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phenopackets / domain-analysis

The goal of this repository is to collect and develop domain analysis content for the phenotypic domain.
https://phenopackets-analysis.rtfd.io/
Apache License 2.0
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Karyotypic sex #10

Open ShahimEssaid opened 3 years ago

ShahimEssaid commented 3 years ago

For page: https://phenopackets-analysis.readthedocs.io/en/latest/domain-entities/karyotypic-sex.html

ShahimEssaid commented 3 years ago

What code should we use for the Observation.code to capture the Phenopackets values seen here: https://phenopackets-schema.readthedocs.io/en/latest/karyotypicsex.html

I'm using the following in the Observation profile for now: https://browser.ihtsdotools.org/?perspective=full&conceptId1=312948004&edition=MAIN/2020-07-31&release=&languages=en

@pnrobinson @rrfreimuth @mellybelly

pnrobinson commented 3 years ago

SNOMED does not have codes that actually denote karyotypic sex for all of the elements we need. I was not able to find other such elements. Would it be a simpler solution just to provide a list of Strings? Karyotypic sex would also be in scope for HPO and we could add terms there if that does not work, but since there are situations where people might use phenopackets without HPO, I wonder if strings would be the better solution?

ShahimEssaid commented 3 years ago

I'm not sure what is meant by strings. But, yes, some strings that will be treated as codes in a CodeSystem and ValueSet so they can be used in profiles would work. For now we can go with a SNOMED code that is sort of close until we define the new stuff. We can have multiple options, not just one, but for profiling we'll need to recommend one. Additional codings of the same concept can be included in the data if available.

I'll finish and push the profile we started earlier today to show what I'm referring to.

pnrobinson commented 3 years ago

I meant like in Patient.gender, "Indicates that the value is taken from a set of controlled strings defined elsewhere". Arguably this would be easier to implement than using codes that might not be easily available.