Laboratory LOINC Workshop – Chicago, IL!                    LOINC!         Introduction and Mapping Boot Camp!            ...
Acknowledgements!LOINC Development Team!Kathy Mercer, Jaci Phillips, Ian Pyle, David Baorto,Fran Brahmi!!RELMA Development...
Overview!1.  Origins of LOINC!2.  LOINC 101!3.  Using RELMA!4.  Searching and Mapping to LOINC!5.  Approaches to Mapping a...
Origins of LOINC!The lingua franca of clinical observation exchange!
Soda or Pop?!                    what you see in the order list                                                 !Lab A!   ...
Logical           Observation           Identi"ers           Names and           Codes!A universal code system that facili...
If an observation is a questionand the observation value isan answer…  !LOINC provides codes for   !questions   !Other voc...
What is my patient’shemoglobin level?!718-7:Hemoglobin:MCnc:Pt:Bld:Qn!
How fast does mypatient usually walk?!41959-8:Walking speed:Vel:1W^mean:^Patient:Qn:Calculated
Indiana Network for Patient Care!   HL7 v.2.X Message!MSH|^~&|HOSPITAL_A|SAMPLE_HOSPITAL_A|||$YearMonthDay|||||||||||||||P...
Result with a Coded Value!   Data type ofresult (OBX-5) is a      This code is          This code is coded element!       ...
Laboratory LOINC!
Clinical LOINC!
The LOINC Community!Open. Nimble. Pragmatic.!
Open Development!Worldwide distribution at no cost!End-user content additions!Welcome all comers!Volunteers!!
Regenstrief Institute!Steward!Developer of content!Developer of tools!Developer of community!Distributor!Voice!!
LOINC Codes Over Time By Release!70,000!          LOINC Codes!          Lab Codes!60,000!                                 ...
loinc.org members!12,000!10,000! 8,000! 6,000! 4,000! 2,000!          11 new members per day!               330 new member...
11,100+ users in 141 countries!
Downloads: ~1100/month!
6,900 views!           !  100 views!  260 views!
International Adoption!participation, translation, implementation!
LOINC Submitters!Since 2009, 84 organizations from 14 countries!
LOINC Translators!   18 organizations!
New and Updated!Estonian!French!German!Greek!Italian!Spanish!
In-progress!Catalan!Dutch!French!Russian!!
Large Implementations!SIGA Saúde project !Canada Health Infoway!ePSOS!Assistance publique - Hôpitaux de Paris!Hong Kong Ho...
US Adoption!A few key highlights!
US Federal Agencies!       NLM!        VA!       DoD!       IHS!       NCI!       CDC!
Other Key US Adoptions!        HITSP!        eLINCS!       NAACCR!        CDISC!      NCQA/HEDIS!         HL7!        HIPA...
EHR Incentive   Programa.k.a. “Meaningful Use”!
New Frontiers inContent Modeling!
Standardized Assessments!
Purpose!Assessments are widely used…!…and not unlike other clinical observations!!
LOINC could be a           !!  master question "le           and uniform representation !
Panels/Forms Available as   Separate Download!
Currently in LOINC!US Government Forms!   CARE, MDSv2, MDSv3, OASIS B1, OASIS C, RFC!   US Surgeon General’s Family Health...
Translational Research Variables!
LOINC 101!LOINC for newbs (not nOObs)!
The LOINC Distribution!
http://search.loinc.org!
Anatomy of a LOINC Term!       5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA!         5193-8!                    ...
NOT part of a LOINC Name!Testing instrument!Speci"c details about the specimen!Priority (e.g. STAT)!Where testing was done...
Component!    The substance or entity that is measured,             evaluated, or observed!Sodium!Glucose!Brucella sp. org...
Component Structure                                      !      Analyte Name^Challenge^Adjustments                        ...
Property!                      * the most di"cult LOINC axis!The characteristic or attribute of the analyte that      is m...
Property!                       * the most di"cult LOINC axis!Fully Named Properties!                                    m...
Common Property Issues!               Fraction versus Ratio!Fraction = Part/Whole!    !NFr: % Eosinophils / leukocytes!   ...
Timing!The interval of time over which the observation          or measurement was made!Pt!       point in time!12H!      ...
System!The system (context) or specimen type upon which the               observation was made.!Ser!          serum!Ser/Pl...
System Structure!                  System^Super System!Super System!Patient is the default!Used to indicate!   blood produ...
Scale!Qn!     Quantitative!!           continuous numeric!!           optional operator!Ord! Ordinal!!           Ranked se...
Method!Only needed if interpretation a#ected!  Di#erent normal ranges!  Test sensitivity!Listed at the generic level!  Agg...
LOINC Parts !Uses !translation, synonymy, building hierarchies,creating display names, linking descriptions!
Hierarchies!LOINC class !Each LOINC axis!Multi-axial!    Component | System!    Separate download!    !!    !
RELMA®!REgenstrief LOINC Mapping Assistant!
We’ll Cover!RELMA “Boot Camp”!Mapping tips/pitfalls!Get started!
What’s it Good For?!Browse LOINC!Map your local terms to LOINC!   !import/export!   !translate local words to LOINC-speak!...
Get RELMA!
http://search.loinc.org!
RELMA Highlights!Hierarchies!Search!Enhanced details view!Common test list!Panels and forms!Export, copy, paste!
Search Syntax!Google-like!AND, OR, -<word>, +<word>!Limit by category (e.g. micro)!Wildcards (? and *)!!    Assumes EXACT ...
More RELMA Features !User Speci"ed Search Limits !Selectable trees for:! Class! Multiaxial (component/system)! System (spe...
Installing RELMA!
Installation Steps!Need Windows (or a VM on a Mac)!Got disk space? 2Gb is recommended!Start installer <drive>:RELMASetup!S...
File Locations!Database and Ancillary Files!Windows XP!    !  C:Documents and SettingsAll UsersDocumentsRELMAWindows Vista...
Running RELMA!
Main Menu/Welcome Screen!     File->Set Preferred Language!
Select Linguistic Variant(s)!
LOINC Terms with Spanish Linguistic Variant!                                All Spanish!                                  ...
Simple Search!
Search Window!enter search terms                 !                                      limit to common tests             ...
Search Window!          Help!              !    “common tests”   relative frequency!
New RELMA Help"le!
Context Menu!right click to bring up    context menu   !
Setting User Preferences!
Set User Preferences!               select User Preferences                                     !                 from the...
Set User Preference Dialog!                     File locations: !              (see prior slide for location)             ...
User Map Screen Preferences!             Include/exclude battery terms                                         !          ...
Importing Local Termsinto RELMA!
4 Ways to Build LMOF!1.  Hand enter!              bad!2.  Make your own table !    bad!3.  Import text "le from    good!  ...
Make a Local Dataset!Extract from Your Test Catalog! Battery code! Battery description or name! *Local code ! *Test descri...
Make a Delimited Text File!Need separate "elds!Use any delimiter!Fields in any order!Required "elds (minimum):!  Local Cod...
Importing Local Terms!1.  Start it up!2.  Find local term "le!C:Documents and SettingsAll UsersDocumentsRELMASamplesC:User...
Example Tab-Delimited File!
Importing Local Files!             select “Import Local Terms                from Delimited File”!                  or jus...
Navigate to File Location!               select File andstored in !                 sample "les click Open                ...
Open File in RELMA!                               Give it a name!                        (RELMA allows multiple sets in   ...
Open File in RELMA!     oh "ddlesticks!!!                     !
Match Your Fields!                assign LMOF attribute!
Match Your Fields!                choose "eld name!
Now You’re Ready!!minimum assignments                  !                               Do It!                             ...
After import, RELMA willsearch for words it does not         recognize!
Alternate Import (best)!Nothing closer to the truth than real data!
Big Pile of HL7 Messages!!RELMA parses into dataset!    OBR ID!    OBR description!    OBX ID!    OBX description!    Samp...
Generate Local term "le from HL7 messages !                       select Import Terms from                                ...
Select File to Import!                  select HL7 "le!
Specify HL7 File Name and Sample Size!name the local term "le (working set)!                     select the number of     ...
HL7 Messages Data Statistics!
Your turn!         ! Import Local Terms                  !(or sample OBX "le)!
Cleaning Your Data!A little time upfront saves more later!                                          photo via Mu#et!
Prep Your Data for Mapping!Improve mapping success!  !Expand abbreviations!  !Ignore “administrative” words!  !Standardize...
RELMA Cleaning Tools!                use this tool to edit                  unknown terms   !
Review Unknown Local Terms!         may re-scan "le for          unknown terms   !
Replace Local Terms! Assign LMOF Attribute  replacement options !                     !
RELMA Cleaning Tools!                use this tool to make                 global substitutions                           ...
Term Substitution!save this global substitution  for only this working set!
Clean Up!        !Take some time to  clean up your    sample "le!
Reviewing yourLocal Terms!
Change Local Term File!             Select the Working Set                                  !
Manual Enter/Edit !           View/Add/Edit Local Terms                                   !
Edit Term Dialog!                                        EditAddDelete Terms                                              ...
New Terms added to LMOF!click on “Edit Term” to see        sample data!                              new battery code!
Sample Results for Observation!                    Sample Values from                        Messages !
Search Local Term File!Calcium!                  Enter Keyword from any                                  Return to Full Li...
Export Local Term File!Delimiters supported:! Tab, comma, bar (|)                   !
Searching andMapping to LOINC !what RELMA was born to do!                             Photo via Jeffrey Beall!
Hit It!               !Are you working on the    right local "le?                   !
Core Mapping Screen Features!Customizable grid !   Export results grid!Sort by columns!      Stores mappings!View term det...
Mapping Screen !          View or edit local term!        Navigate through the local terms                                ...
Con"gure Grid!                        Select elements to display!                                          Reorder grid el...
Quick choice buttons!Viewing LOINC term detail!
View Local Term Details!          Select level of          detail to display!
Select detail display level!Select level of detail to         display!
Standard Mapping Screen!Begin a search !(or hit “enter”)               !
Initial Mapping Results!                   Fiddlesticks !#*$%!!                       What now??? !  Click toshow words  u...
Initial Mapping Results!Use term    Number of LOINC    Battery termscheckbox!   terms containing    included in           ...
Revised Mapping Results!                        Number of                         matching                       records f...
Re-revised Mapping Results!               Click any column               header to re-sort                               !...
Standard Mapping Screen!                   CANINE DISTEMPER VIRUS IFEnter keywords here!                             Clear...
Ad hoc term search!
Tabbed Access to Functions!    Navigate to Functions     from Mapping Page  !          Switch between Grid and            ...
Tree View!
Tree View!  Can map to terms                 Cannot map to  with LOINC Codes!                    terms                    ...
Assigning a LOINC Map!                     Click “Map” Button!                        (or doubleclick)                    ...
Adding Mapping Comments!Check with Frank in Chemistry          If comments        option is selected,         prompt appea...
Assigning a LOINC Map!  LOINC Term   Assigned!
View LOINC Term Details!                                 View details for a                                speci"c LOINC T...
LOINC Term Details!                                Can scroll down a single                                    formatted p...
LOINC Term Details: Panels!
View Panel Children!Select View Panel Children    from context menu  !
Panel Children!
Con"gure Export Options!                    Output options                                 !                              ...
Excel Export Format!
More on Search Syntax!Tips and Tricks!                    Photo via Jeffrey Beall!
Wildcards!“*” replaces any number of characters!  GLUC*!  *COSE!  GLU*SE!“?” replaces a single character!  GLUCOS?!  ?LUCO...
Search Quali"ers !            Detailed help available!Includes Glucuronidase,      Glucosidase,Glucosylceramidase, etc.!
Search in a Field!Field!       Example!LOINC!       loinc:12628-4!Component!   component:chemotherapy!Property!    glucose...
Other Cool Tricks!Use parentheses!!(flu OR rhinovirus) -haemophilus! component:(norepinephrine creatinine)!Fuzzy search (~...
Limiting Your Searches!Sometimes 60,000 terms is too many!
Setting Search Limits!Reduces number of candidate terms!Many, many options!Hierarchy allows domain restrictions!
with great power comes  great responsibility!                          Photo via [cipher]!
Setting Search Limits!click Hierarchy & Search Limits tab!
Search Constraints!                                         Attribute trees                                               ...
Terms Consistent with Units!               Only terms consistent                with mmol/L appear !
Quick Access Toggles For Common Restrictions!                 On/O# Toggles                             !
Specimen Restriction!              Specimen              constraints                        !
Terms Consistent with Specimen !                           CSF           enter default             specimen!
Terms Consistent with Specimen !Only CSF Terms are     returned!
Setting Search Limits!Methodless Terms     Override Methodless Terms   Restriction!              Restriction!
Limit to Methodless Terms!
Limit to Methodless Terms!only Methodless terms appear!
Methodless Only Unchecked!         All terms returned!
Methodless Only Checked!                     Only Methodless                      terms returned! Di#er in one ormore comp...
Conditional Methodless!                   More terms                    returned!No methodlessterm; all shown!
Setting Search Limits!         Limit to Lab Tests Only!        (No Clinical LOINC Terms) !
Setting Search Limits!           Empirically derived common tests                                          !              ...
A brief aside…!Developing convenience sets!                               photo via x-ray delta one!
A Few Tests Give Most Results!                                                100%!Cumulative Laboratory Observation Volum...
Setting Search Limits!      include Trial, Deprecated or     Discouraged LOINC codes with            returned terms  !
LOINC Term Status!Trial!! as the concept and associated attributes may change.  Concept is experimental in nature. Use wit...
Include Deprecated LOINC Terms!Can’t map to a deprecated term!Warning before mapping to discouraged term!      Discouraged...
LOINC Hierarchies – Class Tree!          Three top-level             branches !                            Tree Navigation...
Before Class Restriction!              Most terms have class of “CHAL”                                            !Large n...
Hierarchies!       Restrict eligible tests         to non-challenge        chemistry tests only !
Following Class Restriction!  Only Non-ChallengeChemistry tests returned!
A Reminder About Search Limits!                  Indicates that you’ve got                   something set over here !
Component Hierarchy!             “right click” for context menu                with “view details” option!      Show the L...
Details Screen: LOINC Part!
Show Associated LOINCs!
Hierarchy Wrap-up!All trees operate the same way!All grids operate the same way!Tree is searchable !Combine tree limits wi...
Search Hints and Tips!Zero hit keywords are ignored!    !(may need to rephrase)!!Common causes of Zero results!    !Too ma...
RELMA’s Auto Mapper!Starting with our best guesses may save you time!
What Does It Do?!Batch processes local term "le to getN- closest candidate LOINCs!!Uses words and units from local terms!!...
Recent Improvements!Faster. Way faster.!Better clean-up routine!New specimen guesser!Better local to LOINC word "nder!Brea...
Does it Work?!Lab terms (internal analysis)!            !#1 ranking: 60-70ish%!            !In Top 5: 70-80ish%!!Radiology...
(Lab) Auto Mapper!                                     launch it here!a couple of options                  !      print re...
Intelligent Mapper - Mapping Screen!
Mapping Guidance andApproaches to SpecialDomains!Top N, Reportable Conditions, Newborn Screening!
Not just an IT problem!
Get real.!units, results, experts!
Don’t be a one hit wonder.!
Additional Pearls andGuidance!Clem McDonald, MD!Director, Lister Hill National Center for Biomedical Communications – Nati...
Other               RELMA ®Features!Oh yes, there’s more!!
Using Your Mapped Terms!You’ve done the work. Now reap the glory.!                                             photo via j...
Con"gure Export Format!Context Sensitive Export     Con"guration!
LMOF Export Con"guration!Select Export Format!                        Select Fields to Export                             ...
Printing Mapped Terms!                            Click Print button to PreviewMay highlight terms to be               out...
Custom Export Con"guration!    Select the Format you wish             to Export                     !    Select the Fields...
Excel™ Export!
Export Terms Dialog!Select Term Set              !                                          Select Delimiter              ...
More RELMA Fun!Parts, Panels, and Proposing New Terms!
LOINC Part Search!Works just like the term search!Handy for looking at descriptions!
Parts Search!
Parts Search!   only parts that havedescriptions, references, etc                            !
Panels, Forms, and Surveys!Wanted to make it easy to "nd!Special features for browsing!
Panels, Forms and Survey Review!                           Review Panels, Forms and                                   Surv...
Government Forms!
Laboratory Panels!         Double-click panel           name to see           components   !
Expanded Panel Detail!
Clinical Panels!      Find where a term has            been used !
LOINC Term Panel Usage!
Other Survey Instruments!
Proposing New LOINC Terms!LOINC grows because you ask.!
Proposing a New Term!Are you sure?!Give us all you got!RELMA is best!Send them in groups!
What We Need!•    Local test/observation name!•    Local order (panel) name!•    Description of the test !•    Name of sen...
Propose new LOINC terms!                    Select Propose a                         LOINC !
Your Info!Navigate through   Create new term, proposed terms!   save current term                      or Exit form!      ...
Use Existing Terms as Template!        Click the Propose           Term button !                            Select your cl...
Use Existing Terms as Template!                     All required                  components "lled in!
Review Proposed Terms!                   Review your new                        terms!
Review Proposed Terms!                   Choose whether to                    send or postpone!                   All prop...
Submitting New Terms!Still need to email us the "le!      !submissions@loinc.org!!More Information!      !http://loinc.org...
http://loinc.org/submissions/new-terms!
photo via milos milosevic!
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full
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2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full

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2011 05 26 - Lab LOINC Tutorial - Chicago - Handout version - full

  1. 1. Laboratory LOINC Workshop – Chicago, IL! LOINC! Introduction and Mapping Boot Camp! Daniel J. Vreeman, PT, DPT, MSc! Assistant Research Professor, Indiana University School of Medicine! Research Scientist, Regenstrief Institute, Inc! Clem McDonald, MD! Director, Lister Hill National Center for Biomedical Communications – National Library of Medicine !05.26.2011! dvreeman@regenstrief.org! © 2011!
  2. 2. Acknowledgements!LOINC Development Team!Kathy Mercer, Jaci Phillips, Ian Pyle, David Baorto,Fran Brahmi!!RELMA Development Team!John Hook, Mark Fisher, Karen Ahmed, AnandhiSowmyan, James Dennis!!LOINC Committee!Supporters: NLM, Regenstrief, CHITREC,Metropolitan Chicago Healthcare Council,Chicago Department of Public Health!
  3. 3. Overview!1.  Origins of LOINC!2.  LOINC 101!3.  Using RELMA!4.  Searching and Mapping to LOINC!5.  Approaches to Mapping and Domain-speci"c Help!6.  Other RELMA features!7.  Your turn!
  4. 4. Origins of LOINC!The lingua franca of clinical observation exchange!
  5. 5. Soda or Pop?! what you see in the order list !Lab A! Lab B!Test Name: Lyme Disease Serology! Test Name: Lyme Disease Antibody!Measures: B. burgdorferi Ab IgG! Measures: B. burgdorferi Ab IgM!Method: ELISA! Method: Immune blot!Scale: quantitative! Scale: qualitative!e.g.: Titer 1:40! e.g.: Positive!! !LOINC Code = 5062-5! LOINC Code = 6321-4!
  6. 6. Logical Observation Identi"ers Names and Codes!A universal code system that facilitates exchange, pooling, and processing of results!
  7. 7. If an observation is a questionand the observation value isan answer… !LOINC provides codes for !questions !Other vocabularies provide !codes for the answers!
  8. 8. What is my patient’shemoglobin level?!718-7:Hemoglobin:MCnc:Pt:Bld:Qn!
  9. 9. How fast does mypatient usually walk?!41959-8:Walking speed:Vel:1W^mean:^Patient:Qn:Calculated
  10. 10. Indiana Network for Patient Care! HL7 v.2.X Message!MSH|^~&|HOSPITAL_A|SAMPLE_HOSPITAL_A|||$YearMonthDay|||||||||||||||PID|||$patientId$||$patientName$|||||||||||||||||||| LocalCode^LocalName^CodeSystem^LOINCcode^LOINCname^CodeSystemPV1|||||||$attendingDoctor$||$consultingDoctor$||||||||OBR|1|||012^CBC/Auto Diff^HSPA^57021-8^CBC W Auto Diff^LN||$reqDate|||||||||OBX|2|NM|123^WBC^HSP_A^26464-8^Leukocytes [#/volume] in Blood^LN||10.8|K/MM3|||||F|OBX|3|NM|234^RBC^HSP_A^26453-1^Erythrocytes [#/volume] in Blood^LN||4.82|MIL/MM3|||||F|OBX|4|NM|345^HGB^HSP_A^718-7^Hemoglobin [Mass/volume] in Blood^LN||15.7|GM/DL|||||F|OBX|5|NM|456^HCT^HSP_A^20570-8^Hematocrit [Volume Fraction] of Blood^LN||45|%|||||||F| !" Message Processor! !" Institutional Repository!
  11. 11. Result with a Coded Value! Data type ofresult (OBX-5) is a This code is This code is coded element! from LOINC! from SNOMED! OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT Code identifying this observation ! Code identifying the(what are these results? result (L. monocytogenes)! Listeria culture)!
  12. 12. Laboratory LOINC!
  13. 13. Clinical LOINC!
  14. 14. The LOINC Community!Open. Nimble. Pragmatic.!
  15. 15. Open Development!Worldwide distribution at no cost!End-user content additions!Welcome all comers!Volunteers!!
  16. 16. Regenstrief Institute!Steward!Developer of content!Developer of tools!Developer of community!Distributor!Voice!!
  17. 17. LOINC Codes Over Time By Release!70,000! LOINC Codes! Lab Codes!60,000! Slope = 2200!50,000! Slope = 600!40,000!30,000!20,000!10,000! laboratory terms only! 0!
  18. 18. loinc.org members!12,000!10,000! 8,000! 6,000! 4,000! 2,000! 11 new members per day! 330 new members per month! 0!
  19. 19. 11,100+ users in 141 countries!
  20. 20. Downloads: ~1100/month!
  21. 21. 6,900 views! ! 100 views! 260 views!
  22. 22. International Adoption!participation, translation, implementation!
  23. 23. LOINC Submitters!Since 2009, 84 organizations from 14 countries!
  24. 24. LOINC Translators! 18 organizations!
  25. 25. New and Updated!Estonian!French!German!Greek!Italian!Spanish!
  26. 26. In-progress!Catalan!Dutch!French!Russian!!
  27. 27. Large Implementations!SIGA Saúde project !Canada Health Infoway!ePSOS!Assistance publique - Hôpitaux de Paris!Hong Kong Hospital Authority!Red Agrolab!BiTAC! Lots more…success is often silent!
  28. 28. US Adoption!A few key highlights!
  29. 29. US Federal Agencies! NLM! VA! DoD! IHS! NCI! CDC!
  30. 30. Other Key US Adoptions! HITSP! eLINCS! NAACCR! CDISC! NCQA/HEDIS! HL7! HIPAA! HIE’s!
  31. 31. EHR Incentive Programa.k.a. “Meaningful Use”!
  32. 32. New Frontiers inContent Modeling!
  33. 33. Standardized Assessments!
  34. 34. Purpose!Assessments are widely used…!…and not unlike other clinical observations!!
  35. 35. LOINC could be a !! master question "le and uniform representation !
  36. 36. Panels/Forms Available as Separate Download!
  37. 37. Currently in LOINC!US Government Forms! CARE, MDSv2, MDSv3, OASIS B1, OASIS C, RFC! US Surgeon General’s Family Health Portrait!Brief Interview for Mental Status (BIMS)!Confusion Assessment Method (CAM)!Geriatric Depression Scale (GDS)!HIV Signs and Symptoms Checklist!Home Health Care Classi"cation!howRU!Living with HIV (LIV-HIV)!Morse Fall Scale!OMAHA!PHQ (9 and 2)!Quality Audit Marker (QAM)!!
  38. 38. Translational Research Variables!
  39. 39. LOINC 101!LOINC for newbs (not nOObs)!
  40. 40. The LOINC Distribution!
  41. 41. http://search.loinc.org!
  42. 42. Anatomy of a LOINC Term! 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA! 5193-8! LOINC Code!Hepatitis B virus surface Ab! Component ! ACnc ! Property Measured! Pt ! Timing! Ser ! System! Qn! Scale! EIA! Method! There are six major LOINC axes !
  43. 43. NOT part of a LOINC Name!Testing instrument!Speci"c details about the specimen!Priority (e.g. STAT)!Where testing was done!Who did the test!Test interpretation!Anything not part of naming the test!Stu# carried in other parts of HL7 message!
  44. 44. Component! The substance or entity that is measured, evaluated, or observed!Sodium!Glucose!Brucella sp. organism!In$uenza A Virus antigen!Cytomegalovirus antibody!Lipids.total! 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA!
  45. 45. Component Structure ! Analyte Name^Challenge^Adjustments !Formal analyte name! Calcium! Specify “subanalytes”! Coronavirus Ag! May have subclasses! Calcium.ionized! ! !Challenge! 1H post 100 g Glucose PO! Two parts separated <time delay>post<challenge type>! by “post”! !! !Adjustments! Adjusted to pH 7.4!
  46. 46. Property! * the most di"cult LOINC axis!The characteristic or attribute of the analyte that is measured, evaluated, or observed.!Major Categories:! !mass! !substance! !catalytic activity! !arbitrary! !number! 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA!
  47. 47. Property! * the most di"cult LOINC axis!Fully Named Properties! mg/dL!MCnc! mass concentration! umol/L!SCnc! substance concentration! mg/g!MCnt! mass content ! U/L!CCnc! catalytic concentration!Prid! presence or identity!Imp! impression!Type! “kind of”! Property is related to units of measure! 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA!
  48. 48. Common Property Issues! Fraction versus Ratio!Fraction = Part/Whole! !NFr: % Eosinophils / leukocytes! !SFr: % HGB which is A2!! photo via jurvetson!Ratio = multiple analytes from same system! !MCrto: BUN/Creatinine in urine!!Relative Ratio = measures from di"erent system! !RelRto: actual to normal control!!
  49. 49. Timing!The interval of time over which the observation or measurement was made!Pt! point in time!12H! 12 hour collection!24H! 24 hour collection! Non-Pt timings are often ! found with Rate Property!
  50. 50. System!The system (context) or specimen type upon which the observation was made.!Ser! serum!Ser/Plas! serum or plasma!Bld! whole blood !Ur! urine!Flu! body #uid! photo via AlishaV!Tiss! tissue!XXX! speci$ed elsewhere ! 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA!
  51. 51. System Structure! System^Super System!Super System!Patient is the default!Used to indicate! blood product unit! bone marrow donor! fetus! photo via Xurble! 818-5:A Ag:ACnc:Pt:RBC^BPU:Ord: ! 11670-7:Blood $ow.mean:Vel:Pt:Aortic arch^fetus:Qn:US.doppler !
  52. 52. Scale!Qn! Quantitative!! continuous numeric!! optional operator!Ord! Ordinal!! Ranked set (1+, 2+, 3+)! photo via puuikibeach !Nom! Nominal!! unranked collection!! Taxonomy (e.g. bacteria)!Nar! Narrative! 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA!
  53. 53. Method!Only needed if interpretation a#ected! Di#erent normal ranges! Test sensitivity!Listed at the generic level! Agglutination! Immunoassay! Probe with target ampli"cation! 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
  54. 54. LOINC Parts !Uses !translation, synonymy, building hierarchies,creating display names, linking descriptions!
  55. 55. Hierarchies!LOINC class !Each LOINC axis!Multi-axial! Component | System! Separate download! !! !
  56. 56. RELMA®!REgenstrief LOINC Mapping Assistant!
  57. 57. We’ll Cover!RELMA “Boot Camp”!Mapping tips/pitfalls!Get started!
  58. 58. What’s it Good For?!Browse LOINC!Map your local terms to LOINC! !import/export! !translate local words to LOINC-speak! !manual/automated mapping!
  59. 59. Get RELMA!
  60. 60. http://search.loinc.org!
  61. 61. RELMA Highlights!Hierarchies!Search!Enhanced details view!Common test list!Panels and forms!Export, copy, paste!
  62. 62. Search Syntax!Google-like!AND, OR, -<word>, +<word>!Limit by category (e.g. micro)!Wildcards (? and *)!! Assumes EXACT MATCH! unless you use wildcards!
  63. 63. More RELMA Features !User Speci"ed Search Limits !Selectable trees for:! Class! Multiaxial (component/system)! System (specimen)! Component! Method!
  64. 64. Installing RELMA!
  65. 65. Installation Steps!Need Windows (or a VM on a Mac)!Got disk space? 2Gb is recommended!Start installer <drive>:RELMASetup!Specify installation directory keep default!Two database "les installed! RELMA.MDB – LOINC terms database! LMOF3.MDB – Local Master Observation File!Two sample "les included !Run it!!
  66. 66. File Locations!Database and Ancillary Files!Windows XP! ! C:Documents and SettingsAll UsersDocumentsRELMAWindows Vista and 7!!C:UsersPublicDocumentsRELMA!Sample "les!Windows XP! !C:Documents and SettingsAll UsersDocumentsRELMASamplesWindows Vista and 7!!C:UsersPublicDocumentsRELMASamples !
  67. 67. Running RELMA!
  68. 68. Main Menu/Welcome Screen! File->Set Preferred Language!
  69. 69. Select Linguistic Variant(s)!
  70. 70. LOINC Terms with Spanish Linguistic Variant! All Spanish! !
  71. 71. Simple Search!
  72. 72. Search Window!enter search terms ! limit to common tests ! limit to speci"c units !
  73. 73. Search Window! Help! ! “common tests” relative frequency!
  74. 74. New RELMA Help"le!
  75. 75. Context Menu!right click to bring up context menu !
  76. 76. Setting User Preferences!
  77. 77. Set User Preferences! select User Preferences ! from the File Menu! ...or from Welcome Screen!
  78. 78. Set User Preference Dialog! File locations: ! (see prior slide for location) ! startup screen preference!
  79. 79. User Map Screen Preferences! Include/exclude battery terms ! add comments on mappings !
  80. 80. Importing Local Termsinto RELMA!
  81. 81. 4 Ways to Build LMOF!1.  Hand enter! bad!2.  Make your own table ! bad!3.  Import text "le from good! your test catalog! !4.  Import from real HL7 best! v2.x messages !
  82. 82. Make a Local Dataset!Extract from Your Test Catalog! Battery code! Battery description or name! *Local code ! *Test description or name! Include method if important! Units! Example Values! Laboratory Section!
  83. 83. Make a Delimited Text File!Need separate "elds!Use any delimiter!Fields in any order!Required "elds (minimum):! Local Code! Local Description! Units (highly recommended)!
  84. 84. Importing Local Terms!1.  Start it up!2.  Find local term "le!C:Documents and SettingsAll UsersDocumentsRELMASamplesC:UsersPublicDocumentsRELMASamples3.  Name your working set!4.  Identify "eld delimiter in your "le!5.  Match your "elds to LMOF attributes!6.  Import!!
  85. 85. Example Tab-Delimited File!
  86. 86. Importing Local Files! select “Import Local Terms from Delimited File”! or just click here!
  87. 87. Navigate to File Location! select File andstored in ! sample "les click Open RELMA Directory !
  88. 88. Open File in RELMA! Give it a name! (RELMA allows multiple sets in one LMOF database) !select your delimiter ! Import button!
  89. 89. Open File in RELMA! oh "ddlesticks!!! !
  90. 90. Match Your Fields! assign LMOF attribute!
  91. 91. Match Your Fields! choose "eld name!
  92. 92. Now You’re Ready!!minimum assignments ! Do It! !
  93. 93. After import, RELMA willsearch for words it does not recognize!
  94. 94. Alternate Import (best)!Nothing closer to the truth than real data!
  95. 95. Big Pile of HL7 Messages!!RELMA parses into dataset! OBR ID! OBR description! OBX ID! OBX description! Sample results:! actual values, units, abnormal #ags, normal ranges! ! !
  96. 96. Generate Local term "le from HL7 messages ! select Import Terms from HL7 File!
  97. 97. Select File to Import! select HL7 "le!
  98. 98. Specify HL7 File Name and Sample Size!name the local term "le (working set)! select the number of sample values ! select which codes to store!
  99. 99. HL7 Messages Data Statistics!
  100. 100. Your turn! ! Import Local Terms !(or sample OBX "le)!
  101. 101. Cleaning Your Data!A little time upfront saves more later! photo via Mu#et!
  102. 102. Prep Your Data for Mapping!Improve mapping success! !Expand abbreviations! !Ignore “administrative” words! !Standardize idiosyncratic words! !Standardize time references!RELMA can help!
  103. 103. RELMA Cleaning Tools! use this tool to edit unknown terms !
  104. 104. Review Unknown Local Terms! may re-scan "le for unknown terms !
  105. 105. Replace Local Terms! Assign LMOF Attribute replacement options ! !
  106. 106. RELMA Cleaning Tools! use this tool to make global substitutions !
  107. 107. Term Substitution!save this global substitution for only this working set!
  108. 108. Clean Up! !Take some time to clean up your sample "le!
  109. 109. Reviewing yourLocal Terms!
  110. 110. Change Local Term File! Select the Working Set !
  111. 111. Manual Enter/Edit ! View/Add/Edit Local Terms !
  112. 112. Edit Term Dialog! EditAddDelete Terms ! Export Terms! Search Terms by Keyword!Text alignment option! Print Preview List !
  113. 113. New Terms added to LMOF!click on “Edit Term” to see sample data! new battery code!
  114. 114. Sample Results for Observation! Sample Values from Messages !
  115. 115. Search Local Term File!Calcium! Enter Keyword from any Return to Full List ! Field!
  116. 116. Export Local Term File!Delimiters supported:! Tab, comma, bar (|) !
  117. 117. Searching andMapping to LOINC !what RELMA was born to do! Photo via Jeffrey Beall!
  118. 118. Hit It! !Are you working on the right local "le? !
  119. 119. Core Mapping Screen Features!Customizable grid ! Export results grid!Sort by columns! Stores mappings!View term details!
  120. 120. Mapping Screen ! View or edit local term! Navigate through the local terms !Quick select button list ! Custom Grid Con"guration!
  121. 121. Con"gure Grid! Select elements to display! Reorder grid elements ! Visually resize elements !Reset Default Con"guration!
  122. 122. Quick choice buttons!Viewing LOINC term detail!
  123. 123. View Local Term Details! Select level of detail to display!
  124. 124. Select detail display level!Select level of detail to display!
  125. 125. Standard Mapping Screen!Begin a search !(or hit “enter”) !
  126. 126. Initial Mapping Results! Fiddlesticks !#*$%!! What now??? ! Click toshow words used in search!
  127. 127. Initial Mapping Results!Use term Number of LOINC Battery termscheckbox! terms containing included in keyword ! search!
  128. 128. Revised Mapping Results! Number of matching records found! Units restrictionselected by default!
  129. 129. Re-revised Mapping Results! Click any column header to re-sort ! Number of matchingMatch units records found!unselected!
  130. 130. Standard Mapping Screen! CANINE DISTEMPER VIRUS IFEnter keywords here! Clear all input "elds !
  131. 131. Ad hoc term search!
  132. 132. Tabbed Access to Functions! Navigate to Functions from Mapping Page ! Switch between Grid and Tree Views !
  133. 133. Tree View!
  134. 134. Tree View! Can map to terms Cannot map to with LOINC Codes! terms representing LOINC parts !Tree Navigation Buttons!
  135. 135. Assigning a LOINC Map! Click “Map” Button! (or doubleclick) ! Highlight correct term !
  136. 136. Adding Mapping Comments!Check with Frank in Chemistry If comments option is selected, prompt appears !
  137. 137. Assigning a LOINC Map! LOINC Term Assigned!
  138. 138. View LOINC Term Details! View details for a speci"c LOINC Term ! Right clicking on a LOINCterm brings up a Task Menu !
  139. 139. LOINC Term Details! Can scroll down a single formatted page ! Can scroll throughChange to expanded returned subset of details view! terms ! Change text size!
  140. 140. LOINC Term Details: Panels!
  141. 141. View Panel Children!Select View Panel Children from context menu !
  142. 142. Panel Children!
  143. 143. Con"gure Export Options! Output options ! Include!Save con"guration column headers ! and/or export!
  144. 144. Excel Export Format!
  145. 145. More on Search Syntax!Tips and Tricks! Photo via Jeffrey Beall!
  146. 146. Wildcards!“*” replaces any number of characters! GLUC*! *COSE! GLU*SE!“?” replaces a single character! GLUCOS?! ?LUCOSE! GLUC?SE!
  147. 147. Search Quali"ers ! Detailed help available!Includes Glucuronidase, Glucosidase,Glucosylceramidase, etc.!
  148. 148. Search in a Field!Field! Example!LOINC! loinc:12628-4!Component! component:chemotherapy!Property! glucose property:CCnc!Timing! glucose timing:24H!System! glucose system:CSF!Scale! glucose scale:Nar!Method! mycobacterium method:EIA!Class! glucose class:UA!
  149. 149. Other Cool Tricks!Use parentheses!!(flu OR rhinovirus) -haemophilus! component:(norepinephrine creatinine)!Fuzzy search (~)!!Bergdorferi~
  150. 150. Limiting Your Searches!Sometimes 60,000 terms is too many!
  151. 151. Setting Search Limits!Reduces number of candidate terms!Many, many options!Hierarchy allows domain restrictions!
  152. 152. with great power comes great responsibility! Photo via [cipher]!
  153. 153. Setting Search Limits!click Hierarchy & Search Limits tab!
  154. 154. Search Constraints! Attribute trees ! Local Unit Constraint: ! Default is “ON”! LOINC term status !Prede"ned, general search constraints !
  155. 155. Terms Consistent with Units! Only terms consistent with mmol/L appear !
  156. 156. Quick Access Toggles For Common Restrictions! On/O# Toggles !
  157. 157. Specimen Restriction! Specimen constraints !
  158. 158. Terms Consistent with Specimen ! CSF enter default specimen!
  159. 159. Terms Consistent with Specimen !Only CSF Terms are returned!
  160. 160. Setting Search Limits!Methodless Terms Override Methodless Terms Restriction! Restriction!
  161. 161. Limit to Methodless Terms!
  162. 162. Limit to Methodless Terms!only Methodless terms appear!
  163. 163. Methodless Only Unchecked! All terms returned!
  164. 164. Methodless Only Checked! Only Methodless terms returned! Di#er in one ormore components !
  165. 165. Conditional Methodless! More terms returned!No methodlessterm; all shown!
  166. 166. Setting Search Limits! Limit to Lab Tests Only! (No Clinical LOINC Terms) !
  167. 167. Setting Search Limits! Empirically derived common tests ! (99.8% of INPC volume)!Next Release: Top 2000 fromhumungous sample!
  168. 168. A brief aside…!Developing convenience sets! photo via x-ray delta one!
  169. 169. A Few Tests Give Most Results! 100%!Cumulative Laboratory Observation Volume (%)! 90%! 80%! 70%! 60%! 50%! 40%! 30%! 20%! 10%! 0%! 0! 500! 1000! 1500! 2000! 2500! 3000! 3500! 4000! Number of Laboratory Observation Codes (N)! Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775. !
  170. 170. Setting Search Limits! include Trial, Deprecated or Discouraged LOINC codes with returned terms !
  171. 171. LOINC Term Status!Trial!! as the concept and associated attributes may change. Concept is experimental in nature. Use with cautionDiscouraged!! mappings to this concept are discouraged although Concept is not recommended for current use. New existing mappings may continue to be valid in! context.Deprecated! Concept is retired and should not be used, but it is retained in LOINC for historical purposes.
  172. 172. Include Deprecated LOINC Terms!Can’t map to a deprecated term!Warning before mapping to discouraged term! Discouraged LOINC Terms appear as an inverted triangle! Deprecated LOINC Terms appear as strikethrough text with a “Do Not” symbol!
  173. 173. LOINC Hierarchies – Class Tree! Three top-level branches ! Tree Navigation Buttons!
  174. 174. Before Class Restriction! Most terms have class of “CHAL” !Large number of candidate terms !
  175. 175. Hierarchies! Restrict eligible tests to non-challenge chemistry tests only !
  176. 176. Following Class Restriction! Only Non-ChallengeChemistry tests returned!
  177. 177. A Reminder About Search Limits! Indicates that you’ve got something set over here !
  178. 178. Component Hierarchy! “right click” for context menu with “view details” option! Show the LOINC Codes associated with these components !
  179. 179. Details Screen: LOINC Part!
  180. 180. Show Associated LOINCs!
  181. 181. Hierarchy Wrap-up!All trees operate the same way!All grids operate the same way!Tree is searchable !Combine tree limits with others! “Mulligan” button!
  182. 182. Search Hints and Tips!Zero hit keywords are ignored! !(may need to rephrase)!!Common causes of Zero results! !Too many keywords! !Limits and keyword contradictions! !Local term weirdness!!Units are GREAT discriminators!
  183. 183. RELMA’s Auto Mapper!Starting with our best guesses may save you time!
  184. 184. What Does It Do?!Batch processes local term "le to getN- closest candidate LOINCs!!Uses words and units from local terms!!Produces a ranked list for your review!
  185. 185. Recent Improvements!Faster. Way faster.!Better clean-up routine!New specimen guesser!Better local to LOINC word "nder!Break ties with frequency data!
  186. 186. Does it Work?!Lab terms (internal analysis)! !#1 ranking: 60-70ish%! !In Top 5: 70-80ish%!!Radiology terms! !#1 ranking: 80-90ish%! !In Top 5: 90ish%! !Using CPT-based restriction helped! !(but we couldn’t distribute it)! 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.!
  187. 187. (Lab) Auto Mapper! launch it here!a couple of options ! print report or work through the ranked list when done !
  188. 188. Intelligent Mapper - Mapping Screen!
  189. 189. Mapping Guidance andApproaches to SpecialDomains!Top N, Reportable Conditions, Newborn Screening!
  190. 190. Not just an IT problem!
  191. 191. Get real.!units, results, experts!
  192. 192. Don’t be a one hit wonder.!
  193. 193. Additional Pearls andGuidance!Clem McDonald, MD!Director, Lister Hill National Center for Biomedical Communications – National Library of Medicine !
  194. 194. Other RELMA ®Features!Oh yes, there’s more!!
  195. 195. Using Your Mapped Terms!You’ve done the work. Now reap the glory.! photo via janeandd!
  196. 196. Con"gure Export Format!Context Sensitive Export Con"guration!
  197. 197. LMOF Export Con"guration!Select Export Format! Select Fields to Export ! Save Con"guration and Export !
  198. 198. Printing Mapped Terms! Click Print button to PreviewMay highlight terms to be output! printed!
  199. 199. Custom Export Con"guration! Select the Format you wish to Export ! Select the Fields you wish to Export !
  200. 200. Excel™ Export!
  201. 201. Export Terms Dialog!Select Term Set ! Select Delimiter !Check Fields you wish to export!
  202. 202. More RELMA Fun!Parts, Panels, and Proposing New Terms!
  203. 203. LOINC Part Search!Works just like the term search!Handy for looking at descriptions!
  204. 204. Parts Search!
  205. 205. Parts Search! only parts that havedescriptions, references, etc !
  206. 206. Panels, Forms, and Surveys!Wanted to make it easy to "nd!Special features for browsing!
  207. 207. Panels, Forms and Survey Review! Review Panels, Forms and Surveys !Review Panels, Forms and Surveys !
  208. 208. Government Forms!
  209. 209. Laboratory Panels! Double-click panel name to see components !
  210. 210. Expanded Panel Detail!
  211. 211. Clinical Panels! Find where a term has been used !
  212. 212. LOINC Term Panel Usage!
  213. 213. Other Survey Instruments!
  214. 214. Proposing New LOINC Terms!LOINC grows because you ask.!
  215. 215. Proposing a New Term!Are you sure?!Give us all you got!RELMA is best!Send them in groups!
  216. 216. What We Need!•  Local test/observation name!•  Local order (panel) name!•  Description of the test !•  Name of send out lab (if applicable)!•  Name of healthcare organization that stimulated the request for this term (if you are submitting on behalf of someone else)!•  Units of measure (for quantitative observations)!•  Answer lists (for qualitative observations)!•  Sample results, reports (if applicable)!•  Package inserts, test kit documentation (if applicable)!•  Vendor, instrument, and/or reagent kit used to perform this test (if applicable)!•  Description of the project or activity that stimulated the request for this term, or any other documentation you have!
  217. 217. Propose new LOINC terms! Select Propose a LOINC !
  218. 218. Your Info!Navigate through Create new term, proposed terms! save current term or Exit form! Suggested LOINC Name!
  219. 219. Use Existing Terms as Template! Click the Propose Term button ! Select your closest match!
  220. 220. Use Existing Terms as Template! All required components "lled in!
  221. 221. Review Proposed Terms! Review your new terms!
  222. 222. Review Proposed Terms! Choose whether to send or postpone! All proposed terms fully editable!
  223. 223. Submitting New Terms!Still need to email us the "le! !submissions@loinc.org!!More Information! !http://loinc.org/submissions!!LOINC Submissions Policy! !http://loinc.org/submissions-policy!! !!
  224. 224. http://loinc.org/submissions/new-terms!
  225. 225. photo via milos milosevic!

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