Stream: genomics
Topic: GenomicsBase profile on genomics-reporting IG
Nicolas Riss | Arkhn (Mar 03 2021 at 09:37):
Hello everyone :smile:
I have a small question about the GenomicsBase profile (http://hl7.org/fhir/uv/genomics-reporting/genomics-base.html)
Why does the interpretation attribute has 0..0 cardinality ?
According to me, it could be interesting to keep it, for example for variant.component:copy-number that inherits from GenomicsBase profile
Thanks in advance for your explanations :smile:
Bret H (Mar 03 2021 at 14:04):
It was thought to be confusing with the effort to pull-out interpretation to profiles on observation.
Bret H (Mar 03 2021 at 14:04):
- Observation.interpretation
Definition
A categorical assessment of an observation value. For example, high, low, normal.
Control 0..0
Binding Codes identifying interpretations of observations.
The codes SHALL be taken from ObservationInterpretationCodes; other codes may be used where these codes are not suitable
Type CodeableConcept
Requirements
For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.
Alternate Names Abnormal Flag
Comments
Historically used for laboratory results (known as 'abnormal flag' ), its use extends to other use cases where coded interpretations are relevant. Often reported as one or more simple compact codes this element is often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result.
Invariants Defined on this element
ele-1: All FHIR elements must have a @value or children (: hasValue() or (children().count() > id.count()))
Bret H (Mar 03 2021 at 14:06):
also I would recommend looking to our build STU2: http://build.fhir.org/ig/HL7/genomics-reporting/ depending on where your work is at.. also: http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-overall-interpretation.html
Bret H (Mar 03 2021 at 14:08):
Curious, what o you have in mind for interpretation in the copy-number component?
Kevin Power (Mar 03 2021 at 15:21):
I will add that this has changed in our upcoming release: See here https://jira.hl7.org/browse/FHIR-24879
Nicolas Riss | Arkhn (Mar 03 2021 at 15:43):
Oh cool ! I didn't see you published a STU2 build !
The case I imagine was for cancerous cell, my idea was to use the copy-number.interpretation attribute to indicate if it is higher than the normal cells
Thanks for all these answers, it's a lot clearer
Bret H (Mar 03 2021 at 15:57):
Tumor normal testing has been a topic in the CG calls. @Patrick Werner can you remind me where we left off with Tumor Normal testing? Thanks
Bret H (Mar 03 2021 at 15:57):
was there a zulip thread
Last updated: Apr 12 2022 at 19:14 UTC
