Tutorial (Do not modify) - Add species to NCPI Patient

[znatty22]

A Patient in the NCPI FHIR model can represent either a human or an animal. In the forseable future, the clinical data that will be ingested into the NCPI FHIR server will only contain Patients that are either Homo sapiens (humans) or Canis lupus subspecies familiaris (domestic dogs).

The NCPI Patient StructureDefinition should be modified to include an attribute to capture it's species and that attribute should be restricted to the above two values. Details of the requested extension can be found here: <TBD - NCPI FHIR modeling spreadsheet link>

The following should be implemented to close this issue:

• [ ] Species Extension
• [ ] Species CodeSystem and ValueSet to capture snomedct codes for Homo sapiens and Canis lupus subspecies familiaris
• [ ] Bind species extension to NCPI Patient StructureDefinition
• [ ] Update the NCPI Patient example with a value for species

[allisonheath]

(Just as an example based on the representation meeting)

To better understand the best representation for this information, we need some more background and use cases for this field before we proceed with implementation.

For example, from KFDRC, we have a collaboration with KOMP2 to functionally test variants and resulting phenotypes. We would like to bring this information into the same FHIR server with the original human patients whose genomic/phenotypic data provide the hypothesis for this testing. So we would consider these mice as "patients" with their own set of phenotypic data.

There also exists an animal extension in HL7 that we might be able to leverage: https://www.hl7.org/fhir/extension-patient-animal.html.

[allisonheath]

I am going to leave this issue open for the time being - at least through the next larger FHIR WG meeting as an example but we will eventually close it out. If species is a real use case for the NCPI model (and it seems like it may be), then a separate ticket should be created.