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Agenda for Upcoming Meeting

September 8, 2017, 1:30PM

  • NCI insertion: finished, taking 14 hours to complete.   
    • Laura findings:

      • I see a couple of these… they have a demoted atom and in demotions bin but there is no 2nd concept or demotion rel.

        • CN# 101298 One CUI C0205447
        • TODO: look into

      • The PAR and CHD are wrong.

        What is listed as CHD are actually the PAR of  this concept. If you look at context for SNOMED for example, Finding of HIV status is a PAR.

        • CN# 262978 HIV negative finding CUI C0481430

        • TODO: deploy code updates

      • For the list of checklists, can we have it that the newest ones created are on the 1st page? So the order is newest to oldest?

        • Not a sorting issue, but an insertion when creating.  Also,  feel this is lower priority.

        • TODO: refresh page after creation of new checklist

  • Post-query processing for concepts_id_1,concepts_id_2 bins.
    • An issue for QA bins, and for demotions ME bin
    • Example: after MTH_2017AA insertion, it took 42620.183 seconds (12 hours) to process ME 'demotions'. So no cycles.
      • 16,152 conceptId pairs returned by query, 1994 clusters ended up in bin
        • 6653237 - 981810
        • 981810 - 6653237
        • 682110 - 6653664
        • 6653664 - 682110
      • 3716 entries in parChd.
        • Parent 6660138 went through 130+ iterations of getDescendents
        • 6660138=[6660140,6660141,6660142,6660143,6660144,6660145,6660146]
        • 6660140=[6660141,6660142,6660143,6660144,6660145,6660146]
        • 6660141=[6660142,6660143,6660144,6660145,6660146]
        • 6660142=[6660143,6660144,6660145,6660146]
        • 6660143=[6660144,6660145,6660146]
        • 6660144=[6660145,6660146]
        • 6660145=[6660146]
        • 6660146=[]
      • Checking to make sure child hasn't already been processed before running
  • Process export/import issue
    • Export updated so JSON contains parameters
    • Import needs to be able to incorporate JSON parameters into algorithm properties
  • MTH_2017AA insertion
    • Still no NEEDS_REVIEW checklists
      • Precomputed Merges - all lines set to N|N
      • Generated Merges - changeStatus set to false
    • MEME4 vs. MEME5 merge scripts review

September 1, 2017, 1:30PM

  • QA Bins: post-query processing for concepts_id_1,concepts_id_2 bins never finishes
  • Continue term type suppressability discussion

    • Per the UMLS reference manual:

      Code Block

      Suppressible

      flag.

      Values

      =

      O,

      E,

      Y,

      or

      N

      O:

      All

      obsolete

      content,

      whether

      they

      are

      obsolesced

      by

      the

      source

      or

      by

      NLM.

      These

      will

      include

      all

      atoms

      having

      obsolete

      TTYs,

      and

      other

      atoms

      becoming

      obsolete

      that

      have

      not

      acquired

      an

      obsolete

      TTY

      (e.g.

      RxNorm

      SCDs

      no

      longer

      associated

      with

      current

      drugs,

      LNC

      atoms

      derived

      from

      obsolete

      LNC

      concepts).

      E:

      Non-obsolete

      content

      marked

      suppressible

      by

      an

      editor.

      These

      do

      not

      have

      a

      suppressible

      SAB/TTY

      combination.

      Y:

      Non-obsolete

      content

      deemed

      suppressible

      during

      inversion.

      These

      can

      be

      determined

      by

      a

      specific

      SAB/TTY

      combination

      explicitly

      listed

      in

      MRRANK.

      N:

      None

      of

      the

      above

    • Per Stephanie:

      Code BlockI am looking at cases where tty = AB or HS && suppressible != "Y". For most of them, a simple change to NCI & ISO3166-2 would do it. I think if we explain it to NCI they will ok it -- Laura will understand, and we should probably run it by Tracey/Rob/Larry in case they have any concerns or foresee any gotchas. For the others that come in through UMLS ... I think the but a few come from RxNorm which has its own rules so I'm pretty sure they're intentional and I'm hesitant to change it. I would be ok changing the two "HS" cases to "Y" but then it would be different from the UMLS. Not sure if that

      I am  looking at cases where tty = AB or HS && suppressible != “Y”.     For most of them, a simple change to NCI & ISO3166-2 would do it.  I think if we explain it to NCI they will ok it -- Laura will understand, and we should probably run it by Tracey/Rob/Larry in case they have any concerns or foresee any gotchas.  For the others that come in through UMLS … I think the but a few come from RxNorm which has its own rules so I’m pretty sure they’re intentional and I’m hesitant to change it.   I would be ok changing the two “HS” cases to “Y” but then it would be different from the UMLS.  Not sure if that matters.

  • Review umlscui.txt issues

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