Strand should be constrained from integer - 2016-09 core #391

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    • Type: Change Request
    • Resolution: Persuasive
    • Priority: Medium
    • FHIR Core (FHIR)
    • DSTU2
    • Clinical Genomics
    • MolecularSequence (was Sequence)
    • Resource Sequence -
    • Hide

      Based on implementation of wiki page, so far there is no better way to constrain an integer into only two possible values. (Same as coordinatSystem)

      We propose add notes both in resource page and genomics implement page to help people understand choice of strand in different terminology systems:

      Proposed wording:

      There are lots of definition concerning with the Directionality of DNA or RNA. Here strand element in Sequence resource is defined to have constraints with value +1 and -1 , to indicate what is the direction for nucleotide series. In order to avoid confusion, we use +1 to express the "plus" strand (5' to 3') and -1 to express the "minus" strand (3' to 5'). Here is a very simple mapping that indicates which number the expression will be represented.

      +1 * -1*

      Watson Crick

      Sense Antisense

      positive negative

      Here is a small-scale example: if 5' GCGATATCGCAAA 3' is the data, then GC..AAA is plus strand while AAA..CG is the minus strand.

      Check preview at:

      https://bcl-lab.github.io/FHIR_CG_web/sequence.html#10.4.4.2

      Show
      Based on implementation of wiki page, so far there is no better way to constrain an integer into only two possible values. (Same as coordinatSystem) We propose add notes both in resource page and genomics implement page to help people understand choice of strand in different terminology systems: Proposed wording: There are lots of definition concerning with the Directionality of DNA or RNA. Here strand element in Sequence resource is defined to have constraints with value +1 and -1 , to indicate what is the direction for nucleotide series. In order to avoid confusion, we use +1 to express the "plus" strand (5' to 3') and -1 to express the "minus" strand (3' to 5'). Here is a very simple mapping that indicates which number the expression will be represented. +1 * -1* Watson Crick Sense Antisense positive negative Here is a small-scale example: if 5' GCGATATCGCAAA 3' is the data, then GC..AAA is plus strand while AAA..CG is the minus strand. Check preview at: https://bcl-lab.github.io/FHIR_CG_web/sequence.html#10.4.4.2
    • David Kreda/Clem McDownload: 25-0-2
    • Enhancement
    • Non-substantive
    • DSTU2

      Comment:

      strand datatype is currently integer; should be more constrained than that along with definition; eg +/-, or +1/-1, or 1/0, etc

      Summary:

      Strand should be constrained from integer

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

              Created:
              Updated:
              Resolved: