Sequence as definitional?

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    • Type: Change Request
    • Resolution: Persuasive with Modification
    • Priority: Medium
    • FHIR Core (FHIR)
    • STU3
    • Clinical Genomics
    • MolecularSequence (was Sequence)
    • 10.6
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      Proposal:

      Change the extra note on the Sequence resource to pose a slightly different question.

      The Clinical Genomics committee has identified overlaps and redundancies between content in the Sequence Resource and content in observation profiles in the evolving Implementation Guide for Clinical Genomics Reporting [http://hl7.org/fhir/uv/genomics-reporting/index.html. The committee is considering options for modifying the _ _resource _ _and anticipates potential changes being brought forward in an upcoming ballot.

      http://build.fhir.org/sequence.html

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      Proposal: Change the extra note on the Sequence resource to pose a slightly different question. The Clinical Genomics committee has identified overlaps and redundancies between content in the Sequence Resource and content in observation profiles in the evolving Implementation Guide for Clinical Genomics Reporting [http://hl7.org/fhir/uv/genomics-reporting/index.html . The committee is considering options for modifying the _ _resource _ _and anticipates potential changes being brought forward in an upcoming ballot. http://build.fhir.org/sequence.html
    • Bob M / Gil : 16-0-3
    • Non-substantive
    • STU3

      http://hl7.org/fhir/2018May/sequence.html

      There's a question of whether Sequence should be a definitional resource. I understand this to mean that Sequence would refer to a nucleotide or protein sequence, but not necessarily be tied to a particular Specimen or Patient. This is attractive in that it could be reused, and it's reuse could be a subject of analyis (eg., how many Patients have Observations that point to a particular Sequence. While attractive, I'm having a hard time figuring out how to implement such a system. How do go about finding out if a Sequence already exists in the FHIR server and whether I should I reuse it? What if the sequence I observed it a sub-sequence of an existing Sequence resource? or if it is an extension of it by only a couple of nucleotides? Seems like it would be better if this was left to the research systems hosting this information. If we are going to change Sequence to be definitional, then we also need to develop guidance and example workflows in its use. Or perhaps have both SequenceDefinition which may be reused in Sequence instances for observed sequences?

            Assignee:
            Unassigned
            Reporter:
            Bob Milius
            Watchers:
            1 Start watching this issue

              Created:
              Updated:
              Resolved: