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20080609 Loinc Workshop

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2008 06 09 - Laboratory LOINC Workshop and Tutorial

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20080609 Loinc Workshop

  1. 1. Using RELMA Or… In Search of the Missing LOINC © 2007 Regenstrief Institute & James Case James T. Case MS, DVM, PhD Professor, Clinical Diagnostic Informatics California Animal Health and Food Safety Laboratory University of California, Davis Laboratory LOINC Meeting – June 2008
  2. 2. Acknowledgements <ul><li>RELMA Development Team </li></ul><ul><ul><li>John Hook, Mark Fisher, Ryan Phillips, Karen Ahmad, and more! </li></ul></ul><ul><li>Kathy Mercer </li></ul><ul><li>Clem McDonald </li></ul><ul><li>Dan Vreeman </li></ul><ul><li>The Lab LOINC Committee </li></ul><ul><li>Funding Support </li></ul><ul><ul><li>NLM, Regenstrief Institute, NCI, CDC </li></ul></ul>© 2007 Regenstrief Institute & James Case
  3. 3. What will we cover today? <ul><li>Installing RELMA </li></ul><ul><li>Setting personal preferences </li></ul><ul><li>Loading a Local Observation File (LMOF) </li></ul><ul><li>Preparing LMOF for Mapping </li></ul><ul><li>Review of Map Screen Functions </li></ul><ul><li>Setting Search Limits </li></ul><ul><li>Mapping Local Terms to LOINC </li></ul><ul><li>Viewing LOINC Term Details </li></ul><ul><li>Proposing/Submitting New LOINC Terms </li></ul><ul><li>Exporting/Printing Mapped Terms </li></ul><ul><li>Mapping your own LMOF data </li></ul>
  4. 4. Goals of Health Information Standards <ul><li>Interoperability – the ability to exchange information between organizations </li></ul><ul><li>Comparability – the ability to ascertain the equivalence of data from different sources </li></ul><ul><li>Data Quality – the measurement of completeness, accuracy and precision </li></ul>
  5. 5. Levels of Interoperability <ul><li>Basic – allows messages to be exchanged between computer systems </li></ul><ul><ul><li>Word processing documents, spreadsheets </li></ul></ul><ul><li>Functional – describes the standard syntax (format) of the message </li></ul><ul><ul><li>Document templates, forms, data structures </li></ul></ul><ul><ul><li>Message standards </li></ul></ul><ul><li>Semantic – requires use of standard vocabularies within the message </li></ul>
  6. 6. Comparability <ul><li>Meaning of the data is consistent when shared among different parties </li></ul><ul><li>Common terminology required </li></ul><ul><ul><li>Should work in the background </li></ul></ul><ul><li>Not just words </li></ul><ul><ul><li>Codes – uniquely identifies terms </li></ul></ul><ul><ul><li>Classification – groups related terms </li></ul></ul><ul><ul><li>Vocabulary – specialized, precise terms that remove ambiguity </li></ul></ul>
  7. 7. Potential Uses of Health Data are Constrained by Data Quality Factors <ul><li>Data quality issues </li></ul><ul><ul><li>Different for client communications vs. analysis </li></ul></ul><ul><ul><li>Often constrained by external forces </li></ul></ul><ul><ul><ul><li>E.g. criteria for diagnosis often differs from the criteria for reporting </li></ul></ul></ul><ul><li>Unidirectional effect of data consolidation </li></ul><ul><ul><li>Detailed -> General </li></ul></ul><ul><ul><li>General -> Detailed </li></ul></ul>
  8. 8. The Problem <ul><li>“ In attempting to arrive at the truth, I have applied everywhere for information, 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 questions… They would show [subscribers] how their money was being spent [and] what amount of good was really being done with it…” </li></ul>Florence Nightingale - Notes on a Hospital, 1873
  9. 9. Why LOINC? <ul><li>“ Within one laboratory, local jargon terms may be used which are usually well understood between colleagues, but would not be sufficiently widely known for communication with the outside world.” </li></ul><ul><li>U. Forsum et al., Pure Appl. Chem 72:555-745, 2000 Properties and Units in the Clinical Laboratory Sciences Part VII. Properties and Units in Clinical Microbiology </li></ul>
  10. 10. Test comparisons <ul><li>Lab A </li></ul><ul><li>Test Name: Lyme Disease Serology </li></ul><ul><li>Measures: B. burgdorferi Ab IgG </li></ul><ul><li>Method: ELISA </li></ul><ul><li>Scale: quantitative </li></ul><ul><li>e.g.: Titer 1:40 </li></ul><ul><li>Lab B </li></ul><ul><li>Test Name: Lyme Disease Antibody </li></ul><ul><li>Measures: B. burgdorferi Ab IgM </li></ul><ul><li>Method: Immune blot </li></ul><ul><li>Scale: qualitative </li></ul><ul><li>e.g.: Positive </li></ul>LOINC Code = 5062-5 LOINC Code = 6321-4 What you see in the order list
  11. 11. LOINC ® 101
  12. 12. Anatomy of a LOINC Term 5193-8 LOINC Code Hepatitis B virus surface Ab ACnc Pt Ser Qn EIA Component Property Measured Timing System Scale Method There are six major LOINC axes 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
  13. 13. What is NOT part of a LOINC Name? <ul><li>The instrument used in testing </li></ul><ul><li>Specific details about the specimen </li></ul><ul><li>Priority (e.g. STAT) </li></ul><ul><li>Where testing was done </li></ul><ul><li>Who did the test </li></ul><ul><li>Test interpretation </li></ul><ul><li>Anything that is not an intrinsic part of the name of the result </li></ul><ul><li>Other things that are carried in; </li></ul><ul><ul><li>The OBX segment </li></ul></ul><ul><ul><li>An HL7 Version 3 Observation Object </li></ul></ul>
  14. 14. Component/Analyte The substance or entity that is measured, evaluated, or observed <ul><li>- Sodium </li></ul><ul><li>- Glucose </li></ul><ul><li>- Brucella sp. organism </li></ul><ul><li>- Influenza A Virus antigen </li></ul><ul><li>Cytomegalovirus Virus antibody </li></ul><ul><li>Lipids.Total </li></ul>5193-8: Hepatitis B virus surface Ab :ACnc:Pt:Ser:Qn:EIA
  15. 15. Component/Analyte Structure <ul><li>Formal name of Analyte (e.g. Calcium) </li></ul><ul><ul><li>Must specify any “subanalyte” </li></ul></ul><ul><ul><ul><li>e.g. Coronavirus Ag </li></ul></ul></ul><ul><ul><li>May have a subclass – separated by “.” </li></ul></ul><ul><ul><ul><li>e.g. Calcium.Free </li></ul></ul></ul><ul><li>Challenge - e.g, 1H post 100 gm Glucose PO </li></ul><ul><ul><li>Two subparts separated by “post” </li></ul></ul><ul><ul><li><time delay> post <challenge type> </li></ul></ul><ul><li>Adjustments/corrections </li></ul><ul><ul><li>E.g. Adjusted to pH 7.4 </li></ul></ul>Analyte Name^Challenge^Adjustments
  16. 16. <ul><li>Mass: Observations reported with mass (milligrams, grams, etc.) in the numerator of their units of measure </li></ul><ul><li>Substance: Observations reported with moles or milliequivalents in the numerator of their units of measure </li></ul><ul><li>Catalytic activity: Observations that report enzymatic activity </li></ul><ul><li>Arbitrary: Results that report arbitrary units in the numerator of their units of measure </li></ul><ul><li>Number: Counts </li></ul>Property* The characteristic or attribute of the analyte that is measured, evaluated, or observed the most difficult LOINC axis Major Categories 5193-8:Hepatitis B virus surface Ab: ACnc :Pt:Ser:Qn:EIA
  17. 17. <ul><li>MCnc – mass concentration (mass/unit vol) </li></ul><ul><li>MCnt – mass content (mass/unit mass) </li></ul><ul><li>NCnc – number concentration (number/unit vol) </li></ul><ul><li>TmStp – time </li></ul><ul><li>CCnc – catalytic concentration (activity) </li></ul><ul><li>Prid – presence or identity </li></ul><ul><li>Imp – impression/interpretation </li></ul><ul><li>Find – subjective or objective observation </li></ul><ul><li>Type – “Kind-of” </li></ul>Property* the most difficult LOINC axis Combine Major Categories with Subtypes for Full Property 5193-8:Hepatitis B virus surface Ab: ACnc :Pt:Ser:Qn:EIA
  18. 18. Common Issues with LOINC Properties <ul><li>Fraction = Part/whole </li></ul><ul><ul><li>Number fraction (NFr): % Eosinophils </li></ul></ul><ul><ul><li>Substance fraction (SFr): % HGB which is A2 </li></ul></ul><ul><li>Ratio = Measures from the same system </li></ul><ul><ul><li>Mass concentration ratio - MCrto </li></ul></ul><ul><ul><ul><li>e.g., BUN/Creat in urine specimen </li></ul></ul></ul><ul><ul><li>Substance ratio-SCrto </li></ul></ul><ul><ul><ul><li>Urea/Creatinine expressed as mmol/L (SI units) </li></ul></ul></ul><ul><li>Relative Ratio = Measures from different systems </li></ul><ul><ul><li>RelRto – multiple of the median </li></ul></ul><ul><ul><li>RlTm – time from actual and normal control </li></ul></ul>Fraction (proportion) vs. Ratio a/a+b vs. a/b
  19. 19. <ul><li>Pt - at a point in time </li></ul><ul><li>12H - a twelve hour collection </li></ul><ul><li>24H - a twenty four hour collection </li></ul>Timing* *non-Pt timings are usually associated with Ratio Property The interval of time over which the observation or measurement was made
  20. 20. System The system (context) or specimen type upon which the observation was made. Super System Second subpart (^). When not included, “patient” is the default. Used to indicated blood product unit (BPU), a bone marrow donor, or a fetus.
  21. 21. <ul><li>Qn - quantitative </li></ul><ul><ul><li>Continuous numeric (real, integer, ratio) </li></ul></ul><ul><ul><li>Optional operator (>,  ,  , <) </li></ul></ul><ul><li>Ord - ordinal </li></ul><ul><ul><li>a ranked set of possible values (1+, 2+, 3+) </li></ul></ul><ul><li>Nom - nominal </li></ul><ul><ul><li>an unranked collection of possible values </li></ul></ul><ul><ul><li>a taxonomy (e.g list of bacteria) </li></ul></ul><ul><li>Nar - narrative </li></ul><ul><ul><li>free text narrative (e.g., visit note) </li></ul></ul>Scale
  22. 22. Scale (Special) <ul><li>OrdQn – Ordinal or Quantitative </li></ul><ul><ul><li>Primarily used for antimicrobial observations e.g. MIC reported as resistant, intermediate, susceptible or as the mm diameter of the inhibition zone </li></ul></ul><ul><ul><li>Use is discouraged </li></ul></ul><ul><li>Multi – structured text “globs” </li></ul><ul><ul><li>e.g. chromatography output </li></ul></ul><ul><ul><li>Use is discouraged </li></ul></ul><ul><li>Doc – Clinical documents </li></ul><ul><li>Set – Clinical attachments (headers) </li></ul>
  23. 23. Method <ul><li>Methods only needed if interpretation affected </li></ul><ul><ul><li>Different normal ranges </li></ul></ul><ul><ul><li>Test Sensitivity </li></ul></ul><ul><li>Listed only at the generic level </li></ul><ul><ul><li>Agglutination </li></ul></ul><ul><ul><li>Immunoassay </li></ul></ul><ul><ul><li>Probe with target amplification </li></ul></ul>
  24. 24. Mapping Terms to LOINC Things to Remember <ul><li>The thing ordered is not always the thing measured: </li></ul><ul><ul><li>Blood Culture – live organism(s) identified </li></ul></ul><ul><ul><li>VDRL – Treponema pallidum Ab </li></ul></ul><ul><ul><li>Urinalysis – lots of different things </li></ul></ul><ul><li>The question (what am I measuring?) is not the answer (e.g. Pos) </li></ul><ul><ul><li>You are mapping the question, not the answer! </li></ul></ul><ul><li>You must know the specifics of the component being tested for (what is this test actually measuring?) </li></ul>
  25. 25. RELMA ® Regenstrief LOINC Mapping Assistant
  26. 26. Purpose of Tutorial <ul><li>“Eliminate” need to read the User’s Manual </li></ul><ul><li>Become familiar with RELMA features </li></ul><ul><li>Provide some insight into mapping tips/pitfalls </li></ul><ul><li>Help begin the mapping process for your institution </li></ul><ul><li>Note: Most screen shots from version 3.24(early release) </li></ul>
  27. 27. New in this Version (rel. 3.24) <ul><li>Determine which panels have any of or all of a group of LOINCs. </li></ul><ul><li>LOINC Details new display type, &quot;Custom Display&quot;. </li></ul><ul><li>Custom Export - Select columns to send to the Clipboard, Excel, a CSV file, or email program. </li></ul><ul><li>Exporting mapped local terms to a delimited file support LOINC parts </li></ul><ul><ul><li>Component, Property, Time, System, Scale, and Method of mapped terms. </li></ul></ul><ul><li>Row numbers now displayed on restriction trees and multi-axial tree search results. </li></ul><ul><li>Grids allow switch between word-wrapped and truncated cell contents. </li></ul><ul><ul><li>Truncated cells display an ellipsis (...) </li></ul></ul>
  28. 28. New in this Version (rel. 3.24) <ul><li>Context menu now has the &quot;Propose a LOINC&quot; action. </li></ul><ul><li>When adding or editing a local term, can use the context menu. </li></ul><ul><li>When displaying LOINC/Part Details, you can type a LOINC/Part number into the LOINC/Part number box, hit Enter, and RELMA will display that LOINC/Part. </li></ul><ul><li>Then, that LOINC/Part is added to the end of the list of displayed LOINCs/Parts. </li></ul><ul><li>The Change Submission form now lists the name of the local term file, the number of local terms in the file, the number of mapped terms, the number of unmapped terms, and the percentage of mapped terms. </li></ul><ul><li>When RELMA is set to ask for a comment at each mapping, if no comment is supplied the mapping is not performed. </li></ul>
  29. 29. New in this Version (rel. 3.24) <ul><li>Units from the original submission are included as part of the example units on the LOINC Details. </li></ul><ul><li>On the LOINC Details display, externally defined answers are now explicitly shown as externally defined. </li></ul><ul><li>Importing HL7 switches to the local term file of the HL7 import. </li></ul><ul><li>Switching preferred language from the User Preferences form immediately loads the language. </li></ul><ul><li>Support for searching the LOINC database in multiple languages. </li></ul><ul><li>The HIPAA HL7 attachments displays have been modifed to display on the &quot;Panels, Forms & Surveys&quot; form. </li></ul>
  30. 30. <ul><li>Manual and automated mapping assistant </li></ul><ul><li>Same free use as LOINC (see license) </li></ul><ul><li>Comes with the LOINC files and indexes </li></ul><ul><li>Developed in Visual Basic (No API) </li></ul><ul><li>RELMA tools transform local words in local file </li></ul><ul><ul><li>User creates file of local term/name and codes </li></ul></ul><ul><li>Assigns LOINC term to local test/battery code </li></ul>RELMA Functions
  31. 32. Highlights <ul><li>Browseable Hierarchies </li></ul><ul><li>Display search results in tree view </li></ul><ul><li>Enhanced “details” view of terms/parts </li></ul><ul><ul><li>References </li></ul></ul><ul><ul><li>Descriptions </li></ul></ul><ul><ul><li>Sample units </li></ul></ul><ul><li>Empirically-derived common test list </li></ul><ul><li>Special features for panels/forms </li></ul><ul><li>Enhanced export/copy-paste options </li></ul>
  32. 33. <ul><li>For a given test, users can select LOINC records containing: </li></ul><ul><ul><li>A particular category of test (e.g., microbiology) </li></ul></ul><ul><ul><li>Any selected word in the input term </li></ul></ul><ul><ul><li>Additional keyed in word(s) </li></ul></ul><ul><ul><li>Wild cards of ? and * </li></ul></ul><ul><ul><li>Any intersection of the above </li></ul></ul>RELMA
  33. 34. RELMA Logic <ul><li>Not  #<word A> </li></ul><ul><li>Or  <word A> | <word B > </li></ul><ul><li>And  <word B> <word A> </li></ul>
  34. 35. <ul><li>For a given test: </li></ul><ul><li>User can select LOINC records containing: </li></ul><ul><ul><li>A set of words connected by ANDs or Ors </li></ul></ul><ul><ul><li>Wild cards of ? and * </li></ul></ul><ul><ul><li>Selected classes, systems, components, </li></ul></ul><ul><ul><li>Any intersection of the above </li></ul></ul><ul><li>Note: </li></ul><ul><ul><li>RELMA assumes exact match on word unless user adds terminal “*” to indicate wild card. </li></ul></ul>RELMA Search logic
  35. 36. Additional RELMA Features <ul><li>User Specified Search Limits </li></ul><ul><li>Selectable trees for: </li></ul><ul><ul><li>Class </li></ul></ul><ul><ul><li>System (specimen) </li></ul></ul><ul><ul><li>Component </li></ul></ul><ul><ul><li>Method </li></ul></ul>
  36. 37. Installing RELMA®
  37. 38. Installation Steps <ul><li>Make sure you have enough free disk space! </li></ul><ul><ul><li>At least 250Mb are needed </li></ul></ul><ul><li>From CD </li></ul><ul><ul><li>Start – Run – D:RELMASetup </li></ul></ul><ul><li>Specify installation directory </li></ul><ul><ul><li>Life will be easier if you accept the default </li></ul></ul><ul><li>Two database files installed </li></ul><ul><ul><li>RELMA.MDB – LOINC Terms Database </li></ul></ul><ul><ul><li>LMOF3.MDB – Local Master Observation File </li></ul></ul><ul><li>Two sample files copied (C:Program FilesRELMA) </li></ul><ul><li>Run from Start – (All) Programs – Regenstrief – RELMA </li></ul>
  38. 39. Running RELMA®
  39. 40. Copyright Screen © 2006 Regenstrief Institute & James Case
  40. 41. Main Menu/Welcome Screen © 2006 Regenstrief Institute & James Case Click File, Set Preferred Language
  41. 42. Select Linguistic Variant(s)
  42. 43. LOINC Terms with Spanish Linguistic Variant Spanish!
  43. 44. Welcome Screen
  44. 45. Setting User Preferences
  45. 46. Select User Preferences From the File Menu Set User Preferences
  46. 47. Set User Preference Dialog © 2006 Regenstrief Institute & James Case User Name or Initials File Locations Startup Screen Preference RELMA Color Scheme
  47. 48. RELMA Color Schemes Predefined Schemes Create, Save, Delete custom color schemes Customize Colors
  48. 49. User Map Screen Preferences Click Map Screen Tab
  49. 50. Importing Local Terms into RELMA
  50. 51. 4 Ways to Load LMOF Files <ul><li>Direct entry into LMOF from within RELMA (painful) </li></ul><ul><li>Create an Access table that mimics the LMOF structure (less painful but tedious) </li></ul><ul><ul><li>Appendix A: RELMA Manual </li></ul></ul><ul><li>Create a delimited ASCII file from your local test catalog (good choice) </li></ul><ul><li>Load directly from HL7 v2.x messages (best? choice) </li></ul><ul><ul><li>Pulls data from OBR and OBX segments </li></ul></ul>
  51. 52. Constructing a Local Dataset <ul><li>Create extract of your test catalog with: </li></ul><ul><ul><li>Battery/Panel Code </li></ul></ul><ul><ul><li>Battery/Panel Description or Name </li></ul></ul><ul><ul><li>Local Code </li></ul></ul><ul><ul><li>Test Description or Name </li></ul></ul><ul><ul><ul><li>Include Method if Important </li></ul></ul></ul><ul><ul><li>Units </li></ul></ul><ul><ul><li>Example Values </li></ul></ul><ul><ul><li>Laboratory Section </li></ul></ul>
  52. 53. Creating Delimited ASCII File <ul><li>RELMA can’t parse free text </li></ul><ul><ul><li>Need to create separate fields </li></ul></ul><ul><li>Can use any of these delimiters </li></ul><ul><ul><li>Tab, Semicolon, Comma, Space </li></ul></ul><ul><ul><li>Can define your own (“|” character recommended) </li></ul></ul><ul><li>Fields can be in any order </li></ul><ul><li>Minimum required fields </li></ul><ul><ul><li>Local Code </li></ul></ul><ul><ul><li>Local Description </li></ul></ul><ul><ul><li>Units (highly recommended) </li></ul></ul>
  53. 54. Entering New Local Terms into RELMA
  54. 55. Manual Enter/Edit © 2006 Regenstrief Institute & James Case View/Add/Edit Local Terms
  55. 56. Edit Term Dialog Add New Test Print Preview List Text alignment option Custom Export Format
  56. 57. Add Local Term Form Click to Add to Current Working File MICRO BUBPLAG BUBONIC PLAGUE – RRT PCR
  57. 58. Print Preview Local Term File
  58. 59. Text Alignment Truncated vs. Wrapped Truncated terms end with ellipsis
  59. 60. Custom Export Options Output Options
  60. 61. Exported as Excel File
  61. 62. Steps to Import Local Terms <ul><li>Click Import Local Terms Button from Main Menu </li></ul><ul><ul><li>a) File>Import Local Terms from Delimited File </li></ul></ul><ul><li>Locate your local terms text file </li></ul><ul><ul><li>Sample file loaded into C:Program FilesRELMA </li></ul></ul><ul><li>Name your Working Set </li></ul><ul><ul><li>LMOF database can contain multiple work sets </li></ul></ul><ul><li>Define default section (Optional) </li></ul><ul><li>Identify file delimiter </li></ul><ul><li>Assign fields to LMOF attributes </li></ul><ul><ul><li>Ignore fields you don’t need </li></ul></ul><ul><ul><li>Combine fields if needed </li></ul></ul><ul><li>Check “Case-sensitive” if needed </li></ul><ul><li>Click Import . </li></ul>
  62. 63. Example Delimited File © 2006 Regenstrief Institute & James Case
  63. 64. Importing Local Files © 2006 Regenstrief Institute & James Case Select Import Local Terms
  64. 65. Open File in RELMA © 2006 Regenstrief Institute & James Case Name your working set. RELMA allows multiple sets in LMOF database Select your delimiter Import Button
  65. 66. Open File in RELMA © 2006 Regenstrief Institute & James Case
  66. 67. Fields Segregated © 2006 Regenstrief Institute & James Case Assign LMOF Attribute
  67. 68. Ready to Import © 2006 Regenstrief Institute & James Case Now you can click this button!
  68. 69. Alternative (best) Way <ul><li>Use large set of HL7 messages </li></ul><ul><li>Automatically make dataset of: </li></ul><ul><ul><li>OBR ID </li></ul></ul><ul><ul><li>OBR description </li></ul></ul><ul><ul><li>OBX ID </li></ul></ul><ul><ul><li>OBX description </li></ul></ul><ul><ul><li>Sample of results with </li></ul></ul><ul><ul><ul><li>Real values </li></ul></ul></ul><ul><ul><ul><li>Units </li></ul></ul></ul><ul><ul><ul><li>Abnormal flags </li></ul></ul></ul><ul><ul><ul><li>Normal ranges </li></ul></ul></ul>
  69. 70. Generate Local term file from HL7 messages Select Import Terms from HL7 File
  70. 71. Select File to Import Select HL7 File
  71. 72. Specify HL7 File Name and Sample Size Name the Local Term File (working set)
  72. 73. HL7 Messages Data Statistics © 2006 Regenstrief Institute & James Case
  73. 74. New Terms added to LMOF New Battery Code Sample Data
  74. 75. <ul><li>Import the two sample files provided </li></ul><ul><ul><li>Import_Sample_OBR.txt </li></ul></ul><ul><ul><ul><li>Contains battery code and description </li></ul></ul></ul><ul><ul><li>Import_Sample_OBX.txt </li></ul></ul><ul><ul><ul><li>Contains test code and description </li></ul></ul></ul><ul><li>Create 2 working sets </li></ul>Lenny L’OINC says: “ Load the Sample Files Into RELMA now!”
  75. 76. Cleaning your data
  76. 77. Preparing your Data for Mapping <ul><li>Improve mapping success by: </li></ul><ul><ul><li>Expanding abbreviations </li></ul></ul><ul><ul><li>Standardizing colloquial terms </li></ul></ul><ul><ul><li>Ignoring “administrative” terms </li></ul></ul><ul><ul><li>Standardizing time references </li></ul></ul><ul><li>Can be done prior to importing </li></ul><ul><li>Better to use tools built into RELMA </li></ul>
  77. 78. Preparing your Data for Mapping <ul><li>Find local Words not in LOINC </li></ul><ul><ul><li>Tools>Concepts in Local Term File Unknown to RELMA </li></ul></ul><ul><ul><li>Creates a list of local terms in your file not found in LOINC </li></ul></ul><ul><ul><li>Only needs to be run once per working set </li></ul></ul><ul><ul><li>Can be printed or saved as a file </li></ul></ul><ul><ul><li>Autosearches LOINC terminology </li></ul></ul><ul><ul><li>Global Replace, Interactive Replace, Ignore </li></ul></ul>
  78. 79. RELMA Cleaning Tools Use this tool to find unknown terms
  79. 80. Scanning Local Terms
  80. 81. Replace Local Terms © 2006 Regenstrief Institute & James Case Assign LMOF Attribute Replacement Options
  81. 82. RELMA Cleaning Tools Use this tool to make global substitutions
  82. 83. Term Substitution Save this global substitution for only this working set
  83. 84. Mapping Local Terms
  84. 85. Mapping Local Terms <ul><li>Select “ Map Local Terms to LOINC ” from Welcome Screen </li></ul><ul><li>Select your Working Set to Map </li></ul><ul><ul><li>File>Change Local term File </li></ul></ul><ul><li>Select the subset of terms to work with: </li></ul><ul><ul><li>All </li></ul></ul><ul><ul><li>Mapped </li></ul></ul><ul><ul><li>Unmapped </li></ul></ul><ul><li>Set your Search Limits </li></ul><ul><ul><li>Set Search Limits Button </li></ul></ul>
  85. 86. Standard Mapping Window Features <ul><li>Resizeable grid </li></ul><ul><li>Reorder Grid columns </li></ul><ul><li>View details of LOINC term </li></ul><ul><li>Sort by column </li></ul><ul><ul><li>Click column </li></ul></ul><ul><ul><li>Custom Sort </li></ul></ul><ul><li>Print or export results grid Spell check squiggly line to signify words not known to RELMA </li></ul>
  86. 87. Mapping Screen View or edit local term
  87. 88. View Local Term Details © 2006 Regenstrief Institute & James Case
  88. 89. Standard Mapping Screen Begin a search
  89. 90. Initial Mapping Results Click to show words used in search EEK! What’ll I do?!
  90. 91. Initial Mapping Results Use term checkbox Number of LOINC terms containing keyword Battery terms included in search
  91. 92. Revised Mapping Results Number of matching records found Match units selected by default
  92. 93. Re-revised Mapping Results Number of matching records found Match units unselected
  93. 94. Standard Mapping Screen Clear all input fields
  94. 95. Cleared Mapping Screen Enter keywords here CANINE DISTEMPER VIRUS IF
  95. 96. Ad hoc term search
  96. 97. Standard Mapping Screen Navigate through the local terms Show entire local term file
  97. 98. Show all terms Displays printed report format
  98. 99. © 2006 Regenstrief Institute & James Case
  99. 100. Additional Search Screen Options Navigate to viewed screens View Mode: Grid (default) or Tree (new)
  100. 101. Tree View <ul><li>Replaces “Group” View in prior versions </li></ul><ul><li>Still in beta </li></ul><ul><li>Results displayed hierarchically </li></ul><ul><ul><li>Defined by the multi-axial hierarchy in search restrictions </li></ul></ul><ul><li>Map to a term in tree by clicking Map button of double clicking term </li></ul><ul><ul><li>Only rows that have LOINC Codes </li></ul></ul>
  101. 102. Tree View Cannot map to these Can map to these
  102. 103. Assigning a LOINC Map Highlight correct term Click “Map” Button (or doubleclick)
  103. 104. Adding Mapping Comments If comments option is selected, prompt appears Check with Frank in Chemistry
  104. 105. Assigning a LOINC Map LOINC Term Assigned
  105. 106. View LOINC Term Details Right clicking on a LOINC term brings up a Task Menu View details for a specific LOINC Term
  106. 107. LOINC Term Details Can scroll through returned subset of terms Change to expanded details view Change text size Can scroll down a single formatted page
  107. 108. Expanded Details View
  108. 109. Expanded Details View
  109. 110. Using Wildcards in Searches <ul><li>“*” replaces any number of characters </li></ul><ul><ul><li>GLUC* </li></ul></ul><ul><ul><li>*COSE </li></ul></ul><ul><ul><li>GLU*SE </li></ul></ul><ul><li>“?” replaces a single character </li></ul><ul><ul><li>GLUCOS? </li></ul></ul><ul><ul><li>?LUCOSE </li></ul></ul><ul><ul><li>GLUC?SE </li></ul></ul>
  110. 111. Other Search Qualifiers <ul><li>“ #” represents the “NOT” operator </li></ul><ul><ul><li>#GLUCOSE – terms without the Word Glucose </li></ul></ul><ul><li>“ |” is the “OR” operator </li></ul><ul><ul><li>GLUCOSE | LACTOSE </li></ul></ul><ul><li>Can have multiple “OR”s per box </li></ul><ul><li>Can Mix OR and NOT and Wildcards </li></ul>
  111. 112. Limiting Searches
  112. 113. Setting Search Limits <ul><li>Narrows search to specific subset of LOINC terms </li></ul><ul><li>Reduces number of candidate terms </li></ul><ul><li>Limits can be applied to all components </li></ul><ul><li>Component attribute can be further restricted by number of words </li></ul><ul><li>Tree structure allows for hierarchical constraints </li></ul>
  113. 114. RELMA - Search Constraints <ul><li>Controls general search constraints including: </li></ul><ul><ul><li>Limit to LOINC terms compatible with submitted units </li></ul></ul><ul><ul><li>Force match with any specimen contained in name </li></ul></ul><ul><ul><li>Methodless terms only ( now enhanced ) </li></ul></ul><ul><ul><li>Limit to components with N or fewer words in their name </li></ul></ul><ul><ul><li>Pop up search timing statistics after each search </li></ul></ul><ul><li>Use carefully or search may not be successful </li></ul><ul><ul><li>(Note parallel control switches at bottom of screen) </li></ul></ul>
  114. 115. Setting Search Limits Click Hierarchy & Search Limits Button
  115. 116. Setting search limits <ul><li>Can also set most of them by toggling buttons at the bottom of the screen </li></ul>Toggle Buttons
  116. 117. Search Constraints Predefined, general search constraints Attribute trees Local Unit Constraint: Now defaults to “ON”
  117. 118. Terms Consistent with Units Only terms consistent with mmol/L appear
  118. 119. Setting Search Limits Specimen constraints
  119. 120. Terms Consistent with Specimen CSF Enter default Specimen
  120. 121. Terms Consistent with Specimen Only CSF Terms are returned
  121. 122. Setting Search Limits Methodless Terms Restriction Override Methodless Terms Restriction
  122. 123. Limit to Methodless Terms
  123. 124. Limit to Methodless Terms Only Methodless Terms Appear
  124. 125. More on Methodless Terms <ul><li>Some LOINC categories do not have methodless terms </li></ul><ul><li>Checking methodless only will remove these from view on results grid </li></ul><ul><li>Checking additional box allows these to be seen </li></ul>
  125. 126. Methodless Only Unchecked All terms returned
  126. 127. Methodless Only Checked Only Methodless terms returned
  127. 128. Conditional Methodless More terms returned
  128. 129. Setting Search Limits Limit to Lab Tests Only (No Clinical LOINC Terms)
  129. 130. Setting Search Limits Limit to lab tests that comprise 99.8% of INPC volume
  130. 131. Setting Search Limits Limit Number of Words in the Component Attribute
  131. 132. Limit Number of Component Words Without Limit Applied: 698 terms returned
  132. 133. Limit Number of Component Words With Limit Applied: 64 terms returned Restriction appears on Toggle Bar (cannot toggle off)
  133. 134. Setting Search Limits Include Deprecated LOINC Codes with Returned Terms
  134. 135. Include Deprecated LOINC Terms Deprecated LOINC Terms appear as Strikethrough Text with a “Do Not” Symbol
  135. 136. Favor Property Restriction Favor one type of property over others
  136. 137. Order/Observation Restriction Order or Observation preference
  137. 138. LOINC Hierarchies – Class Tree Three top-level branches Tree Navigation Buttons
  138. 139. Before Class Restriction Large number of candidate terms Many terms have class of “CHAL”
  139. 140. Search Trees chal Restrict eligible tests to non-challenge chemistry tests only
  140. 141. Following Class Restriction Only Non-Challenge Chemistry tests returned
  141. 142. Improvements to Trees Continued reorganization to provide a Specimen hierarchy
  142. 143. Improved Hierarchy for Component Show the LOINC Codes associated with these components
  143. 144. Show Associated LOINCs Click on details for more information about the selection
  144. 145. Details Screen
  145. 146. Tree Export Tools Save tree data to a file Export tree data to Excel Send Tree data as email
  146. 147. RELMA - Tree Features <ul><li>All trees operate the same way </li></ul><ul><li>Shows terms spelled out </li></ul><ul><li>Can expand and collapse parts or all of tree. </li></ul><ul><li>Tree is string searchable </li></ul><ul><li>Search can be based on one or more branches of a tree with or without other criteria </li></ul><ul><li>Tabs are marked with an asterisk if criteria selected </li></ul>
  147. 148. Navigating through the Mapping Process
  148. 149. <ul><li>Limit effort to one lab section at a time and focus expertise </li></ul><ul><li>Chemistry and hematology will be easiest </li></ul><ul><li>Consider prioritizing by frequency </li></ul>LOINC Mapping Tactics
  149. 150. Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc . 2007;:771-775.
  150. 151. More LOINC Mapping Tactics <ul><li>Try using method-less terms first </li></ul><ul><ul><li>Specific methods can be transmitted in: </li></ul></ul><ul><ul><ul><li>OBX–17 (v2.x), Observation.methodCode (v3.0) </li></ul></ul></ul><ul><li>Examine local units or real results to verify correct properties </li></ul><ul><ul><li>Properties are rarely distinguishable in tests </li></ul></ul><ul><li>You don’t have to do it all at one sitting </li></ul><ul><ul><li>Use the “Unmapped” function to return where you left off </li></ul></ul><ul><li>With every release - Update previous mappings to identify deprecated terms </li></ul>
  151. 152. Common Mapping Issues <ul><li>Locally Defined Test Name Ambiguity </li></ul><ul><ul><li>Reuse of local test code </li></ul></ul><ul><li>“ Analyte-free” Local Test Names </li></ul><ul><li>Incongruent Value sets (Scale ambiguity) </li></ul><ul><li>Result vs. Interpretation </li></ul><ul><li>Available LOINC Terms too Specific </li></ul><ul><li>Available LOINC Terms too General </li></ul><ul><li>Panel vs. Discrete Test </li></ul><ul><ul><li>Common in Microbiology </li></ul></ul>
  152. 153. Using your Mapped Terms <ul><li>Print results of LOINC Mapping </li></ul><ul><li>Export to File </li></ul>
  153. 154. Intelligent Mapper <ul><li>Run in batch mode to find N- closest terms </li></ul><ul><li>Can then use this output to do final mapping </li></ul><ul><li>Again units are VERY important </li></ul><ul><li>Can pick all limits available to regular mapping </li></ul><ul><li>With Radiology can use CPT to help </li></ul><ul><li>Intelligent Mapper Radiology References </li></ul><ul><ul><li>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. </li></ul></ul><ul><ul><li>Vreeman DJ and McDonald CJ. Automated Mapping of Local Radiology Terms to LOINC. Proc AMIA Symp. 2005;769-773. </li></ul></ul>
  154. 155. Picking the Intelligent Mapper
  155. 156. Intelligent Mapper Start Screen
  156. 157. Intelligent Mapper - Mapping Screen
  157. 158. Exporting Mapped Terms Export Terms to Delimited File
  158. 159. Export Terms Dialog Check Fields you wish to export Select Delimiter
  159. 160. Output File © 2006 Regenstrief Institute & James Case Mapped terms include LOINC code
  160. 161. Other RELMA ® Features
  161. 162. Panels, Forms and Survey Review New Menu Function: Review Panels, Forms and Surveys
  162. 163. Government Forms Form Name Component LOINC terms
  163. 164. Laboratory panels Expand category to see panels Double-click panel name to see components
  164. 165. Expanded Panel Detail
  165. 166. Expanded Clinical Panel © 2006 Regenstrief Institute & James Case
  166. 167. Clinical Panels New Feature: Find where a term has been used
  167. 168. LOINC Term Usage 35089-2, 35090-0
  168. 169. LOINC Term Panel Usage
  169. 170. Other Survey Instruments
  170. 171. HIPAA Attachments View Various HIPAA Attachments
  171. 172. HIPPA Attachment Tree
  172. 173. Expanded Attachment Data
  173. 174. Can’t find the term you want?
  174. 175. Search Hints and Tips <ul><li>Keywords with zero frequency are ignored </li></ul><ul><ul><li>May need to rephrase – use synonym </li></ul></ul><ul><li>Some causes for no returned terms </li></ul><ul><ul><li>Too many keywords in search – uncheck some </li></ul></ul><ul><ul><li>Limits applied that don’t make sense </li></ul></ul><ul><ul><ul><li>E.g. Method-less tests plus Method tree set to EIA </li></ul></ul></ul><ul><ul><li>Did not find and revise words not in RELMA </li></ul></ul><ul><ul><ul><li>Local units not in RELMA </li></ul></ul></ul><ul><li>Units are GREAT discriminators </li></ul><ul><li>You may have tests that need to be added to LOINC </li></ul>
  175. 176. Proposing New LOINC Terms
  176. 177. Proposing New Terms <ul><li>Make sure the term is really needed </li></ul><ul><ul><li>Think of other names for the same concept </li></ul></ul><ul><ul><li>Avoid detailed methods or localizations </li></ul></ul><ul><ul><li>Is the distinction really important? </li></ul></ul><ul><li>Supply sufficient annotation to justify the new term </li></ul><ul><ul><li>Package inserts, sample reports (email to Regenstrief) </li></ul></ul><ul><ul><li>The more the better! </li></ul></ul><ul><li>Construct new terms within RELMA </li></ul><ul><ul><li>File>Propose a LOINC </li></ul></ul><ul><ul><li>Linked to the “trees” to allow browsing </li></ul></ul><ul><li>Can review and submit them to LOINC from within RELMA </li></ul>
  177. 178. Propose new LOINC terms Select Propose a LOINC
  178. 179. Propose new LOINC terms Navigate through proposed terms Create new term, save current term or Exit form
  179. 180. Preview Proposed Terms Review your new terms
  180. 181. Preview Proposed Terms All proposed terms fully editable Choose whether to send or postpone X X X X
  181. 182. Use Existing Terms as Template Select your closest match Click the Propose Term button
  182. 183. Use Existing Terms as Template All required components filled in
  183. 184. Using LOINC and SNOMED Together
  184. 185. Where do LOINC and SNOMED Fit? <ul><li>LOINC represents the question: </li></ul><ul><ul><li>Is there any Botulism toxin in my specimen? (33708-9) </li></ul></ul><ul><ul><li>Organisms identified in specimen? (634-6) </li></ul></ul><ul><li>SNOMED represents the answer: </li></ul><ul><ul><li>Negative (SCTID 260385009) </li></ul></ul><ul><ul><li>E. coli O157:H7 (SCTID 103429008) </li></ul></ul>Remember:
  185. 186. Where do LOINC and SNOMED Fit? <ul><li>In an HL7 message, LOINC may be used: </li></ul><ul><ul><li>In OBR-4 (Universal Service Identifier) </li></ul></ul><ul><ul><li>In OBX-3 (Observation Identifier </li></ul></ul><ul><li>SNOMED may be used: </li></ul><ul><ul><li>In OBX-5 (where nominal values are needed) </li></ul></ul><ul><ul><li>Almost anyplace else in an HL7 message where coded values are needed </li></ul></ul>
  186. 187. OBX: With a Coded Value OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT The code is from SNOMED The code is from LOINC OBX-5: Data A code for L. monocytogenes A code that identifies the data type in OBX-5 as a coded element OBX-3:A code that identifies the data in OBX-5 (Listeria culture)
  187. 188. HL7 2.5 Example (ER-7 format) <ul><li>MSH|^~&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01| LABGL1199510221838581| P| 2.3||| NE| NE </li></ul><ul><li>PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^ </li></ul><ul><li>Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090 </li></ul><ul><li>OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult </li></ul><ul><li>^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN </li></ul><ul><li>OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837 </li></ul><ul><li>OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility Panel^ LN||| 199812300934||||||||Bacterial isolate| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN </li></ul><ul><li>OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate ^SCT|||||| F||| 199812300934|| CA20837 </li></ul><ul><li>OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934|| CA20837 </li></ul><ul><li>OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F||| 199812300934|| CA20837 </li></ul>First Order OBR (Culture and ID) First Result Value (SNOMED) First Result Description OBX (LOINC) Second Order OBR (Susceptibility)
  188. 189. Q and A Session
  189. 190. Exercise Map your own data
  190. 191. Need RELMA? http://tinyurl.com/2vrms7

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