2010 06 07 - LOINC Workshop

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2010 06 07 - LOINC Workshop

  1. 1. Laboratory  LOINC  Meeting  –  December  2010   James  T.  Case  MS,  DVM,  PhD   Health  Program  Specialist,  SNOMED  CT   National  Library  of  Medicine   ©2010 Regenstrief Institute and James Case
  2. 2. Acknowledgements   •  RELMA  Development  Team   •  John  Hook,  Mark  Fisher,  Karen  Ahmad,  Craig  Kelker   •  Dan  Vreeman   •  Clem  McDonald   •  Kathy  Mercer   •  The  Lab  LOINC  CommiFee   •  Funding  Support   •  NLM,  Regenstrief  InsJtute,  NCI,  CDC   ©2010 Regenstrief Institute and James Case
  3. 3. What  will  we  cover  today?   •  Overview  of  LOINC   •  Reviewing  new  RELMA  features!   •  Installing  RELMA   •  SeMng  personal  preferences   •  Loading  a  Local  ObservaJon  File  (LMOF)   •  Searching  for  a  LOINC  Term   •  Preparing  LMOF  for  Mapping   •  Review  of  Map  Screen  FuncJons   •  SeMng  Search  Limits   •  Mapping  Local  Terms  to  LOINC   •  Viewing  LOINC  Term  Details   •  Proposing/SubmiMng  New  LOINC  Terms   •  ExporJng/PrinJng  Mapped  Terms   •  Mapping  your  own  LMOF  data     ©2010 Regenstrief Institute and James Case
  4. 4. Why  are  we  doing  this?   Goals  of  Health  Information  Standards   •  Interoperability  –  the  ability  to  exchange   informaJon  between  organizaJons   •  Comparability  –  the  ability  to  ascertain  the   equivalence  of  data  from  different  sources   •  Data  Quality  –  the  measurement  of   accessibility,  completeness,  accuracy  and   precision  (and  more)   ©2010 Regenstrief Institute and James Case
  5. 5. Levels  of  Interoperability   •  Basic  –  allows  data  to  be  exchanged  between   computer  systems   •  Word  processing  documents,  text  messages     •  Func7onal  –  describes  the  standard  syntax   (format)  of  the  data   •  Document  templates,  forms,  data  structures   •  Message  standards   •  Seman7c  –  requires  use  of  standard   vocabularies  within  the  data   ©2010 Regenstrief Institute and James Case
  6. 6. Comparability   •  Meaning  of  the  data  is  consistent  when  shared   among  different  parJes   •  Erysipelas  –  Human  skin  disease;  Streptococcus  Grp  A   •  Erysipelas  –  Animal  SepJcemia/dermaJJs;  Erysipelothrix   rhusiopathiae   •  Common  terminology  required   •  Should  work  in  the  background   •  Not  just  words   •  Codes  –  uniquely  idenJfies  terms   •  ClassificaJon  –  groups  related  terms   •  Vocabulary  –  specialized,  precise  terms  that  remove   ambiguity   ©2010 Regenstrief Institute and James Case
  7. 7. Potential  Uses  of  Health  Data  are   Constrained  by  Data  Quality  Factors   •  Data  quality  issues   •  Different  for  client  communicaJons  vs.  analysis   •  O]en  constrained  by  external  forces   •  E.g.  criteria  for  diagnosis  o]en  differs  from  the  criteria   for  reporJng   •  UnidirecJonal  effect  of  data  consolidaJon   •  Detailed   General   •  General      Detailed   ©2010 Regenstrief Institute and James Case
  8. 8. The  Problem   “In  aFempJng  to  arrive  at  the  truth,  I  have  applied   everywhere  for  informaJon,  but  in  scarcely  an   instance  have  I  been  able  to  obtain  hospital   records  fit  for  any  purpose  of  comparison.    If  they   could  be  obtained,  they  would  enable  us  to   decide  many  other  quesJons…  They  would  show   [subscribers]  how  their  money  was  being  spent   [and]  what  amount  of  good  was  really  being  done   with  it…”   Florence  Nightingale  -­  Notes  on  a  Hospital,  1873   ©2010 Regenstrief Institute and James Case
  9. 9. Test  comparisons   What  you  see  in  the  order  list   Lab  A   Lab  B   Test  Name:  Lyme  Disease  Serology   Test  Name:  Lyme  Disease  An7body   Measures:  B.  burgdorferi  Ab  IgG   Measures:  B.  burgdorferi  Ab  IgM   Method:  ELISA   Method:  Immune  blot   Scale:  quan7ta7ve   Scale:  qualita7ve   e.g.:  Titer  1:40   e.g.:  Posi7ve   ©2010 Regenstrief Institute and James Case
  10. 10. Why  LOINC?   “Within  one  laboratory,  local  jargon  terms   may  be  used  which  are  usually  well   understood  between  colleagues,  but   would  not  be  sufficiently  widely  known  for   communicaJon  with  the  outside  world.”   U.  Forsum  et  al.,  Pure  Appl.  Chem  72:555-­‐745,  2000  Proper3es  and  Units  in  the  Clinical   Laboratory  Sciences  Part  VII.    Proper3es  and  Units  in  Clinical  Microbiology   ©2010 Regenstrief Institute and James Case
  11. 11. LOINC®  101   ©2010 Regenstrief Institute and James Case
  12. 12. Anatomy  of  a  LOINC  Term   5193-­8:Hepatitis  B  virus  surface  Ab:ACnc:Pt:Ser:Qn:EIA   5193-­‐8   LOINC  Code   Hepa77s  B  virus  surface  Ab   Component   ACnc   Property  Measured   Pt   Timing   Ser   System   Qn   Scale   EIA   Method   There  are  six  major  LOINC  axes   ©2010 Regenstrief Institute and James Case
  13. 13. What  is  NOT  part  of  a  LOINC  Name?   •  The  instrument  used  in  tesJng   •  Specific  details  about  the  specimen   •  Priority  (e.g.  STAT)   •  Where  tesJng  was  done   •  Who  did  the  test   •  Test  interpretaJon   •  Anything  that  is  not  an  intrinsic  part  of  the  name  of   the  result   •  Other  things  that  are  carried  in;   •  The  OBR  or  OBX  segment   •  An  HL7  Version  3  ObservaJon  Object   ©2010 Regenstrief Institute and James Case
  14. 14. Component/Analyte   The  substance  or  enJty  that  is  measured,   evaluated,  or  observed   -­‐  Sodium   -­‐  Glucose   -­‐  Brucella  sp.  organism   -­‐  Influenza  A  Virus  anJgen   -­‐  Cytomegalovirus  Virus  anJbody   -­‐  Lipids.Total   5193-­8:Hepatitis  B  virus  surface  Ab:ACnc:Pt:Ser:Qn:EIA   ©2010 Regenstrief Institute and James Case
  15. 15. Component/Analyte  Structure   Analyte  Name^Challenge^Adjustments   •  Formal  name  of  Analyte  (e.g.  Calcium)   •  Must  specify  any  “subanalyte”   •  e.g.    Coronavirus  Ag   •  May  have  a  subclass  –  separated  by  “.”   •  e.g.  Calcium.Free   •  Challenge  -­‐  e.g,  1H  post  100  gm  Glucose  PO   •  Two  subparts  separated  by  “post”   •  <Jme  delay>  post  <challenge  type>   •  Adjustments/correcJons   •  E.g.  Adjusted  to  pH  7.4   ©2010 Regenstrief Institute and James Case
  16. 16. Property   the  most  difficult  LOINC  axis   The  characterisJc  or  aFribute  of  the  analyte  that  is   measured,  evaluated,  or  observed   Major  Categories   •  Mass:  ObservaJons  reported  with  mass  (milligrams,  grams,  etc.)   in  the  numerator  of  their  units  of  measure   •  Substance:  ObservaJons  reported  with  moles  or  milliequivalents   in  the  numerator  of  their  units  of  measure   •  Cataly7c  ac7vity:  ObservaJons  that  report  enzymaJc  acJvity     •  Arbitrary:  Results  that  report  arbitrary  units  in  the  numerator  of   their  units  of  measure   •  Number:  Counts   5193-­8:Hepatitis  B  virus  surface  Ab:ACnc:Pt:Ser:Qn:EIA ©2010 Regenstrief Institute and James Case  
  17. 17. Property   the  most  difficult  LOINC  axis   Combine  Major  Categories  with  Subtypes  for  Full  Property   •  MCnc  –  mass  concentraJon  (mass/unit  vol)   •  MCnt  –  mass  content  (mass/unit  mass)   •  NCnc  –  number  concentraJon  (number/unit  vol)   •  TmStp  –  Jme   •  CCnc  –  catalyJc  concentraJon  (acJvity)   •  Prid  –  presence  or  idenJty   •  Imp  –  impression/interpretaJon   •  Find  –  subjecJve  or  objecJve  observaJon   •  Type  –  “Kind-­‐of”   5193-­8:Hepatitis  B  virus  surface  Ab:ACnc:Pt:Ser:Qn:EIA ©2010 Regenstrief Institute and James Case  
  18. 18. Common  Issues  with  LOINC  Properties   FracJon  (proporJon)  vs.  RaJo   a/a+b  vs.  a/b   •  FracJon  =  Part/whole   •  Number  fracJon  (NFr):    %  Eosinophils   •  Substance  fracJon  (SFr):  %  HGB  which  is  A2   •  RaJo  =  Measures  mulJple  analytes  from  the  same   system  (specimen)   •  Mass  concentraJon  raJo  -­‐  MCrto   •  e.g.,  BUN/Creat  in  urine  specimen   •  Substance  raJo-­‐SCrto   •  Urea/CreaJnine  expressed  as  mmol/L  (SI  units)   •  RelaJve  RaJo  =  Measures  from  different  systems   •  RelRto  –  mulJple  of  the  median   •  RlTm  –  Jme  from  actual  Institute and ormal  control   ©2010 Regenstrief and  n James Case
  19. 19. Timing*   The  interval  of  Jme  over  which  the  observaJon  or   measurement  was  made   •  Pt  -­‐  at  a  point  in  Jme   •  12H  -­‐  a  twelve  hour  collecJon   •  24H  -­‐  a  twenty  four  hour  collecJon   *non-­‐Pt  Jmings  are  usually  associated  with  RaJo  Property   ©2010 Regenstrief Institute and James Case
  20. 20. System   The  system  (context)  or  specimen  type  upon  which   the  observaJon  was  made.   •  Ser  -­‐  Serum   •  Gast  –  Gastric  fluid/contents   •  Bld  -­‐  Whole  blood  (RBC)   •  Food  –  Food  or  feedstuff   •  Ur-­‐  Urine   •  Tiss  –  Tissue   •  BldA  -­‐  Arterial  blood   •  XXX  –  To  be  specified  in   •  Liver  -­‐  Liver   another  part  of  the  message     •  Flu  –  Body  Fluid,  unspecified   Super  System   Second  subpart  (^).  When  not  included,  “paJent”  is  the   default.  Used  to  indicated  blood  product  unit  (BPU),  a  bone   marrow  donor,  or  a  fetus.   ©2010 Regenstrief Institute and James Case
  21. 21. Scale   •  Qn  -­‐  quanJtaJve     •  ConJnuous  numeric  (real,  integer,  raJo)   •  OpJonal  operator  (>,  ≥,  ≤,  <)   •  When  assay  detecJon  limits  are  exceeded   •  Ord  -­‐  ordinal     •  a  ranked  set  of  possible  values  (1+,  2+,  3+)   •  Nom  -­‐  nominal     •  an  unranked  collecJon  of  possible  values   •  a    taxonomy  (e.g  list  of  bacteria)   •  Nar  -­‐  narraJve     •  free  text  narraJve  (e.g.,  visit  note)   ©2010 Regenstrief Institute and James Case
  22. 22. Scale  (Special)   •  OrdQn  –  Ordinal  or  QuanJtaJve   •  Primarily  used  for  anJmicrobial  observaJons  e.g.   MIC  reported  as  resistant,  intermediate,  suscepJble   or  as  the  mm  diameter  of  the  inhibiJon  zone   •  Use  is  discouraged   •  MulJ  –  structured  text  “globs”   •  e.g.  chromatography  output   •  Use  is  discouraged   •  Doc  –  Clinical  documents   •  Set  –  Clinical  aFachments  (headers)   ©2010 Regenstrief Institute and James Case
  23. 23. Method   •  Methods  only  needed  if  interpretaJon  affected   •  Different  normal  ranges   •  Test  SensiJvity   •  Listed  only  at  the  generic  level   •  AggluJnaJon   •  Immunoassay   •  Probe  with  target  amplificaJon   ©2010 Regenstrief Institute and James Case
  24. 24. Mapping  Terms  to  LOINC   Things  to  Remember   •  The  thing  ordered  is  not  always  the  thing  measured:   •  Blood  Culture  –  live  organism(s)  idenJfied   •  VDRL  –  Treponema  pallidum  Ab   •  Urinalysis  –  lots  of  different  things   •  The  quesJon  (what  am  I  measuring?  e.g.  Glucose)  is   not  the  answer  (e.g.  90  mg/dl)   •  You  are  mapping  the  quesJon,  not  the  answer!   •  You  must  know  the  specifics  of  the  component  being   tested  for  (what  is  this  test  actually  measuring?)   ©2010 Regenstrief Institute and James Case
  25. 25. What  is  in  LOINC?   Content   •  Term  structures   •  SubmiFed  units,  Example  UCUM  units   •  aiming  toward  preferred  units  sorJng   •  Synonyms   •  Answer  lists  for  categorical    variables   (Some)   •  Text  descripJons  –  links  to  info  sources   about  individual  tests     •  Panel  structures   •  Foreign  language  translaJons     ©2010 Regenstrief Institute and James Case 25
  26. 26. Regenstrief  LOINC  Mapping  Assistant   ©2010 Regenstrief Institute and James Case
  27. 27. Purpose  of  Tutorial   •  “Eliminate”  need  to  read  the  User’s  Manual   •  Become  familiar  with  RELMA  features   •  Provide  some  insight  into  mapping  Jps/pi}alls   •  Help  begin  the  mapping  process  for  your   insJtuJon   ©2010 Regenstrief Institute and James Case
  28. 28. RELMA  Functions   •  Manual  and  automated  mapping  assistant   •  Same  free  use  as  LOINC  (see  license)   •  Comes  with  the  LOINC  files  and  indexes   •  Now  migrated  to  MS  .NET  environment.   •  RELMA  tools  transform  local  words  in  local  file   •  User  creates  file  of  local  term/name  and  codes   •  Assigns  LOINC  term  to  local  test/baFery  code   •  Context  sensiJve  hierarchies  for  local  use.   ©2010 Regenstrief Institute and James Case
  29. 29. New  in  This  Version  (Rel.  4.4)     •  New  LOINC  status  values   •  Ac7ve  (current)  -­‐  LOINC  term  is  in  acJve  use   •  Trial  (new)  -­‐  LOINC  term  is  under  development,   so  it  may  change.   •  Discouraged  (new)  -­‐  LOINC  retained  for   backward  compaJbility;  should  not  be  used  for   new  mappings.   •  Deprecated  (current)  -­‐  LOINC  has  been   deprecated;  replace  all  mappings  to   replacement  term  LOINC.                                       ©2010 Regenstrief Institute and James Case
  30. 30. New  in  This  Version  (Rel.  4.4)     •  "Part  Search"  -­‐  new  tab  on  mapping  form   •  lets  you  search  for  common  LOINC  Parts  using   Google-­‐like  query  syntax  (Lucene).   •  Ability  to  select  the  type  of  LOINC  details   display  from  the  right-­‐click  menu:   •  View  Details  –  Simple   •  View  Details  –  Comprehensive   •  View  Details  –  Custom   (When  viewing  Parts,  selecJng  any  of  these  performs  the  idenJcal   "View  Details"  acJon  for  Parts.)   ©2010 Regenstrief Institute and James Case
  31. 31. New  in  This  Version  (Rel.  4.4)     •  "View  Panel  Children“  -­‐  context  menu   •  displays  children  of  a  selected  LOINC  panel  in  a   grid  on  a  new  form.     •  all  normal  right-­‐click  acJons  on  the  LOINCs  in   this  grid  are  available.   •  Custom  Export     •  export  all  row   •  only  the  selected  rows.   •  The  mapping  screen  now  lets  you  type  in   the  local  term  file  entry  #  so  you  can  go  to   that  term  directly.   ©2010 Regenstrief Institute and James Case
  32. 32. New  in  This  Version  (Rel.  4.4)     •  LOINC  and  Part  grid  (flat)  search  results   now  preserve  their  sort  order  between   searches  when  you  use  the  Sort  Grid  right-­‐ click  acJon.   •  For  example,  if  you  search  LOINC  for  OPIATES,   "Sort  Grid"  ascending  by  the  Component,  then   search  for  MORPHINE,  the  search  results  for   MORPHINE  will  be  sorted  by  Component.   •  The  View  All  Working  Set  Terms  screen   now  has  an  "Export  Local  Term  File"  buFon.   ©2010 Regenstrief Institute and James Case
  33. 33. New  in  This  Version  (Rel.  4.4)     •  Upon  compleJon  of  a  text  or  HL7  import,  a   summary  will  appear  showing  the  results.     A]er  user  confirmaJon  of  the  results,  the   process  to  idenJfy  unrecognizable  concepts   (baFery,  test,  or  units)  will  start   automaJcally,  showing  words  that  RELMA   cannot  use  for  synonyms.   •  The  Custom  Display  now  gives  you  finer-­‐ grained  control  over  what  LOINC  Part   informaJon  you  see.   ©2010 Regenstrief Institute and James Case
  34. 34. New  in  This  Version  (Rel.  4.4)     •  Search  result  grids/trees  now  display  an   example  UCUM  units  column,  located  just   before  the  example  units  column.   •  Search  result  grids/trees  now  display  the   HL7  CDA  document  secJon  column,  located   just  a]er  the  Order/ObservaJon  column.   •  New  shortcuts   •  Ctrl-­‐E  –  Export     •  Ctrl-­‐P  –  Print   ©2010 Regenstrief Institute and James Case
  35. 35. LOINC  Web  Site   ©2010 Regenstrief Institute and James Case
  36. 36. What’s  available  to  download?   •  RELMA  -­‐  mapping  and  browsing  tool   •  HL7  message  converter-­‐  Makes  a  database   suitable  for  mapping   •  HL7  lint  (finds  bad  messages)   •  LOINC  database  and  spreadsheets     •  LOINC  User  guide;  RELMA  User  Guide   •  Tools  to  assist  language  translaJons  by  part   •  Tools  for  building  databases  to  map  from   HL7  messages   ©2010 Regenstrief Institute and James Case 36
  37. 37. RELMA  Highlights   •  Browseable  Hierarchies   •  Display  search  results  in  tree  view   •  Enhanced  “details”  view  of  terms/parts   •  References   •  DescripJons   •  Sample  units   •  Empirically-­‐derived  common  test  list   •  Special  features  for  panels/forms   •  Enhanced  export/copy-­‐paste  opJons   ©2010 Regenstrief Institute and James Case
  38. 38. RELMA  Mapping  Window     Search  Logic   For  a  given  test:   •  User  can  select  LOINC  records  containing:   •  A  set  of  words  connected  by  ANDs  or    Ors   •  AddiJonal  keyed  in  words   •  A  parJcular  category  of  test  (e.g.  microbiology)   •  Wild  cards  of  ?  and  *     •  Selected  classes,  systems,  components,     •  Any  intersecJon  of  the  above   Notes:   RELMA  assumes  exact  match  on  word  unless  user  adds   terminal  “*”  to  indicate  wild  card.   This  is  being  migrated  to  Lucene  searching  in  future   releases   ©2010 Regenstrief Institute and James Case
  39. 39. RELMA  Logic   Not    →    #<word  A>   Or  →        <word  A>    |    <word  B  >   And  →        <word  B>  <word  A>   ©2010 Regenstrief Institute and James Case
  40. 40. Additional  RELMA  Features     •  User  Specified  Search  Limits     •  Selectable  trees  for:   •  Class   •  MulJaxial  (component/system)   •  System  (specimen)   •  Component   •  Method   ©2010 Regenstrief Institute and James Case
  41. 41. Installing RELMA® ©2010 Regenstrief Institute and James Case
  42. 42. Installation  Steps   •  Make  sure  you  have  enough  free  disk  space!   •  2Gb  is  recommended   •  From  CD  -­‐  Start  –  Run  –  D:RELMASetup   •  Specify  installaJon  directory   •  Life  will  be  easier  if  you  accept  the  default   •  Two  database  files  installed   •  RELMA.MDB  –  LOINC  Terms  Database   •  LMOF3.MDB  –  Local  Master  ObservaJon  File   •  Two  sample  files  included     •  Run  from  Start  –  (All)  Programs  –  Regenstrief  –  RELMA   ©2010 Regenstrief Institute and James Case
  43. 43. File  Locations     New  for  this  version! •  Database  and  Ancillary  Files   •  Windows  XP  =  C:Documents  and  SeMngsAll  Users DocumentsRELMA   •  Windows  Vista  =  C:UsersPublicDocumentsRELMA   •  Windows  7  =  C:UsersPublicDocumentsRELMA   •  Sample  files   •  Windows  XP  =  C:Documents  and  SeMngsAll  Users DocumentsRELMASamples   •  Windows  Vista  =  C:UsersPublicDocumentsRELMA Samples   •  Windows  7  =  C:UsersPublicDocumentsRELMA Samples   ©2010 Regenstrief Institute and James Case
  44. 44. Running RELMA® Version 4.4 ©2010 Regenstrief Institute and James Case
  45. 45. Copyright  Screen   ©2010 Regenstrief Institute and James Case
  46. 46. Main  Menu/Welcome  Screen   Click  File,  Set  Preferred   Language   ©2010 Regenstrief Institute and James Case
  47. 47. Select  Linguistic  Variant(s)   ©2010 Regenstrief Institute and James Case
  48. 48. LOINC  Terms  with  Spanish  Linguistic  Variant   Spanish!   ©2010 Regenstrief Institute and James Case
  49. 49. Setting  User  Preferences   ©2010 Regenstrief Institute and James Case
  50. 50. Set  User  Preferences   Select  User  Preferences   From  the  File  Menu   ...or  from  Welcome  Screen   ©2010 Regenstrief Institute and James Case
  51. 51. Set  User  Preference  Dialog   New  File  Locations:   Now  stored  in  All  Users/Documents   Startup  Screen  Preference   ©2010 Regenstrief Institute and James Case
  52. 52. User  Map  Screen  Preferences   Click  Map  Screen  Tab   Include/Exclude  Battery  Terms   Add  comments  on  Mappings   ©2010 Regenstrief Institute and James Case
  53. 53. Importing  Local   Terms  into  RELMA   ©2010 Regenstrief Institute and James Case
  54. 54. 4  Ways  to  Load  LMOF  Files   •  Direct  entry  into  LMOF  from  within  RELMA  (painful)   •  Handy  for  individual  entries/edits   •  Create  an  Access  table  that  mimics  the  LMOF  structure   (less  painful  but  tedious)   •  Appendix  A:    RELMA  Manual   •  Create  a  delimited  ASCII  file  from  your  local  test   catalog  (good  choice)   •  Load  directly  from  HL7  v2.x  messages   •  Pulls  data  from  OBR  and  OBX  segments   •  Stores  NTE  segment  data   ©2010 Regenstrief Institute and James Case
  55. 55. Constructing  a  Local  Dataset   Create  extract  of  your  test  catalog  with:   •  BaFery/Panel  Code   •  BaFery/Panel  DescripJon  or  Name   •  *Local  Code     •  *Test  DescripJon  or  Name   •  Include  Method  if  Important   •  Units   •  Example  Values   •  Laboratory  SecJon   ©2010 Regenstrief Institute and James Case
  56. 56. Creating  Delimited  ASCII  File   •  RELMA  can’t  parse  free  text   •  Need  to  create  separate  fields   •  Can  use  any  of  these  delimiters   •  Tab,  Semicolon,  Comma,  Space   •  Can  define  your  own   •  Fields  can  be  in  any  order   •  Minimum  required  fields     •  Local  Code   •  Local  DescripJon   •  Units  (highly  recommended)   ©2010 Regenstrief Institute and James Case
  57. 57. Entering  New  Local  Terms     into  RELMA   ©2010 Regenstrief Institute and James Case
  58. 58. Manual  Enter/Edit     View/Add/Edit  Local  Terms   ©2010 Regenstrief Institute and James Case
  59. 59. Edit  Term  Dialog   EditAddDelete  Terms   Export  (New  function)   Search  Terms  by  Keyword   Text  alignment  option   Print  Preview  List   ©2010 Regenstrief Institute and James Case
  60. 60. Export  Local  Term  File   Delimiters  supported:   Tab,  comma,  bar  (|)   ©2010 Regenstrief Institute and James Case
  61. 61. Add  Local  Term   MICRO! BUBPLAG! BUBONIC PLAGUE – RRT PCR! Click  to  Add  to  Current   Working  File   ©2010 Regenstrief Institute and James Case
  62. 62. Search  Local  Term  File   Enter  Keyword  from  any   Return  to  Full  List   Field   ©2010 Regenstrief Institute and James Case
  63. 63. Print  Preview  Local  Term  File   ©2010 Regenstrief Institute and James Case
  64. 64. Steps  to  Import  Local  Terms   1.  Click  Import Local Terms  BuFon  from  Main  Menu       a) File>Import Local Terms from Delimited File   2.  Locate  your  local  terms  text  file   a)  E.g.  WinXP  Sample  files  loaded  into  C:Documents  and   SeMngsAll  UsersShared  DocumentsRELMA   3.  Name  your  Working  Set   a)  LMOF  database  can  contain  mulJple  work  sets   4.  Define  default  secJon  (OpJonal)   5.  IdenJfy  file  delimiter     6.  Assign  fields  to  LMOF  aFributes   a)  Ignore  fields  you  don’t  need   b)  Combine  fields  if  needed   7.  Check  “Case-­‐sensiJve”  if  needed   8.  Click  Import.   ©2010 Regenstrief Institute and James Case
  65. 65. Local  Term  File  Options   ©2010 Regenstrief Institute and James Case
  66. 66. Example  Tab-­Delimited  File   ©2010 Regenstrief Institute and James Case
  67. 67. Importing  Local  Files   Select  Import  Local  Terms   from  Delimited  File   ©2010 Regenstrief Institute and James Case
  68. 68. Navigate  to  File  Location   Select  File  iles  stored  ipen Sample  e and  Click  O n     RELMA  Directory   ©2010 Regenstrief Institute and James Case
  69. 69. Open  File  in  RELMA   Name  your  working  set.     RELMA  allows  multiple  sets  in   LMOF  database   Select  your  delimiter   Import  Button   ©2010 Regenstrief Institute and James Case
  70. 70. Open  File  in  RELMA   ©2010 Regenstrief Institute and James Case
  71. 71. Fields  Segregated   Assign LMOF Attribute Choose  eield  name   ©2010 Regenstrief Institute and James Case
  72. 72. Ready  to  Import   Minimum  assignments   Now  you  can  click  the   Import  button!   ©2010 Regenstrief Institute and James Case
  73. 73. Post-­Processing  of  Local  File   New  Feature!   •  A]er  import,  RELMA  Searches  for  terms   (words)  that  it  does  not  recognize   •  Stored  in  a  file  for  future  reconciliaJon   ©2010 Regenstrief Institute and James Case
  74. 74. Change  Local  Term  File   Select  the  Working  Set   ©2010 Regenstrief Institute and James Case
  75. 75. Alternative  Pragmatic  Way   •  Use  large  set  of  HL7  messages   •  AutomaJcally  make  dataset  of:   •  OBR  ID   •  OBR  descripJon   •  OBX  ID   •  OBX  descripJon   •  Sample  of  results    with     •  Real  values   •  Units   •  Abnormal  flags   •  Normal  ranges   ©2010 Regenstrief Institute and James Case
  76. 76. Generate  Local  term  eile  from  HL7  messages     Select  Import  Terms  from   HL7  File   ©2010 Regenstrief Institute and James Case
  77. 77. Select  File  to  Import   Select  HL7  File   ©2010 Regenstrief Institute and James Case
  78. 78. Specify  HL7  File  Name  and  Sample  Size   Name  the  Local  Term   File  (working  set)   Select  the  number  of   sample  values   Select  which  codes  to  store   ©2010 Regenstrief Institute and James Case
  79. 79. HL7  Messages  Data  Statistics   ©2010 Regenstrief Institute and James Case
  80. 80. New  Terms  added  to  LMOF   Click  on  “Edit  Test  to  see   Sample  Data   New  Battery  Code   ©2010 Regenstrief Institute and James Case
  81. 81. Sample  Results  for  Observation   New  Test  Code   Sample  Values  from   Messages   ©2010 Regenstrief Institute and James Case
  82. 82. Lenny  L’OINC  says:   “Load  the  Sample  Files   Into  RELMA  now!”   •  Import  the  two  sample  files   provided   •  Import_Sample_OBR.txt   •  Contains  baFery  code  and   descripJon   •  Import_Sample_OBX.txt   •  Contains  test  code  and   descripJon   •  Create  2  working  sets   •  Load  your  personal  data  set   ©2010 Regenstrief Institute and James Case
  83. 83. Cleaning  your  data   ©2010 Regenstrief Institute and James Case
  84. 84. Preparing  your  Data  for  Mapping   •  Improve  mapping  success  by:   •  Expanding  abbreviaJons   •  Standardizing  colloquial  terms   •  Ignoring  “administraJve”  terms   •  Standardizing  Jme  references   •  Can  be  done  prior  to  imporJng   •  BeFer  to  use  tools  built  into  RELMA   ©2010 Regenstrief Institute and James Case
  85. 85. RELMA  Cleaning  Tools   Use  this  tool  to  edit   unknown  terms   ©2010 Regenstrief Institute and James Case
  86. 86. Review  Unknown  Local  Terms   May  Re-­Scan  File  for   Unknown  Terms   ©2010 Regenstrief Institute and James Case
  87. 87. Replace  Local  Terms   Assign  LMOF  Attribute Replacement Options     ©2010 Regenstrief Institute and James Case
  88. 88. RELMA  Cleaning  Tools   Use  this  tool  to  make   global  substitutions   ©2010 Regenstrief Institute and James Case
  89. 89. Term  Substitution   Save  this  global  substitution   for  only  this  working  set   ©2010 Regenstrief Institute and James Case
  90. 90. Lenny  L’OINC  says:   “Begin  to  clean  your   data  now!”   •  Using  the  OBR  or  OBX  sample   files,  take  15-­‐20  minutes  to   clean  up  these  unrecognized   terms   •  You  may  use  your  own  data  if   you  wish.   ©2010 Regenstrief Institute and James Case
  91. 91. Searching  for  LOINC  Terms   ©2010 Regenstrief Institute and James Case
  92. 92. Simplieied  Search     Only  Tool   ©2010 Regenstrief Institute and James Case
  93. 93. Search  Window   “Common  Tests”   relative  frequency   Enter  Search  Terms     Limit  to     Specieic   Units   Limit  to  Common     Tests   ©2010 Regenstrief Institute and James Case
  94. 94. Context  Menu   Right  click  to  bring   up  context  menu   ©2010 Regenstrief Institute and James Case
  95. 95. Mapping  Local  Terms   ©2010 Regenstrief Institute and James Case
  96. 96. Mapping  Local  Terms   •  Select  your  Working  Set  to  Map   File>Change Local term File •  •  Select  “Map Local Terms to LOINC”  from   Welcome  Screen   •  Select  the  subset  of  terms  to  work  with:   •  All   •  Mapped   •  Unmapped   •  Set  your  Search Limits •  Set Search Limits BuFon   ©2010 Regenstrief Institute and James Case
  97. 97. Standard  Mapping  Window  Features   •  Customizable  grid   •  View  details  of  LOINC  term   •  Sort  by  column   •  Click  column     •  Custom  Sort   •  Print  or  export  results  grid   •  Spell  check  squiggly  line  to  signify  words   not  known  to  RELMA   ©2010 Regenstrief Institute and James Case
  98. 98. Mapping  Screen     View  or  edit  local  term   New  function!  Enter  local   term  number   Quick  select  button  list   Custom  Grid  Coneiguration   ©2010 Regenstrief Institute and James Case
  99. 99. Coneigure  Grid   Select  elements  to  display   Reorder  grid  elements   Visually  resize  elements   Reset  Default  Coneiguration   ©2010 Regenstrief Institute and James Case
  100. 100. Quick  choice  buttons   Viewing  LOINC  term  detail     ©2010 Regenstrief Institute and James Case
  101. 101. View  Local  Term  Details   Select  level  of  detail  to   display   ©2010 Regenstrief Institute and James Case
  102. 102. New  Feature  –  select  detail  level   New  function!  Select  level   of  detail  to  display   ©2010 Regenstrief Institute and James Case
  103. 103. Standard  Mapping  Screen   Begin  a  search   (or  hit  “enter”)   ©2010 Regenstrief Institute and James Case
  104. 104. Initial  Mapping  Results   EEK!    What’ll  I   do?!   Click  to   show  words   used  in   search   ©2010 Regenstrief Institute and James Case
  105. 105. Initial  Mapping  Results   Use  term   Number  of  LOINC   Battery  terms   checkbox   terms  containing   included  in   keyword   search   ©2010 Regenstrief Institute and James Case
  106. 106. Revised  Mapping  Results   Match  units   Number  of   selected  by   matching   default   records  found   ©2010 Regenstrief Institute and James Case
  107. 107. Re-­revised  Mapping  Results   Number  of   matching   Match  units   records  found   unselected   ©2010 Regenstrief Institute and James Case
  108. 108. Standard  Mapping  Screen   CANINE DISTEMPER VIRUS IF Enter  keywords  here   Clear  all   input  eields   ©2010 Regenstrief Institute and James Case
  109. 109. Ad  hoc  term  search   ©2010 Regenstrief Institute and James Case
  110. 110. Standard  Mapping  Screen   Navigate  through   the  local  terms   ©2010 Regenstrief Institute and James Case
  111. 111. Tabbed  Access  to  Functions   New  function!   Parts  Search   Navigate  to  Functions   from  Mapping  Page   Switch  between  Grid  and   Tree  Views   ©2010 Regenstrief Institute and James Case
  112. 112. Tree  View   ©2010 Regenstrief Institute and James Case
  113. 113. Tree  View   •  Results  displayed  hierarchically   •  Defined  by  the  mulJ-­‐axial  hierarchy  in  search   restricJons  (covered  later)   •  Map  to  a  term  in  tree  by  clicking  Map  buFon   or  double  clicking  term   •  Only  rows  that  have  LOINC  Codes   ©2010 Regenstrief Institute and James Case
  114. 114. Tree  View   Can  map  to  terms   Cannot  map  to   with  LOINC  Codes   terms   representing   LOINC  parts   Tree  Navigation   Buttons   ©2010 Regenstrief Institute and James Case
  115. 115. Assigning  a  LOINC  Map   Click  “Map”  Button     (or  doubleclick)   Highlight  correct   term   ©2010 Regenstrief Institute and James Case
  116. 116. Adding  Mapping  Comments   Check with Frank in Chemistry If  comments   option  is  selected,   prompt  appears   ©2010 Regenstrief Institute and James Case
  117. 117. Assigning  a  LOINC  Map   LOINC  Term   Assigned   ©2010 Regenstrief Institute and James Case
  118. 118. View  LOINC  Term  Details   View  details  for  a   specieic  LOINC  Term   Right  clicking  on  a  LOINC   term  brings  up  a  Task  Menu   ©2010 Regenstrief Institute and James Case
  119. 119. View  Panel  Children  (New  Function!)   Select  View  Panel  Children   from  context  menu   ©2010 Regenstrief Institute and James Case
  120. 120. Panel  Children   ©2010 Regenstrief Institute and James Case
  121. 121. LOINC  Term  Details   Can  scroll  down  a  single   formatted  page   Can  scroll  through   Change  to  expanded   returned  subset  of   details  view     terms   Change  text  size   ©2010 Regenstrief Institute and James Case
  122. 122. Coneigure  Export  Options   Output  Options   Include     Save  Coneiguration   column  headers   and/or  Export   ©2010 Regenstrief Institute and James Case
  123. 123. Excel  Export  Format   ©2010 Regenstrief Institute and James Case
  124. 124. More  on  Searching     Mapping  Screen   ©2010 Regenstrief Institute and James Case
  125. 125. Using  Wildcards  in  Searches   •  Substring  search  supported  by  default   •  “Gluc”  yields  any  terms  with  “gluc”  in  the   component/analyte     •  “*”  replaces  any  number  of  characters   •  GLUC*   •  *COSE   •  GLU*SE   •  “?”  replaces  a  single  character   •  GLUCOS?   •  ?LUCOSE   •  GLUC?SE   ©2010 Regenstrief Institute and James Case
  126. 126. Other  Search  Qualieiers   •  “#”  represents  the  “NOT”  operator   •  #GLUCOSE  –  terms  without  the  Word  Glucose   •  “|”  is  the  “OR”  operator   •  GLUCOSE  |  LACTOSE   •  Can  have  mulJple  “OR”s  per  box   •  Can  Mix  OR  and  NOT  and  Wildcards   ©2010 Regenstrief Institute and James Case
  127. 127. Search  Qualieiers     Includes  Glucuronidase,   Glucosidase,   Glucosylceramidase,  etc.   ©2010 Regenstrief Institute and James Case
  128. 128. Combining  Search  Terms   Exclude  Glucosidase   Reduced  number  of  terms   ©2010 Regenstrief Institute and James Case
  129. 129. Limiting  Searches   ©2010 Regenstrief Institute and James Case
  130. 130. Setting  Search  Limits   •  Narrows  search  to  specific  subset  of  LOINC  terms   •  Reduces  number  of  candidate  terms   •  Limits  can  be  applied  to  all  components   •  Component  aFribute  can  be  further  restricted  by   number  of  words   •  Tree  structure  allows  for  hierarchical  constraints   ©2010 Regenstrief Institute and James Case
  131. 131. General  Search  Constraints   •  Controls  features  including:   •  Limit  to  LOINC  terms  compaJble  with  submiFed  units   •  Forced  match  with  any  specimen  contained  in  name   •  Methodless  terms  only     •  Limit  to  components/analytes  with  N  or  fewer  words  in  their   name   •  Pop  up  search  Jming  staJsJcs  a]er  each  search   •  Use  carefully  or  search  may  not  be  successful    (Note  parallel  control  switches  at  boFom  of  screen)   ©2010 Regenstrief Institute and James Case
  132. 132. Setting  Search  Limits   Click  Hierarchy  &  Search   Limits  Tab   ©2010 Regenstrief Institute and James Case
  133. 133. Setting  search  limits   Can  also  set  most  of  them  by  toggling  buFons   at  the  boFom  of  the  screen     Toggle  Buttons   ©2010 Regenstrief Institute and James Case
  134. 134. Search  Constraints   Attribute  trees   Local  Unit  Constraint:   Now  defaults  to  “ON”   Predeeined,  general  search   constraints   ©2010 Regenstrief Institute and James Case
  135. 135. Terms  Consistent  with  Units   Only  terms  consistent   with  mmol/L  appear   ©2010 Regenstrief Institute and James Case
  136. 136. Setting  Search  Limits   Specimen   constraints   ©2010 Regenstrief Institute and James Case
  137. 137. Terms  Consistent  with  Specimen     CSF Enter  default   Specimen   ©2010 Regenstrief Institute and James Case
  138. 138. Terms  Consistent  with  Specimen     Only  CSF  Terms  are   returned   ©2010 Regenstrief Institute and James Case
  139. 139. Setting  Search  Limits   Methodless  Terms   Override  Methodless  Terms   Restriction   Restriction   ©2010 Regenstrief Institute and James Case
  140. 140. Limit  to  Methodless  Terms   ©2010 Regenstrief Institute and James Case
  141. 141. Limit  to  Methodless  Terms   Only  Methodless   Terms  Appear   ©2010 Regenstrief Institute and James Case
  142. 142. More  on  Methodless  Terms   •  Some  LOINC  categories  do  not  have   methodless  terms   •  Checking  methodless  only  will  remove  these   from  view  on  results  grid   •  Checking  addiJonal  box  allows  these  to  be   seen   ©2010 Regenstrief Institute and James Case
  143. 143. Methodless  Only  Unchecked   All  terms  returned   ©2010 Regenstrief Institute and James Case
  144. 144. Methodless  Only  Checked   Only  Methodless   terms  returned   Differ  in  one  or   more  components   ©2010 Regenstrief Institute and James Case
  145. 145. Conditional  Methodless   More  terms   returned   No  methodless   term;  all  shown   ©2010 Regenstrief Institute and James Case
  146. 146. Setting  Search  Limits   Limit  to  Lab  Tests  Only     (No  Clinical  LOINC  Terms)   ©2010 Regenstrief Institute and James Case
  147. 147. Setting  Search  Limits   Limit  to  lab  tests  that  comprise   99.8%  of  INPC  volume   ©2010 Regenstrief Institute and James Case
  148. 148. Setting  Search  Limits   Limit  Number  of  Words  in  the   Component  Attribute   ©2010 Regenstrief Institute and James Case
  149. 149. Limit  Number  of  Component  Words   Without  Limit  Applied:   838  terms  returned   ©2010 Regenstrief Institute and James Case
  150. 150. Limit  Number  of  Component  Words   Restriction  appears  on   Toggle  Bar     (cannot  toggle  off)   Component  limited  to   1  word   With  Limit  Applied:     69  terms  returned   ©2010 Regenstrief Institute and James Case
  151. 151. Setting  Search  Limits   Include  Deprecated  or   Discouraged  LOINC  Codes   with  Returned  Terms   ©2010 Regenstrief Institute and James Case
  152. 152. Include  Deprecated  LOINC  Terms   -­‐ You  cannot  map  to   deprecated  LOINC  terms   -­‐   You  are  warned  before   mapping  to  discouraged   LOINC  terms   Discouraged  LOINC  Terms  appear  as  an   inverted  triangle     Deprecated  LOINC  Terms  appear  as   Strikethrough  Text  with  a  “Do  Not”   Symbol     ©2010 Regenstrief Institute and James Case
  153. 153. Favor  Property  Restriction   Favor  one  type  of   property  over  others   All  other  components   being  equal  MCnc   only  will  be  displayed   ©2010 Regenstrief Institute and James Case
  154. 154. Order/Observation  Restriction   Order  or  Observation   preference   ©2010 Regenstrief Institute and James Case
  155. 155. LOINC  Hierarchies  –  Class  Tree   Three  top-­level   branches   Tree  Navigation   Buttons   ©2010 Regenstrief Institute and James Case
  156. 156. Before  Class  Restriction   Most  terms  have  class   of  “CHAL”   Large  number  of   candidate  terms   ©2010 Regenstrief Institute and James Case
  157. 157. Search  Trees   chal Restrict  eligible  tests   to  non-­challenge   chemistry  tests  only   ©2010 Regenstrief Institute and James Case
  158. 158. Following  Class  Restriction   Only  Non-­Challenge   Chemistry  tests  returned   ©2010 Regenstrief Institute and James Case
  159. 159. Improvements  to  Trees   Continued  reorganization  to   provide  a  Specimen   hierarchy   ©2010 Regenstrief Institute and James Case
  160. 160. Improved  Hierarchy  for  Component   Click  on  details  for  more   information  about  the   selection   Show  the  LOINC  Codes   associated  with  these   components   ©2010 Regenstrief Institute and James Case
  161. 161. Details  Screen  LOINC  Part   ©2010 Regenstrief Institute and James Case
  162. 162. Show  Associated  LOINCs   ©2010 Regenstrief Institute and James Case
  163. 163. Details  Screen  LOINC  Term   Detailed  Information  on   LOINC  Parts   ©2010 Regenstrief Institute and James Case
  164. 164. Tree  Export  Tools   Export  according  to   Coneiguration     Coneigure  Export  Format     ©2010 Regenstrief Institute and James Case
  165. 165. Tree  Export  Coneiguration   ©2010 Regenstrief Institute and James Case
  166. 166. RELMA  -­  Tree  Features   •  All  trees  operate  the  same  way   •  Shows  terms  spelled  out   •  Can  expand  and  collapse  parts  or  all  of  tree.   •  Tree  is  string  searchable     •  Search  can  be  based  on  one  or  more   branches  of  a  tree  with  or  without  other   criteria   •  Use  “Clear  Most  Limits”  buFon  on  Mapping   Screen  to  remove  all  tree  selecJons   ©2010 Regenstrief Institute and James Case
  167. 167. New  Feature!    LOINC  Part  Search   •  Same  look  as  term  search   •  Uses  “Google-­‐like”  query  language   •  Extremely  fast   •  Include  and  exclude  criteria   •  ParJal  string  matching  (using  wildcards)   •  Demo   •  Campylobacter  fetus,  not  DNA     ©2010 Regenstrief Institute and James Case
  168. 168. Navigating  through  the   Mapping  Process   ©2010 Regenstrief Institute and James Case
  169. 169. LOINC  Mapping  Tactics   •  Limit  effort  to  one  lab  secJon  at  a  Jme  and   focus  experJse   •  Chemistry  and  hematology  will  be  easiest   •  Consider  prioriJzing  by  frequency   ©2010 Regenstrief Institute and James Case
  170. 170. Vreeman  DJ,  Finnell  JT,  Overhage  JM.  A  Rationale  for  Parsimonious  Laboratory  Term   Mapping  by  Frequency.  AMIA  Annu  Symp  Proc.  2007;:771-­775.   ©2010 Regenstrief Institute and James Case
  171. 171. More  LOINC  Mapping  Tactics   •  Try  using  method-­‐less  terms  first   •  Specific  methods  can  be  transmiFed  in:   •   OBX–17  (v2.x),  ObservaJon.methodCode  (v3.0)   •  Examine  local  units  or  real  results  to  verify   correct  properJes   •  ProperJes  are  rarely  disJnguishable  in  tests   •  You  don’t  have  to  do  it  all  at  one  siMng   •  Use  the  “Unmapped”  funcJon  to  return  where  you   le]  off   •  With  every  release  -­‐  Update  previous  mappings   to  idenJfy  deprecated  terms   ©2010 Regenstrief Institute and James Case
  172. 172. Common  Mapping  Issues   •  Locally  Defined  Test  Name  Ambiguity   •  Reuse  of  local  test  code   •  “Analyte-­‐free”  Local  Test  Names   •  Incongruent  Value  sets  (Scale  ambiguity)   •  Result  vs.  InterpretaJon   •  Available  LOINC  Terms  too  Specific   •  Available  LOINC  Terms  too  General   •  Panel  vs.  Discrete  Test   •  Common  in  Microbiology   ©2010 Regenstrief Institute and James Case
  173. 173. Using  your  Mapped  Terms   •  Print  results  of  LOINC  Mapping   •  Export  to  File   ©2010 Regenstrief Institute and James Case
  174. 174. Coneigure  Export  Format   Context  Sensitive  Export   Coneiguration     ©2010 Regenstrief Institute and James Case
  175. 175. LMOF  Export  Coneiguration   Select  Export  Format     Select  Fields  to  Export   Save  Coneiguration  and   Export   ©2010 Regenstrief Institute and James Case
  176. 176. Print  Mapped  Terms  from  View/Add/ Edit  Menu   Click  Print  button  to  Preview   May  highlight  terms  to  be   output   printed   ©2010 Regenstrief Institute and James Case
  177. 177. Formatted  Report  Output   Click  Print  button  to  output   formatted  report   ©2010 Regenstrief Institute and James Case
  178. 178. Custom  Export  Coneiguration   Select  the  Format  you  wish   to  Export   Select  the  Fields  you  wish  to   Export   ©2010 Regenstrief Institute and James Case
  179. 179. Excel™  Export   ©2010 Regenstrief Institute and James Case
  180. 180. Intelligent  Mapper     •  Run  in  batch  mode  to  find  N-­‐  closest  terms   •  Can  then  use  this  output  to  do  final  mapping   •  Again  units  are  VERY  important   •  Can  pick  all  limits  available  to  regular  mapping   •  With  Radiology  can  use  CPT  to  help   •  Intelligent  Mapper  Radiology  References   •  Vreeman  DJ,  McDonald  CJ.  A  Comparison  of  Intelligent  Mapper  and  Document   Similarity  Scores  for  Mapping  Local  Radiology  Terms  to  LOINC.  Proc  AMIA  Symp.   2006;809-­‐813.   •  Vreeman  DJ  and  McDonald  CJ.  Automated  Mapping  of  Local  Radiology  Terms  to   LOINC.  Proc  AMIA  Symp.  2005;769-­‐773.   ©2010 Regenstrief Institute and James Case
  181. 181. Picking  the  Intelligent  Mapper   Begin  by  einding  qualifying   candidates  based  on  local   eile  attributes   ©2010 Regenstrief Institute and James Case
  182. 182. Intelligent  Mapper  Start  Screen   Max  search  time  per  local   May  Apply  Hierarchy   Restrictions  Prior  to  Run term     ©2010 Regenstrief Institute and James Case
  183. 183. Intelligent  Mapper  -­  Mapping  Screen   ©2010 Regenstrief Institute and James Case
  184. 184. Exporting  Mapped  Terms   Export  Terms  to   Delimited  File   ©2010 Regenstrief Institute and James Case
  185. 185. Export  Terms  Dialog   Select  Term  Set   Select  Delimiter   Check  Fields  you   wish  to  export   ©2010 Regenstrief Institute and James Case
  186. 186. Other  RELMA ®   Features   ©2010 Regenstrief Institute and James Case
  187. 187. Panels,  Forms  and  Survey  Review   Review  Panels,  Forms  and   Surveys   Review  Panels,  Forms  and   Surveys   ©2010 Regenstrief Institute and James Case
  188. 188. Government  Forms   Component  LOINC   terms   Form  Name   ©2010 Regenstrief Institute and James Case
  189. 189. Laboratory  panels   Expand  category  to   see  panels     Double-­click   panel  name  to  see   components   ©2010 Regenstrief Institute and James Case
  190. 190. Expanded  Panel  Detail   ©2010 Regenstrief Institute and James Case
  191. 191. Expanded  Clinical  Panel   ©2010 Regenstrief Institute and James Case
  192. 192. Clinical  Panels   Find  where  a  term  has   been  used   ©2010 Regenstrief Institute and James Case
  193. 193. LOINC  Term  Panel  Usage   ©2010 Regenstrief Institute and James Case
  194. 194. Other  Survey  Instruments   ©2010 Regenstrief Institute and James Case
  195. 195. HIPAA  Attachments   View  Various  HIPAA   Attachments     ©2010 Regenstrief Institute and James Case
  196. 196. HIPPA  Attachment  Tree   ©2010 Regenstrief Institute and James Case
  197. 197. Expanded  Attachment  Data   ©2010 Regenstrief Institute and James Case
  198. 198. Context  Specieic  Hierarchies   •  Allows  local  definiJon  of  LOINC  code   hierarchies   •  Template  data  base  is  provided  with   RELMA   •  CONTEXT_SPECIFIC_HIERARCHY_TEMPLATE.mdb   •  Does  not  support  .accdb  format   •  Hierarchies  can  be  displayed  (only)  in   RELMA   •  Codes  and  terms  may  come  from  mulJple   code  systems   ©2010 Regenstrief Institute and James Case
  199. 199.   Access  Context-­Specieic  Hierarchies Select  Context  Specieic   Hierarchies   ©2010 Regenstrief Institute and James Case
  200. 200. Select  Directory   ©2010 Regenstrief Institute and James Case
  201. 201. Context  Specieic  Hierarchies   Locally  deeined   aggregation   ©2010 Regenstrief Institute and James Case
  202. 202. Can’t  eind  the   term  you   want?   ©2010 Regenstrief Institute and James Case
  203. 203. Search  Hints  and  Tips   •   Keywords  with  zero  frequency  are  ignored   •  May  need  to  rephrase  –  use  synonym   •  Some  causes  for  no  returned  terms   •  Too  many  keywords  in  search  –  uncheck  some   •  Limits  applied  that  don’t  make  sense     •  E.g.  Method-­‐less  tests  plus  Method  tree  set  to  EIA   •  Did  not  find  and  revise  words  not  in  RELMA   •  Local  units  not  in  RELMA   •  Units  are  GREAT  discriminators   •  You  may  have  tests  that  need  to  be  added  to   LOINC   ©2010 Regenstrief Institute and James Case
  204. 204. Proposing  New  LOINC  Terms   ©2010 Regenstrief Institute and James Case
  205. 205. Proposing  New  Terms   •  Make  sure  the  term  is  really  needed   •  Think  of  other  names  for  the  same  concept   •  Avoid  detailed  methods  or  localizaJons   •  Is  the  disJncJon  really  important?   •  Supply  sufficient  annotaJon  to  jusJfy  the  new  term   •  Package  inserts,  sample  reports  (email  to  Regenstrief)   •  The  more  the  beFer!   •  Construct  new  terms  within  RELMA   •  File>Propose a LOINC •  Linked  to  the  “trees”  to  allow  browsing   •  Can  review  and  submit  them  to  LOINC  from  within   RELMA   ©2010 Regenstrief Institute and James Case
  206. 206. Propose  new  LOINC  terms   Select  Propose  a   LOINC   ©2010 Regenstrief Institute and James Case
  207. 207. Propose  new  LOINC  terms   Create  new  term,   save  current  term   or  Exit  form   Navigate  through   Required  eields   proposed  terms   ©2010 Regenstrief Institute and James Case
  208. 208. Preview  Proposed  Terms   Review  your  new   terms   ©2010 Regenstrief Institute and James Case
  209. 209. Preview  Proposed  Terms   Choose  whether  to   send  or  postpone   All  proposed  terms   fully  editable   ©2010 Regenstrief Institute and James Case
  210. 210. Use  Existing  Terms  as  Template   Click  the  Propose   Term  button   Select  your  closest   match   ©2010 Regenstrief Institute and James Case
  211. 211. Use  Existing  Terms  as  Template   All  required   components  eilled  in   ©2010 Regenstrief Institute and James Case
  212. 212. Using  LOINC  and  SNOMED   Together   ©2010 Regenstrief Institute and James Case
  213. 213. Where  do  LOINC  and  SNOMED  Fit?   Remember:   •  LOINC  represents  the  quesJon:   •  Is  there  any  Botulism  toxin  in  my  specimen?   (33708-­‐9)   •  Organisms  idenJfied  in  specimen?  (634-­‐6)   •  SNOMED  represents  the  answer:   •  NegaJve  (SCTID  260385009)   •  E.  coli  O157:H7  (SCTID  103429008)   ©2010 Regenstrief Institute and James Case
  214. 214. Where  do  LOINC  and  SNOMED  Fit?   •  In  an  HL7  message,  LOINC  may  be  used:   •  In  OBR-­‐4  (Universal  Service  IdenJfier)   •  In  OBX-­‐3  (ObservaJon  IdenJfier   •  SNOMED  may  be  used:   •  In  OBX-­‐5  (where  nominal  values  are  needed)   •  Almost  anyplace  else  in  an  HL7  message  where   coded  values  are  needed   ©2010 Regenstrief Institute and James Case
  215. 215. OBX:  With  a  Coded  Value   A  code  that   identieies  the   data  type  in     The  code  is   The  code  is   OBX-­5  as  a   from  LOINC   from  SNOMED   coded  element   OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT    OBX-­3:A  code  that   identieies  the  data  in   OBX-­5:  Data   OBX-­5   A  code  for  L.   (Listeria  culture)   monocytogenes   ©2010 Regenstrief Institute and James Case
  216. 216. HL7  2.5  Example  (ER-­7  format)   MSH|^~&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01| LABGL1199510221838581| P| 2.3||| NE| NE First  Order  OBR   PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^ (Culture  and  ID)   Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090alue   First  Result  V (SNOMED)   OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult ^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^ Second  Order  OBR   UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN (Susceptibility)   OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837 OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility Second  Result(s)   First  Result  Description   Panel^esult   199812300934||||||||Bacterial isolate| IN2973^ Schadow^ First   LN|||   (Culture  and  ID) Gunther^^^^   OBXs   OBX  (LOINC)   MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate ^SCT|||||| F||| 199812300934|| CA20837 OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934|| CA20837 OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F||| 199812300934|| CA20837 ©2010 Regenstrief Institute and James Case
  217. 217. Q  and  A  Session   ©2010 Regenstrief Institute and James Case
  218. 218. Exercise   Map  your  own  data   ©2010 Regenstrief Institute and James Case

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