Incorporate CRDC Data Standards Team (DST) minimum metadata elements into CRDCH

[bfurner]

The DST analyzed data dictionaries from a range of projects and produced a report that asserted a set of candidate minimum metadata elements. A majority of these minimum metadata elements are already present in CRDCH v1.0.1, but those that are not need to be included.

Here is the CRDC DST Metadata Standard Reports

[bfurner]

• [ ] Gender: Subject.gender (enum) implement genotypic sex and phenotypic sex and gender attributes directly on Subject - to capture the most recent observation/identification of these characteristics. If we end up needing to capture longitudinal sex/gender data, we may need to use Observations for this. We can also consider capturing it on Subject nd Research Subject - where the later is the sex/gender that applies during a Study.
  • [ ] Principal Investigator Name: ResearchProject.principal_investigator
  • [ ] Subject age at specimen collection Shahim will explore the possibility of making use of the TimePoint entity defined in the CDM
  • [ ] File format and File type Shahim to review CRDCH.Document and FHIR approaches

[ShahimEssaid]

For Specimen subject age at collection, the easiest is a .subject_age_at_collection with a Quantity. We can use a TimePoint instance to represent the point in time when the collection happened. However, this point will also need another point that stands for the subject's birth (an empty one that doesn't have dateTime or a quantity) and the specimen's time point instance then holds the quantity that is the time from birth until collection in the .offsetFromIndex field.

If we want to think of this as simply a value that belongs to the specimen, we should hold it as a quantity directly on the specimen. If we think the time point at which the specimen was collected is important on its own, then we should use a TImePoint instance and an index TimePoint for birth.