic-implication instance with a proposed recommended action (e.g. discontinuing a medication, altering dosage, or "choose alternative medication") one can use the Medication Usage Task, potentially with a MedicationStatement instance. Use genomics-artifact in Therapeutic-implication to supply additional or supporting information, such as CPIC guidelines. In this report example, the text which explains the methodology of the test, was modeled using the PlanDefinition resource (#5 in the schema). The clinical genomics work group has not yet determined the value of providing a profile on PlanDefinition, and requests community feedback on encoding testing methodology details.
Line 139: | Medication Usage Task | The Medication Usage Task is a recommended action Task describing what sort of change (if any) should be made for a specific medication based on an identified finding. This is a computable specific recommendation for action on a specific medication, such as changing a dose. It is a structured means of reporting recommendations. Here tied to a Therapeutic Implication to provide guidance such as changes to a dose or alternative medications. | #Task-PGxRecEx01.html <br/>#Task-PGxRecEx02.html<br/>#Task-PGxRecEx03.html<br/>#Task-PGxRecEx04.html<br/>#Task-PGxRecEx05.html | Not included in this example, ‘Task.focus’ can be used to refer to a MedicationStatement for the patient, if available. <br/>See an alternative example using this pattern at #Task-MedicationRecommendationExample1.html. |
Line 139: | Medication Usage Task | The Medication Usage Task is a recommended action Task describing what sort of change (if any) should be made for a specific medication based on an identified finding. This is a computable specific recommendation for action on a specific medication, such as changing a dose. It is a structured means of reporting recommendations. Here tied to a Therapeutic Implication to provide guidance such as changes to a dose or alternative medications. | #Task-PGxRecEx01.html <br/>#Task-PGxRecEx02.html<br/>#Task-PGxRecEx03.html<br/>#Task-PGxRecEx04.html<br/>#Task-PGxRecEx05.html | Not included in this example, ‘Task.focus’ can be used to refer to a MedicationStatement for the patient, if available. <br/>See an alternative example using this pattern at #Task-MedicationRecommendationExample1.html. |
Line 156: 1. Medication Usage Task - the original eMERGE spec did not structure medication recommendation proposals, which were left in plain text comments.
Bret H (Feb 09 2022 at 16:26):
Remaining figures (I already changed the one on the Theraputic Implication page):
pgx-guidance-figure-2.jpeg ON pharmacogenomics.md
general-relationships.png ON general.xml
These ones I won't change as they are NOT referenced by any pages in the IG currently: 1-general-fig4-other-relationships-new.png and pgx-guidance-Modified v2 schema-overview for PGx exam.jpg
Kevin Power (Feb 09 2022 at 16:42):
Bret H said:
Ok. but which name is right? Medication Recommendation, correct? it is the name of the profile. To be clear, we want to use that name.
Yes that is the right name.
Bret H (Feb 10 2022 at 16:53):
https://jira.hl7.org/browse/FHIR-36005
Bret H (Feb 10 2022 at 18:09):
Thank you! You're saving me the effort. I am ready to push the text changes mentioned in the JIRA
Kevin Power (Feb 10 2022 at 18:19):
Thanks Bret! Perhaps we should wait until we decide on the 'constraint' changes before we apply these?
Bret H (Feb 11 2022 at 20:51):
ok to change now?
Bret H (Feb 11 2022 at 20:52):
PS on the somatic page, I think the best update is to either remove the figure or use:
image.png
any objections?
Kevin Power (Feb 11 2022 at 21:15):
I say use the image you pasted here.
Bret H (Feb 11 2022 at 21:17):
Will do. Can I push the update now? Or still waiting on the branch.
Kevin Power (Feb 11 2022 at 21:18):
Just image updates directly to master are fine, yes. Make sure to sync up locally before you do anything else (the "Fetch origin" option in GitHub Desktop)
Last updated: Apr 12 2022 at 19:14 UTC
