string - 2016-09 core #466

XMLWordPrintableJSON

    • Type: Change Request
    • Resolution: Not Persuasive with Modification
    • Priority: Medium
    • FHIR Core (FHIR)
    • DSTU2
    • Clinical Genomics
    • MolecularSequence (was Sequence)
    • 10.4.6
    • Hide

      Persuasive – add clarification info on string

      In the referenceSeq, there're four ways to represent reference sequence :

      Sequence.referenceSeq.referenceSeqId: Reference sequence id in public database;

      Sequence.referenceSeq.referenceSeqString: Reference sequence string;

      Sequence.referenceSeq.referenceSeqPointer: Reference to observed sequence stored in another sequence entity;

      Sequence.referenceSeq.genomeBuild, Sequence.reference.chromosome: The combination of genome build and chromosome.

      When you choose to use referenceSeqString to record reference sequence, it would be a string like "ACGTTAG".

      Show
      Persuasive – add clarification info on string In the referenceSeq, there're four ways to represent reference sequence : Sequence.referenceSeq.referenceSeqId: Reference sequence id in public database; Sequence.referenceSeq.referenceSeqString: Reference sequence string; Sequence.referenceSeq.referenceSeqPointer: Reference to observed sequence stored in another sequence entity; Sequence.referenceSeq.genomeBuild, Sequence.reference.chromosome: The combination of genome build and chromosome. When you choose to use referenceSeqString to record reference sequence, it would be a string like "ACGTTAG".
    • David Kreda/Clem McDownload: 25-0-2
    • Clarification
    • Non-substantive
    • DSTU2

      Comment:

      What is "string" supposed to be? It is not a phrasing that I have seen in genetics. I assume it is the set of nucleotides which is the part of the normal sequence that gets changed in the variation. But the reference sequence the one that has an ID, is usually a big chunk and is not narrowed down to one sub string. Is this the strand between the ends of the window on the reference sequence? So you are naming a big (probably) reference sequence with your RefSeq ID - which will usually be a whole gene, or larger, or even a whole chromosome, and then narrowing it down to define the part that relates the sample sequence that is different to the reference sequence. Is there a particular use case that needs this levels of complexity? At the beginning you make the point that this is just what is needed for clinical care. Dont think VCF looks like this.

      Summary:

      string

            Assignee:
            Unassigned
            Reporter:
            clemmcdonald
            clemmcdonald
            Watchers:
            2 Start watching this issue

              Created:
              Updated:
              Resolved: