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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:

      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:

      I

      am

      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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