Uploaded image for project: 'FHIR Specification Feedback'
  1. FHIR Specification Feedback
  2. FHIR-25250

FHIR Operations for a genomic data server

    XMLWordPrintableJSON

Details

    • Icon: Change Request Change Request
    • Resolution: Persuasive
    • Icon: Medium Medium
    • Genomics Reporting (FHIR)
    • 1.0 [deprecated]
    • Clinical Genomics
    • genomics [deprecated]
    • Hide
      • Resolution is to merge the $find-subject-variants operation (http://build.fhir.org/ig/HL7/genomics-reporting/branches/fhir_operations/find-subject-variants.html) into the Master branch. (Additional change proposals to the operation are still welcome, and will be managed in the Master branch).
      • Description of $find-subject-variants operation:
      • Use this operation to retrieve variants with precise endpoints from a specified genomic region for a specified patient. If the range in question has been studied, the operation returns variants overlapping the region. If the patient or the specified region has not been studied, the operation returns a 404 error.
      • IN Parameters:
      • subject [1..1]
      • genomicRefSeq [1..1]
      • range (numeric within the ref seq) [1..1]
      • OUT Parameters:
      • regionStudied [0..1]
      • variant [0..*]
      • sequencePhaseRelationships [0..*]
      • Additional resolutions include:
      • operation name: $find-subject-variants
      • context: [base]/$find-subject-variants
      • include discussion of normalization and liftover, including expectations of the server
      Show
      Resolution is to merge the $find-subject-variants operation ( http://build.fhir.org/ig/HL7/genomics-reporting/branches/fhir_operations/find-subject-variants.html ) into the Master branch. (Additional change proposals to the operation are still welcome, and will be managed in the Master branch). Description of $find-subject-variants operation: Use this operation to retrieve variants with precise endpoints from a specified genomic region for a specified patient. If the range in question has been studied, the operation returns variants overlapping the region. If the patient or the specified region has not been studied, the operation returns a 404 error. IN Parameters: subject [1..1] genomicRefSeq [1..1] range (numeric within the ref seq) [1..1] OUT Parameters: regionStudied [0..1] variant [0..*] sequencePhaseRelationships [0..*] Additional resolutions include: operation name: $find-subject-variants context: [base] /$find-subject-variants include discussion of normalization and liftover, including expectations of the server Details of the operation are here: http://build.fhir.org/ig/HL7/genomics-reporting/branches/fhir_operations/find-subject-variants.html
    • Bob D/Kevin P: 13-0-0
    • Enhancement
    • Compatible, substantive

    Description

      Proposal that the next version of the IG include FHIR Operations for a genomic data server (as further described here: https://docs.google.com/presentation/d/1WSqmucM9zaFC24IZJwodCFBvXiwiM5wn0ulRI6Z7z9k/edit

      (An example would be an '$extract-variants' operation, which takes patient ID, chromosome, and region as input, and returns a FHIR Genomics diagnostic report containing variants in the requested region. This proposal is to include operations in the next IG. The specific operations to be included will be subsequently fleshed out).

      Attachments

        Activity

          People

            Unassigned Unassigned
            james.jones James Jones
            Watchers:
            4 Start watching this issue

            Dates

              Created:
              Updated:
              Resolved: