General Feedback - Community Question: Track Informatics Assay(s) in a FHIR Schema

[teslajoy]

How can we track informatics assays within a FHIR schema to ensure they are findable and searchable (using REST API - search parameters of a resource), while maintaining strong associations (tightest links) with core FHIR resources such as Specimen, DocumentReference, Patient, and Observations?

Over the years the informatics community has been capable of efficiently generating large-scale reproducible results associated with specimen(s) of interest using informatics workflow languages such as Nextflow or WDL. By utilizing these workflows in a cloud environment, we can systematically organize analyses results and outcomes according to predefined business rules, leading to streamlined data management and enhanced accessibility.

To organize and translate the data into FHIR, there are two FHIR resources DiagnosticReport and Task that provide provenance to track the assays associated with specimen(s) of interest. However there are Pro's and Con's with each.

Although the naming conventions appears clinical, DiagnosticReport seems to have search parameters with tightest links to core FHIR resources such as Specimen, Patient, Observations, and most importantly DocumentReference's associated with assays that a Task FHIR resource lacks. However, its media field lacks a subfield to define the usage of the DocumentReference ex. input/intermediate/output.

Relevant Link:

github issue : Task vs DiagnosticReport

Suggested Improvements:

• It would be beneficial to include a subfield in DiagnosticReport.media, such as DiagnosticReport.media.use, to specify the type of "grouping" or the intended usage of the DocumentReference (input/intermediate/output).

• It would be beneficial to include a timestamp of type String, allowing us to define anonymized times in research, such as the index date of XYZ (unit: days). This applies to many FHIR resources including DiagnosticReport.

[bwalsh]

See #75

[bwalsh]

Alternatives using "stock" FHIR resources.
Unfortunately, what works in R4 and R6 is problematic for R5.

[bwalsh]

Potential solutions A, B Extension Based

Potential solutions C No Extension needed, Search Parameter

Make Task input and output references searchable

See https://cloud.google.com/healthcare-api/docs/how-tos/fhir-custom-search

Delete the SearchParameters

# if they already exist
curl -X DELETE \
     -H "Authorization: Bearer $(gcloud auth print-access-token)" \
     $FHIR_BASE'/fhir/SearchParameter?url=http://example.org/fhir/SearchParameter/task-input-reference'

curl -X DELETE \
     -H "Authorization: Bearer $(gcloud auth print-access-token)" \
     $FHIR_BASE'/fhir/SearchParameter?url=http://example.org/fhir/SearchParameter/task-output-reference'

Create the SearchParameters

curl -X POST \
     -H "Authorization: Bearer $(gcloud auth print-access-token)" \
     -H "Content-Type: application/fhir+json" \
     -d '{
  "resourceType": "SearchParameter",
  "id": "task-input-reference",
  "url": "http://example.org/fhir/SearchParameter/task-input-reference",
  "name": "input",
  "status": "active",
  "description": "Search for Task.input.value that is a Reference",
  "code": "input",
  "base": [
    "Task"
  ],
  "type": "reference",
  "expression": "Task.input.value",
  "target": [
    "Resource"
  ]
}' \
      $FHIR_BASE'/fhir/SearchParameter'

curl -X POST \
     -H "Authorization: Bearer $(gcloud auth print-access-token)" \
     -H "Content-Type: application/fhir+json" \
     -d '{
  "resourceType": "SearchParameter",
  "id": "task-output-reference",
  "url": "http://example.org/fhir/SearchParameter/task-output-reference",
  "name": "output",
  "status": "active",
  "description": "Search for Task.output.value that is a Reference",
  "code": "output",
  "base": [
    "Task"
  ],
  "type": "reference",
  "expression": "Task.output.value",
  "target": [
    "Resource"
  ]
}' \
      $FHIR_BASE'/fhir/SearchParameter'

See the SearchParameters

curl -X GET \
     -H "Authorization: Bearer $(gcloud auth print-access-token)" \
      $FHIR_BASE'/fhir/SearchParameter'

Re-configure the search (google fhir)

curl -X POST \
    -H "Authorization: Bearer $(gcloud auth application-default print-access-token)" \
    -H "Content-Type: application/json; charset=utf-8" \
    --data "{
        \"canonicalUrls\": [\"http://example.org/fhir/SearchParameter/task-output-reference\",\"http://example.org/fhir/SearchParameter/task-input-reference\"],
    }" \
    $FHIR_BASE":configureSearch"

Re-configure the search (HAPI)

 $FHIR_BASE":$reindex"

Create a Task with Specimen input and DocumentReference output

curl -X POST \
    -H "Authorization: Bearer $(gcloud auth application-default print-access-token)" \
    -H "Content-Type: application/json; charset=utf-8" \
    --data '{
  "resourceType": "Task",
  "status": "draft",
  "intent": "order",
  "input": [
    {
      "type": {"text": "input_specimen"},
      "valueReference": {"reference": "Specimen/4212b378-c69b-5df0-ab79-8f42f62bac5e"}
    }
  ],
  "output": [
    {
      "type": {"text": "output_file"},
      "valueReference": {"reference": "DocumentReference/ccac2a79-31e1-565b-9e92-653f3f9c9524"}
    }
  ]    
}' \
      $FHIR_BASE'/fhir/Task'

Search for the Assay(Task) with Specimen input

curl -X GET \
    -H "Authorization: Bearer $(gcloud auth application-default print-access-token)" \
    $FHIR_BASE'/fhir/Task?input=Specimen/4212b378-c69b-5df0-ab79-8f42f62bac5e'

Find the Specimen and associated Assay (Task)

curl -X GET \
    -H "Authorization: Bearer $(gcloud auth application-default print-access-token)" \
    $FHIR_BASE'/fhir/Specimen?_id=4212b378-c69b-5df0-ab79-8f42f62bac5e&_revinclude:recurse=Task:input'

Search for the task with DocumentReference output

curl -X GET \
    -H "Authorization: Bearer $(gcloud auth application-default print-access-token)" \
    $FHIR_BASE'/fhir/Task?output=DocumentReference/ccac2a79-31e1-565b-9e92-653f3f9c9524'

Find the DocumentReference and associated Assay (Task)

curl -X GET \
    -H "Authorization: Bearer $(gcloud auth application-default print-access-token)" \
    $FHIR_BASE'/fhir/DocumentReference?_id=ccac2a79-31e1-565b-9e92-653f3f9c9524&_revinclude:recurse=Task:output'

[bwalsh]

@teslajoy @RobertJCarroll @JamedFV Consolidated comments on Assay here.