Profile Specimen to include `DocumentReference`

[bwalsh]

Requester information

Please provide the following information:

• Name- Brian Walsh
• Affiliations- OHSU, AnVIL, GA4GH

Request Details

Please provide the following information about what you wanting to accomplish with your model change request:

• Purpose- Capture repository information for files associated directly with Specimen.
• Who it benefits- Researchers using the FHIR endpoint who wish to retrieve all resources associated with Specimen
• Use case- See attached AnVIL snapshot, majority of studies have files associated directly with specimen.

https://github.com/anvilproject/client-apis/blob/pyAnVIL/pyAnVIL/notebooks/figures/AnVIL.png

[torstees]

If your objective is to tie CRAMs/BAMs/VCF/etc to a specimen, we recommend creating a Task for the sequencing task itself (which can link back to the specimen) and point the output of that task to the relevant DocumentReference entry.

[torstees]

We are currently linking Sequence data to Tasks (by way of Document References) and tasks to Specimen.