Using RELMA  Or…In Search of the Missing LOINCLaboratory LOINC Meeting – December 2011   James T. Case MS, DVM, PhD  Healt...
Acknowledgements• LOINC Development TeamClem Mcdonald, Dan Vreemen, Kathy Mercer, JaciPhillips, Ian Pyle, David Baorto, Fr...
What will we cover today?•   Overview of LOINC•   Reviewing new RELMA features!•   Installing RELMA•   Setting personal pr...
©2011 Regenstrief Institute and James Case
Why are we doing this?      Goals of Health Information Standards• Interoperability – the ability to exchange  information...
Levels of Interoperability• Basic – allows data to be exchanged between  computer systems  •   Word processing documents, ...
Comparability• Meaning of the data is consistent when shared  among different parties  •   Erysipelas – Human skin disease...
Potential Uses of Health Data areConstrained by Data Quality Factors• Data quality issues  •   Different for client/patien...
The Problem“In attempting to arrive at the truth, I have applied   everywhere for information, but in scarcely an   instan...
Test comparisons                      What you see in the order listLab A                                             Lab ...
Why LOINC? “Within one laboratory, local jargon terms      may be used which are usually well     understood between colle...
LOINC ®                                      101Emphasis on Laboratory       LOINC       ©2011 Regenstrief Institute and J...
Anatomy of a LOINC Term     5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA        5193-8                          ...
What is NOT part of a LOINC Name?• The instrument used in testing• Specific details about the specimen• Priority (e.g. STA...
Component/AnalyteThe substance or entity that is measured,         evaluated, or observed  -   Sodium  -   Glucose  -   Br...
Component/Analyte Structure      Analyte Name^Challenge^Adjustments• Formal name of Analyte (e.g. Calcium)  •   Must speci...
Property                       the most difficult LOINC axisThe characteristic or attribute of the analyte that is        ...
Property                        the most difficult LOINC axis       Combine Major Categories with Subtypes for Full Proper...
Common Issues with LOINC Properties                 Fraction (proportion) vs. Ratio                          a/a+b vs. a/b...
Timing*The interval of time over which the observation or             measurement was made• Pt - at a point in time• 12H -...
SystemThe system (context) or specimen type upon which           the observation was made.• Ser - Serum                   ...
System Structure                    System^Super System• Super System• Patient is the default• Used to indicate   •   bloo...
Scale• Qn - Quantitative  •   Continuous numeric (real, integer, ratio)  •   Optional operator (>, , , <)       •   When a...
Scale (Special)• OrdQn – Ordinal or Quantitative  •   Primarily used for antimicrobial observations e.g.      MIC reported...
Method• Methods only needed if interpretation affected  •   Different normal ranges  •   Test Sensitivity/Specificity• Gen...
Hierarchies• LOINC ‘class’• Each LOINC axis• Multi-axial •   Component | System •   Separate download              ©2011 R...
Mapping Terms to LOINC                 Things to Remember• The thing ordered is not always the thing measured:   •   Blood...
What is in LOINC?                        Content• Term structures• Submitted units, Example UCUM units  •   aiming toward ...
RELMA®Regenstrief LOINC Mapping Assistant            ©2011 Regenstrief Institute and James Case
Purpose of Tutorial•   “Eliminate” need to read the User’s Manual•   Become familiar with RELMA features•   Provide some i...
RELMA Functions•   LOINC files and indexes•   Manual and automated mapping functions•   Same free use as LOINC (see licens...
New in This Version (Rel. 5.4)• Default - latest copy of LOINC details retrieved from  the loinc.org website.   •   Config...
New in This Version (Rel. 5.4)• "Terms consistent with local units" search  restriction status is saved between editing  s...
LOINC Web Site  ©2011 Regenstrief Institute and James Case
What’s available to download?• RELMA - mapping and browsing tool    •   HL7 message converter- Makes a database        sui...
RELMA Highlights• Browse-able hierarchies of LOINC parts• Display search results in tree view• Enhanced “details” view of ...
Installing RELMA®      ©2011 Regenstrief Institute and James Case
Installation Steps• Make sure you have enough free disk space!   •   2Gb is recommended• From CD - Start – Run – <drive>:R...
File Locations• Database and Ancillary Files  •   Windows XP = C:Documents and SettingsAll      UsersDocumentsRELMA  •   W...
Running RELMA®    Version 5.4    ©2011 Regenstrief Institute and James Case
Copyright Screen    ©2011 Regenstrief Institute and James Case
Main Menu/Welcome Screen       ©2011 Regenstrief Institute and James Case
Set Preferred Language                        Click File, Set Preferred                               Language       ©2011...
Select Linguistic Variant(s)                                       Selecting a translation may                            ...
LOINC Terms with Spanish Linguistic Variant                                                             All Spanish!      ...
Setting User Preferences        ©2011 Regenstrief Institute and James Case
Set User Preferences                                          Select User Preferences                                     ...
Set User Preference Dialog                                           New File Locations:                                  ...
User Map Screen Preferences                                        Click Map Screen Tab                                   ...
Importing LocalTerms into RELMA     ©2011 Regenstrief Institute and James Case
4 Ways to Load LMOF Files• Direct entry into LMOF from within RELMA (painful)   •   Handy for individual entries/edits• Cr...
Constructing a Local DatasetCreate extract of your test catalog with:  •   Battery/Panel Code  •   Battery/Panel Descripti...
Creating Delimited ASCII File• RELMA can’t parse free text  •   Need to create separate fields• Can use any of these delim...
Entering New Local Terms       into RELMA       ©2011 Regenstrief Institute and James Case
Manual Enter/Edit                                View/Add/Edit Local Terms    ©2011 Regenstrief Institute and James Case
Edit Term Dialog                                                              EditAddDelete Terms                         ...
Export Local Term FileDelimiters supported: Tab, comma, bar (|)                        ©2011 Regenstrief Institute and Jam...
Add Local TermMICROBUBPLAGBUBONIC PLAGUE – RRT PCR           Click to Add to Current                Working File          ...
Search Local Term FileCalcium                      Enter Keyword from any                                     Return to Fu...
Print Preview Local Term File          ©2011 Regenstrief Institute and James Case
Steps to Import Local Terms1. Click Import Local Terms Button from Main Menu   a) File>Import Local Terms from Delimited F...
Example Tab-Delimited File        ©2011 Regenstrief Institute and James Case
Importing Local Files                               Select Import Local Terms                                 from Delimit...
Navigate to File Location                                  Select Filefiles stored in                                    S...
Open File in RELMA                                            Name your working set.                                      ...
Fields Segregated                                                 Assign LMOF Attribute                                   ...
Ready to ImportMinimum assignments                                                            Now you can click the       ...
Post-Processing of Local File• After import, RELMA Searches for terms  (words) that it does not recognize• Stored in a fil...
Local Term File Options       ©2011 Regenstrief Institute and James Case
Change Local Term File                                   Select the Working Set                                         Cu...
Alternative Pragmatic Way• Use large set of HL7 messages• Automatically make dataset of:  •   OBR ID  •   OBR description ...
Generate Local term file from HL7 messages                                          Select Import Terms from              ...
Select File to Import                                                  Select HL7 File     ©2011 Regenstrief Institute and...
Specify HL7 File Name and Sample Size                                          Skip import of                             ...
HL7 Messages Data Statistics         ©2011 Regenstrief Institute and James Case
New Terms added to LMOFClick on “Edit Term” to see       Sample Data                                                     N...
Sample Results for Observation                                                       New Test Code                        ...
Lenny L’OINC says: “Load the Sample Files   Into RELMA now!”    • Import the two sample files      provided            •  ...
Cleaning your data    ©2011 Regenstrief Institute and James Case
Preparing your Data for Mapping• Improve mapping success by:  •   Expanding abbreviations  •   Standardizing colloquial te...
RELMA Cleaning Tools                                                  Use this tool to edit                               ...
Review Unknown Local Terms         May Re-Scan File for          Unknown Terms         ©2011 Regenstrief Institute and Jam...
Replace Local Terms   Replacement Options   Assign LMOF Attribute       ©2011 Regenstrief Institute and James Case
RELMA Cleaning Tools                                              Use this tool to make                                   ...
Term SubstitutionSave this global substitution  for only this working set       ©2011 Regenstrief Institute and James Case
Lenny L’OINC says:     “Begin to clean your         data now!”    • Using the OBR or OBX sample      files, take 15-20 min...
Searching for LOINC Terms        ©2011 Regenstrief Institute and James Case
Simplified Search                                            Only Tool©2011 Regenstrief Institute and James Case
Search Window                                                                     Help FileEnter Search Terms             ...
Search WindowHematocrit bld qn                                                           “Common Tests” rank              ...
New RELMA Helpfile     ©2011 Regenstrief Institute and James Case
Context MenuRight click to bring up context menu                       ©2011 Regenstrief Institute and James Case
Mapping Local Terms      ©2011 Regenstrief Institute and James Case
Mapping Local Terms• Select your Working Set to Map  • File>Select Local Term File to Process• Select “Map Local Terms to ...
Standard Mapping Window Features• Customizable grid• View details of LOINC term• Sort by column  •   Click column  •   Cus...
Mapping Screen         View or edit local term          Enter local term numberQuick select button list                Cus...
Configure Grid                         Select elements to display                                                         ...
Quick choice buttonsViewing LOINC term detail         ©2011 Regenstrief Institute and James Case
View Local Term Details                                 Select level of detail to                                         ...
View Local Term Details                                                    Select text size       ©2011 Regenstrief Instit...
Select detail display levelSelect level of detail to        display                            ©2011 Regenstrief Institute...
Standard Mapping Screen                                              EEK! What’llBegin a search                           ...
Standard Mapping Screen  Click toshow words  used in  search              ©2011 Regenstrief Institute and James Case
Initial Mapping Results             Number of LOINC             terms containingUse term                                  ...
Revised Mapping Results Match units                                                  Number of selected by                ...
Re-revised Mapping Results                                                                Number of                       ...
Standard Mapping Screen                 CANINE DISTEMPER VIRUS IFEnter keywords here                             Clear all...
Ad hoc term search    ©2011 Regenstrief Institute and James Case
Standard Mapping Screen      Navigate through       the local terms       ©2011 Regenstrief Institute and James Case
Tabbed Access to Functions    Navigate to Functions     from Mapping Page           Switch between Grid and               ...
Tree View ©2011 Regenstrief Institute and James Case
Tree View• Results displayed hierarchically  •   Defined by the multi-axial hierarchy in search      restrictions (covered...
Tree View  Can map to terms                                                Cannot map to  with LOINC Codes                ...
Assigning a LOINC Map                                       Click “Map” Button                                            ...
Adding Mapping CommentsCheck with Frank in Chemistry          If comments       option is selected,        prompt appears ...
Assigning a LOINC Map  LOINC Term   Assigned       ©2011 Regenstrief Institute and James Case
View LOINC Term Details                                                                     View details for a            ...
LOINC Term Details                                               Can scroll down a single                                 ...
View Panel ChildrenSelect View Panel Children    from context menu                       ©2011 Regenstrief Institute and J...
Panel Children  ©2011 Regenstrief Institute and James Case
Configure Export Options                     Output Options                                                               ...
Excel Export Format     ©2011 Regenstrief Institute and James Case
More on Searching Mapping Screen    ©2011 Regenstrief Institute and James Case
Basic Search SyntaxSpecial        Example                           DefinitionCharacter(s)“ “            Influenza “virus ...
Search Qualifiers                    Detailed help available Includes Glucuronidase,       Glucosidase, Glucosylceramidase...
Combining Search Terms              Exclude Glucosidase                                  Reduced number of terms       ©20...
Advanced Search Syntax               based on Google-like search syntaxParameter      Description+              Term must ...
Applying advanced search       ©2011 Regenstrief Institute and James Case
Limiting Searches    ©2011 Regenstrief Institute and James Case
Setting Search Limits• Narrows search to specific subset of LOINC terms• Reduces number of candidate terms• Limits can be ...
General Search Constraints• Controls features including:   •   Limit to LOINC terms compatible with submitted units   •   ...
Setting Search LimitsClick Hierarchy & Search       Limits Tab                           ©2011 Regenstrief Institute and J...
Setting search limitsCan also set most of them by toggling buttons at the bottom of the screen                            ...
Search Constraints                                                              Attribute trees                           ...
Terms Consistent with Units  New! - Status saved betweenediting sessions                                          Only ter...
Setting Search Limits                                         Specimen                                        constraints ...
Terms Consistent with Specimen                                                       CSF             Enter default        ...
Terms Consistent with SpecimenOnly CSF Terms are     returned                     ©2011 Regenstrief Institute and James Case
Setting Search Limits                                New! - Exclude laterality     ©2011 Regenstrief Institute and James C...
Exclude laterality                                                 Laterality terms    ©2011 Regenstrief Institute and Jam...
Setting Search Limits                                 New! - Restrict to                                 common orders    ...
Restriction to common orders                      Large number of New! Common            candidates  orders rank          ...
Setting Search LimitsMethodless Terms           Override Methodless Terms   Restriction                    Restriction    ...
Limit to Methodless TermsBoth method andmethod-less terms                    ©2011 Regenstrief Institute and James Case
Limit to Methodless TermsOnly Methodless Terms Appear                  ©2011 Regenstrief Institute and James Case
More on Methodless Terms• Some LOINC categories do not have  methodless terms• Checking methodless only will remove these ...
Methodless Only Unchecked            All terms returned        ©2011 Regenstrief Institute and James Case
Methodless Only Checked                                  Only Methodless                                  terms returned D...
Conditional Methodless                             More terms                              returnedNo method-lessterm; all...
Setting Search Limits                   Limit to Lab Tests Only                 (No Clinical LOINC Terms)      ©2011 Regen...
Setting Search Limits                   Limit to common lab tests      ©2011 Regenstrief Institute and James Case
Setting Search LimitsLimit Number of Words in the   Component Attribute                      ©2011 Regenstrief Institute a...
Limit Number of Component Words                                                        Without Limit Applied:             ...
Limit Number of Component Words                 Restriction appears on                       Toggle Bar                   ...
Setting Search Limits       Include Trial, Deprecated or      Discouraged LOINC Codes with             Returned Terms     ...
Include Deprecated LOINC Terms                                          -You cannot map to                                ...
Favor Property Restriction  Favor one type ofproperty over others                                                         ...
Order/Observation RestrictionOrder or Observation    preference                       ©2011 Regenstrief Institute and Jame...
LOINC Hierarchies – Class Tree           Three top-level             branches                                             ...
Before Class Restriction                                                Many terms have class                             ...
Search Trees+Chem* +non                                        Restrict eligible tests                                    ...
Following Class Restriction  Only Non-Challenge   Chemistry tests       returned              ©2011 Regenstrief Institute ...
System Hierarchy   ©2011 Regenstrief Institute and James Case
Component Hierarchy  Click on details for more   information about the          selection               Show the LOINC Cod...
Details Screen LOINC Part        ©2011 Regenstrief Institute and James Case
Show Associated LOINCs       ©2011 Regenstrief Institute and James Case
LOINC Term Details Screen                                        Detailed Information on                                  ...
Tree Export ToolsExport according to  Configuration Configure Export Format                  ©2011 Regenstrief Institute a...
Tree Export Configuration        ©2011 Regenstrief Institute and James Case
RELMA - Tree Features• All trees operate the same way• Shows terms spelled out• Can expand and collapse parts or all of tr...
LOINC Part Search• Same look as term search• Uses “Google-like” query language  •   Extremely fast  •   Include and exclud...
Navigating through the  Mapping Process      ©2011 Regenstrief Institute and James Case
LOINC Mapping Tactics• Limit effort to one lab section at a time and  focus expertise• Chemistry and hematology will be ea...
Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term         Mapping by Frequency. AMIA Annu ...
More LOINC Mapping Tactics• Try using method-less terms first  •   Specific methods can be transmitted in:       •   OBX–1...
Common Mapping Issues• Locally Defined Test Name Ambiguity    •   Reuse of local test code• “Analyte-free” Local Test Name...
Using your Mapped Terms• Print results of LOINC Mapping• Export to File                ©2011 Regenstrief Institute and Jam...
Configure Export FormatContext Sensitive Export     Configuration              ©2011 Regenstrief Institute and James Case
LMOF Export ConfigurationSelect Export Format                                      Select Fields to Export                ...
Print Mapped Terms from View/Add/Edit Menu                                   Click Print button to PreviewMay highlight te...
Formatted Report OutputClick Print button to output      formatted report                    ©2011 Regenstrief Institute a...
Custom Export Configuration      Select the Format you wish               to Export      Select the Fields you wish to    ...
Excel™ Export  ©2011 Regenstrief Institute and James Case
Lab Auto Mapper•   Run in batch mode to find N- closest terms•   Can then use this output to do final mapping•   Again uni...
Picking the Lab Auto Mapper         ©2011 Regenstrief Institute and James Case
Lab Auto Mapper Start Screen   Can restrict search to                       Maximum number of terms      common tests     ...
Lab Auto Mapper Start Screen Local test code                                    Local terms used for                      ...
Lab Auto Mapper - Mapping Screen           ©2011 Regenstrief Institute and James Case
Exporting Mapped Terms                                                    Export Terms to                                 ...
Export Terms DialogSelect Term Set                                                                Select DelimiterCheck Fi...
Other        RELMA®  Features    ©2011 Regenstrief Institute and James Case
Panels, Forms and Survey Review                                     Review Panels, Forms and                              ...
Government Forms              Component LOINC                  terms    Form Name    ©2011 Regenstrief Institute and James...
Laboratory Panels                Expand category to                    see panels                                         ...
Expanded Panel Detail      ©2011 Regenstrief Institute and James Case
Expanded Clinical Panel       ©2011 Regenstrief Institute and James Case
Clinical Panels35089-2, 35090-0                                              Find where a term has                        ...
LOINC Term Panel Usage       ©2011 Regenstrief Institute and James Case
Other Survey Instruments       ©2011 Regenstrief Institute and James Case
HIPAA Attachments                          View Various HIPAA                             Attachments    ©2011 Regenstrief...
HIPPA Attachment Tree      ©2011 Regenstrief Institute and James Case
Expanded Attachment Data        ©2011 Regenstrief Institute and James Case
Can’t find the  term you    want?                 ©2011 Regenstrief Institute and James Case
Search Hints and Tips• Keywords with zero frequency are ignored  •   May need to rephrase – use synonym• Some causes for n...
Proposing New LOINC Terms        ©2011 Regenstrief Institute and James Case
Proposing New Terms• Make sure the term is really needed   •   Think of other names for the same concept   •   Avoid detai...
Propose new LOINC terms                                                    Select Propose a                               ...
Advanced/Simple     toggle        Required fields in            Navigate through                    Create new term,      ...
Preview Proposed Terms                                                    Review your new                                 ...
Review Proposed Terms    James T. Case DVM, PhD                                             301-555-1314    NIH/NLM       ...
Submitting New Terms• Must supply name, organization, phone  and email of submitter• Must select at least one proposed ter...
Use Existing Terms as Template                              Click the Propose                                 Term button ...
Use Existing Terms as Template                                            All required                                    ...
Using LOINC and SNOMED        Together       ©2011 Regenstrief Institute and James Case
Where do LOINC and SNOMED Fit?Remember:• LOINC represents the question:  •   Is there any Botulism toxin in my specimen?  ...
Where do LOINC and SNOMED Fit?• In an HL7 message, LOINC may be used:  •   In OBR-4 (Universal Service Identifier)  •   In...
OBX: With a Coded Value   A code that  identifies the   data type in                       The code is                    ...
HL7 2.5 Example (ER-7 format)MSH|^~&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01|  LABGL1199510221838581| P| 2.3||| NE| NE ...
Q and A Session   ©2011 Regenstrief Institute and James Case
ExerciseMap your own data     ©2011 Regenstrief Institute and James Case
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2011 12 08 - LOINC and RELMA Workshop and Tutorial

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2011 12 08 - LOINC and RELMA Workshop and Tutorial

  1. 1. Using RELMA Or…In Search of the Missing LOINCLaboratory LOINC Meeting – December 2011 James T. Case MS, DVM, PhD Health Program Specialist, SNOMED CT National Library of Medicine ©2011 Regenstrief Institute and James Case
  2. 2. Acknowledgements• LOINC Development TeamClem Mcdonald, Dan Vreemen, Kathy Mercer, JaciPhillips, Ian Pyle, David Baorto, Fran Brahmi• RELMA Development TeamJohn Hook, Mark Fisher, Karen Ahmed, AnandhiSowmyan, James Dennis• LOINC Committee• Supporters:NLM, Regenstrief (including the Indiana Center ofExcellence in Public Health Informatics), RegenstriefFoundation ©2011 Regenstrief Institute and James Case
  3. 3. What will we cover today?• Overview of LOINC• Reviewing new RELMA features!• Installing RELMA• Setting personal preferences• Loading a Local Observation File (LMOF)• Searching for a LOINC Term• Preparing LMOF for Mapping• Review of Map Screen Functions• Setting Search Limits• Mapping Local Terms to LOINC• Viewing LOINC Term Details• Proposing/Submitting New LOINC Terms• Exporting/Printing Mapped Terms• Mapping your own LMOF data ©2011 Regenstrief Institute and James Case
  4. 4. ©2011 Regenstrief Institute and James Case
  5. 5. Why are we doing this? Goals of Health Information Standards• Interoperability – the ability to exchange information between organizations• Comparability – the ability to ascertain the equivalence of data from different sources• Data Quality – the measurement of accessibility, completeness, accuracy and precision (and more) ©2011 Regenstrief Institute and James Case
  6. 6. Levels of Interoperability• Basic – allows data to be exchanged between computer systems • Word processing documents, text messages• Functional – describes the standard syntax (format) of the data • Document templates, forms, data structures • Message standards• Semantic – requires use of standardized content (vocabularies) within the data structure ©2011 Regenstrief Institute and James Case
  7. 7. Comparability• Meaning of the data is consistent when shared among different parties • Erysipelas – Human skin disease; Streptococcus Grp A • Erysipelas – Animal Septicemia/dermatitis; Erysipelothrix rhusiopathiae• Common terminology required • Should work in the background• Words are not enough • Codes – uniquely identify terms • Vocabulary – specialized, precise terms that remove ambiguity • Ontology – describes nature of entities and their relations • Classification – groups related terms ©2011 Regenstrief Institute and James Case
  8. 8. Potential Uses of Health Data areConstrained by Data Quality Factors• Data quality issues • Different for client/patient communications vs. clinical decision support vs. epidemiological analysis • Often constrained by external forces • e.g. criteria for diagnosis often differs from the criteria for reporting• Unidirectional effect of data consolidation • Detailed → General • General → Detailed ©2011 Regenstrief Institute and James Case
  9. 9. The Problem“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…” Florence Nightingale - Notes on a Hospital, 1873 ©2011 Regenstrief Institute and James Case
  10. 10. Test comparisons What you see in the order listLab A Lab BTest Name: Lyme Disease Serology Test Name: Lyme Disease AntibodyMeasures: B. burgdorferi Ab IgG Measures: B. burgdorferi Ab IgMMethod: ELISA Method: Immune blotScale: quantitative Scale: qualitativee.g.: Titer 1:40 e.g.: PositiveLOINC Code = 5062-5 LOINC Code = 6321-4 ©2011 Regenstrief Institute and James Case
  11. 11. 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 communication with the outside world.”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 ©2011 Regenstrief Institute and James Case
  12. 12. LOINC ® 101Emphasis on Laboratory LOINC ©2011 Regenstrief Institute and James Case
  13. 13. Anatomy of a LOINC Term 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA 5193-8 LOINC CodeHepatitis B virus surface Ab Component ACnc Property Measured Pt Timing Ser System Qn Scale EIA Method There are six major LOINC axes ©2011 Regenstrief Institute and James Case
  14. 14. What is NOT part of a LOINC Name?• The instrument used in testing• Specific details about the specimen• Priority (e.g. STAT)• Where testing was done• Who did the test• Test interpretation• 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 Observation Object ©2011 Regenstrief Institute and James Case
  15. 15. Component/AnalyteThe substance or entity that is measured, evaluated, or observed - Sodium - Glucose - Brucella sp. organism - Influenza A Virus antigen - Cytomegalovirus Virus antibody - Lipids.Total 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA ©2011 Regenstrief Institute and James Case
  16. 16. 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” • <time delay> post <challenge type>• Adjustments/corrections • E.g. Adjusted to pH 7.4 ©2011 Regenstrief Institute and James Case
  17. 17. Property the most difficult LOINC axisThe characteristic or attribute of the analyte that is measured, evaluated, or observedMajor Categories• Mass: Observations reported with mass (milligrams, grams, etc.) in the numerator of their units of measure• Substance: Observations reported with moles or milliequivalents in the numerator of their units of measure• Catalytic activity: Observations that report enzymatic activity• 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 ©2011 Regenstrief Institute and James Case
  18. 18. Property the most difficult LOINC axis Combine Major Categories with Subtypes for Full Property• MCnc – mass concentration (mass/unit vol)• MCnt – mass content (mass/unit mass)• NCnc – number concentration (number/unit vol)• TmStp – time• CCnc – catalytic concentration (activity)• Prid – presence or identity• Imp – impression/interpretation• Find – subjective or objective observation• Type – “Kind-of” 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA ©2011 Regenstrief Institute and James Case
  19. 19. Common Issues with LOINC Properties Fraction (proportion) vs. Ratio a/a+b vs. a/b • Fraction = Part/whole • Number fraction (NFr): % Eosinophils • Substance fraction (SFr): % HGB which is A2 • Ratio = Measures multiple analytes from the same system (specimen) • Mass concentration ratio - MCrto • e.g., BUN/Creat in urine specimen • Substance ratio-SCrto • Urea/Creatinine expressed as mmol/L (SI units) • Relative Ratio = Measures from different systems • RelRto • RlTm – time from actual Institute and James Case control ©2011 Regenstrief and normal
  20. 20. Timing*The interval of time over which the observation or measurement was made• Pt - at a point in time• 12H - a twelve hour collection• 24H - a twenty four hour collection *non-Pt timings are usually associated with Rate Property ©2011 Regenstrief Institute and James Case
  21. 21. SystemThe system (context) or specimen type upon which the observation was made.• Ser - Serum • Gast – Gastric• Bld - Whole blood fluid/contents (RBC) • Food – Food or• Ur- Urine feedstuff• BldA - Arterial blood • Tiss – Tissue• Liver - Liver • XXX – To be specified• Flu – Body Fluid, in another part of the unspecified message ©2011 Regenstrief Institute and James Case
  22. 22. 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: 54417-1:ABO+Rh group:Type:Pt:Bld^fetus:Nom: ©2011 Regenstrief Institute and James Case
  23. 23. Scale• Qn - Quantitative • Continuous numeric (real, integer, ratio) • Optional operator (>, , , <) • When assay detection limits are exceeded• Ord - Ordinal • a ranked set of possible values (1+, 2+, 3+)• Nom - Nominal • an unranked collection of possible values • a taxonomy (e.g list of bacteria)• Nar - Narrative • free text narrative (e.g., visit note) ©2011 Regenstrief Institute and James Case
  24. 24. Scale (Special)• OrdQn – Ordinal or Quantitative • Primarily used for antimicrobial observations e.g. MIC reported as resistant, intermediate, susceptible or as the mm diameter of the inhibition zone • Use is discouraged in other contexts• Multi – structured text “globs” • e.g. chromatography output • Use is discouraged• Doc – Clinical documents• Set – Clinical attachments (headers) ©2011 Regenstrief Institute and James Case
  25. 25. Method• Methods only needed if interpretation affected • Different normal ranges • Test Sensitivity/Specificity• Generally listed only at the generic level • Agglutination (limited subtypes) • Immunoassay • Probe with target amplification ©2011 Regenstrief Institute and James Case
  26. 26. Hierarchies• LOINC ‘class’• Each LOINC axis• Multi-axial • Component | System • Separate download ©2011 Regenstrief Institute and James Case
  27. 27. Mapping Terms to LOINC Things to Remember• The thing ordered is not always the thing measured: • Blood Culture – live organism(s) identified • VDRL – Treponema pallidum Ab • Urinalysis – lots of different things• The question (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl) • You are mapping the question, not the answer!• You must know the specifics of the component being tested for (what is this test actually measuring?) ©2011 Regenstrief Institute and James Case
  28. 28. What is in LOINC? Content• Term structures• Submitted units, Example UCUM units • aiming toward preferred units sorting• Synonyms• Answer lists (increasing number)• Text descriptions – links to info sources about individual tests • Panel structures • Foreign language translations ©2011 Regenstrief Institute and James Case
  29. 29. RELMA®Regenstrief LOINC Mapping Assistant ©2011 Regenstrief Institute and James Case
  30. 30. Purpose of Tutorial• “Eliminate” need to read the User’s Manual• Become familiar with RELMA features• Provide some insight into mapping tips/pitfalls• Help begin the mapping process for your institution ©2011 Regenstrief Institute and James Case
  31. 31. RELMA Functions• LOINC files and indexes• Manual and automated mapping functions• Same free use as LOINC (see license)• RELMA tools transform local words in local file • User creates file of local term/name and codes• Assigns LOINC term to local test/battery code• “Common tests” subset to speed mapping• Context sensitive hierarchies for local use.• Flexible “Google-like” search functions ©2011 Regenstrief Institute and James Case
  32. 32. New in This Version (Rel. 5.4)• Default - latest copy of LOINC details retrieved from the loinc.org website. • Configurable from File -> User Preferences -> Details Pages -> Get from Internet. • Build locally File -> User Preferences -> Details Pages -> Build Locally.• Common order rank displayed as "Common Order Rank" in the LOINC Details displays.• New search restriction - "Exclude LOINCs containing left or right“. Bilateral LOINCs and LOINCs without laterality remain in the search results. ©2011 Regenstrief Institute and James Case
  33. 33. New in This Version (Rel. 5.4)• "Terms consistent with local units" search restriction status is saved between editing sessions.• Answer string descriptions displayed with answer string (configurable).• Images are now displayed on Part details pages, if available.• Obsolete LOINC fields deleted from the Details displays -- ANSWERLIST and DEFINITION_DESCRIPTION_HELP. ©2011 Regenstrief Institute and James Case
  34. 34. LOINC Web Site ©2011 Regenstrief Institute and James Case
  35. 35. 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 translations by part• Tools for building databases to map from HL7 messages• New guidance documents for mappers ©2011 Regenstrief Institute and James Case 35
  36. 36. RELMA Highlights• Browse-able hierarchies of LOINC parts• Display search results in tree view• Enhanced “details” view of terms/parts • References • Descriptions • Sample units• Empirically-derived common test list• Empirically-derived common order list• Special features for panels/forms• Enhanced export/copy-paste options ©2011 Regenstrief Institute and James Case
  37. 37. Installing RELMA® ©2011 Regenstrief Institute and James Case
  38. 38. Installation Steps• Make sure you have enough free disk space! • 2Gb is recommended• From CD - Start – Run – <drive>:RELMASetup• Specify installation directory • Life will be easier if you accept the default• Two database files installed • RELMA.MDB – LOINC Terms Database • LMOF3.MDB – Local Master Observation File• Two sample files included• Run from Start – (All) Programs – Regenstrief – RELMA ©2011 Regenstrief Institute and James Case
  39. 39. File Locations• Database and Ancillary Files • Windows XP = C:Documents and SettingsAll UsersDocumentsRELMA • Windows Vista = C:UsersPublicDocumentsRELMA • Windows 7 = C:UsersPublicDocumentsRELMA• Sample files • Windows XP = C:Documents and SettingsAll UsersDocumentsRELMASamples • Windows Vista = C:UsersPublicDocumentsRELMASamples • Windows 7 = C:UsersPublicDocumentsRELMASamples ©2011 Regenstrief Institute and James Case
  40. 40. Running RELMA® Version 5.4 ©2011 Regenstrief Institute and James Case
  41. 41. Copyright Screen ©2011 Regenstrief Institute and James Case
  42. 42. Main Menu/Welcome Screen ©2011 Regenstrief Institute and James Case
  43. 43. Set Preferred Language Click File, Set Preferred Language ©2011 Regenstrief Institute and James Case
  44. 44. Select Linguistic Variant(s) Selecting a translation may require indexes to be built ©2011 Regenstrief Institute and James Case
  45. 45. LOINC Terms with Spanish Linguistic Variant All Spanish! ©2011 Regenstrief Institute and James Case
  46. 46. Setting User Preferences ©2011 Regenstrief Institute and James Case
  47. 47. Set User Preferences Select User Preferences From the File Menu ...or from Welcome Screen ©2011 Regenstrief Institute and James Case
  48. 48. Set User Preference Dialog New File Locations: (See prior slide for location) Startup Screen Preference ©2011 Regenstrief Institute and James Case
  49. 49. User Map Screen Preferences Click Map Screen Tab Auto create search terms Include/Exclude Battery Terms Add comments on Mappings ©2011 Regenstrief Institute and James Case
  50. 50. Importing LocalTerms into RELMA ©2011 Regenstrief Institute and James Case
  51. 51. 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 ©2011 Regenstrief Institute and James Case
  52. 52. Constructing a Local DatasetCreate extract of your test catalog with: • Battery/Panel Code • Battery/Panel Description or Name • *Local Code • *Test Description or Name • Include Method if Important • Units • Example Values • Laboratory Section ©2011 Regenstrief Institute and James Case
  53. 53. 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 Description • Units (highly recommended) ©2011 Regenstrief Institute and James Case
  54. 54. Entering New Local Terms into RELMA ©2011 Regenstrief Institute and James Case
  55. 55. Manual Enter/Edit View/Add/Edit Local Terms ©2011 Regenstrief Institute and James Case
  56. 56. Edit Term Dialog EditAddDelete Terms Export TermsText alignment option Print Preview List ©2011 Regenstrief Institute and James Case
  57. 57. Export Local Term FileDelimiters supported: Tab, comma, bar (|) ©2011 Regenstrief Institute and James Case
  58. 58. Add Local TermMICROBUBPLAGBUBONIC PLAGUE – RRT PCR Click to Add to Current Working File ©2011 Regenstrief Institute and James Case
  59. 59. Search Local Term FileCalcium Enter Keyword from any Return to Full List Field ©2011 Regenstrief Institute and James Case
  60. 60. Print Preview Local Term File ©2011 Regenstrief Institute and James Case
  61. 61. Steps to Import Local Terms1. Click Import Local Terms Button from Main Menu a) File>Import Local Terms from Delimited File2. Locate your local terms text file a) E.g. WinXP Sample files loaded into C:Documents and SettingsAll UsersShared DocumentsRELMA3. Name your Working Set a) LMOF database can contain multiple work sets4. Define default section (Optional)5. Identify file delimiter6. Assign fields to LMOF attributes a) Ignore fields you don’t need b) Combine fields if needed7. Check “Case-sensitive” if needed8. Click Import. ©2011 Regenstrief Institute and James Case
  62. 62. Example Tab-Delimited File ©2011 Regenstrief Institute and James Case
  63. 63. Importing Local Files Select Import Local Terms from Delimited File… ©2011 Regenstrief Institute and James Case
  64. 64. Navigate to File Location Select Filefiles stored in Sample and Click Open RELMA Directory ©2011 Regenstrief Institute and James Case
  65. 65. Open File in RELMA Name your working set. RELMA allows multiple sets in LMOF databaseSelect your delimiter Import Button ©2011 Regenstrief Institute and James Case
  66. 66. Fields Segregated Assign LMOF Attribute Choose field name ©2011 Regenstrief Institute and James Case
  67. 67. Ready to ImportMinimum assignments Now you can click the Import button! ©2011 Regenstrief Institute and James Case
  68. 68. Post-Processing of Local File• After import, RELMA Searches for terms (words) that it does not recognize• Stored in a file for future reconciliation ©2011 Regenstrief Institute and James Case
  69. 69. Local Term File Options ©2011 Regenstrief Institute and James Case
  70. 70. Change Local Term File Select the Working Set Current mapping status ©2011 Regenstrief Institute and James Case
  71. 71. Alternative Pragmatic Way• Use large set of HL7 messages• Automatically make dataset of: • OBR ID • OBR description • OBX ID • OBX description • Sample of results with • Real values • Units • Abnormal flags • Normal ranges ©2011 Regenstrief Institute and James Case
  72. 72. Generate Local term file from HL7 messages Select Import Terms from HL7 File ©2011 Regenstrief Institute and James Case
  73. 73. Select File to Import Select HL7 File ©2011 Regenstrief Institute and James Case
  74. 74. Specify HL7 File Name and Sample Size Skip import of sample valuesName the Local Term Select the number of File (working set) sample values Select which codes to store ©2011 Regenstrief Institute and James Case
  75. 75. HL7 Messages Data Statistics ©2011 Regenstrief Institute and James Case
  76. 76. New Terms added to LMOFClick on “Edit Term” to see Sample Data New Battery Code ©2011 Regenstrief Institute and James Case
  77. 77. Sample Results for Observation New Test Code Sample Values from Messages ©2011 Regenstrief Institute and James Case
  78. 78. Lenny L’OINC says: “Load the Sample Files Into RELMA now!” • Import the two sample files provided • Import_Sample_OBR.txt • Contains battery code and description • Import_Sample_OBX.txt • Contains test code and description • Create 2 working sets • Load your personal data set©2011 Regenstrief Institute and James Case
  79. 79. Cleaning your data ©2011 Regenstrief Institute and James Case
  80. 80. Preparing your Data for Mapping• Improve mapping success by: • Expanding abbreviations • Standardizing colloquial terms • Ignoring “administrative” terms • Standardizing time references• Can be done prior to importing• Better to use tools built into RELMA ©2011 Regenstrief Institute and James Case
  81. 81. RELMA Cleaning Tools Use this tool to edit unknown terms ©2011 Regenstrief Institute and James Case
  82. 82. Review Unknown Local Terms May Re-Scan File for Unknown Terms ©2011 Regenstrief Institute and James Case
  83. 83. Replace Local Terms Replacement Options Assign LMOF Attribute ©2011 Regenstrief Institute and James Case
  84. 84. RELMA Cleaning Tools Use this tool to make global substitutions ©2011 Regenstrief Institute and James Case
  85. 85. Term SubstitutionSave this global substitution for only this working set ©2011 Regenstrief Institute and James Case
  86. 86. 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.©2011 Regenstrief Institute and James Case
  87. 87. Searching for LOINC Terms ©2011 Regenstrief Institute and James Case
  88. 88. Simplified Search Only Tool©2011 Regenstrief Institute and James Case
  89. 89. Search Window Help FileEnter Search Terms Limit to Restrict to “Common Results” Specific Units Restrict to “Common Use Automapper Orders” logic ©2011 Regenstrief Institute and James Case
  90. 90. Search WindowHematocrit bld qn “Common Tests” rank ©2011 Regenstrief Institute and James Case
  91. 91. New RELMA Helpfile ©2011 Regenstrief Institute and James Case
  92. 92. Context MenuRight click to bring up context menu ©2011 Regenstrief Institute and James Case
  93. 93. Mapping Local Terms ©2011 Regenstrief Institute and James Case
  94. 94. Mapping Local Terms• Select your Working Set to Map • File>Select Local Term File to Process• 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 Button ©2011 Regenstrief Institute and James Case
  95. 95. 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 ©2011 Regenstrief Institute and James Case
  96. 96. Mapping Screen View or edit local term Enter local term numberQuick select button list Custom Grid Configuration ©2011 Regenstrief Institute and James Case
  97. 97. Configure Grid Select elements to display Reorder grid elements Visually resize elementsReset Default Configuration ©2011 Regenstrief Institute and James Case
  98. 98. Quick choice buttonsViewing LOINC term detail ©2011 Regenstrief Institute and James Case
  99. 99. View Local Term Details Select level of detail to display ©2011 Regenstrief Institute and James Case
  100. 100. View Local Term Details Select text size ©2011 Regenstrief Institute and James Case
  101. 101. Select detail display levelSelect level of detail to display ©2011 Regenstrief Institute and James Case
  102. 102. Standard Mapping Screen EEK! What’llBegin a search I do?!(or hit “enter”) ©2011 Regenstrief Institute and James Case
  103. 103. Standard Mapping Screen Click toshow words used in search ©2011 Regenstrief Institute and James Case
  104. 104. Initial Mapping Results Number of LOINC terms containingUse term Battery terms keywordcheckbox included in search ©2011 Regenstrief Institute and James Case
  105. 105. Revised Mapping Results Match units Number of selected by matching default records found ©2011 Regenstrief Institute and James Case
  106. 106. Re-revised Mapping Results Number of matching Match units records found unselected ©2011 Regenstrief Institute and James Case
  107. 107. Standard Mapping Screen CANINE DISTEMPER VIRUS IFEnter keywords here Clear all input fields ©2011 Regenstrief Institute and James Case
  108. 108. Ad hoc term search ©2011 Regenstrief Institute and James Case
  109. 109. Standard Mapping Screen Navigate through the local terms ©2011 Regenstrief Institute and James Case
  110. 110. Tabbed Access to Functions Navigate to Functions from Mapping Page Switch between Grid and Tree Views ©2011 Regenstrief Institute and James Case
  111. 111. Tree View ©2011 Regenstrief Institute and James Case
  112. 112. Tree View• Results displayed hierarchically • Defined by the multi-axial hierarchy in search restrictions (covered later)• Map to a term in tree by clicking Map button or double clicking term • Only rows that have LOINC Codes ©2011 Regenstrief Institute and James Case
  113. 113. Tree View Can map to terms Cannot map to with LOINC Codes terms representing LOINC partsTree Navigation Buttons ©2011 Regenstrief Institute and James Case
  114. 114. Assigning a LOINC Map Click “Map” Button (or doubleclick) Highlight correct term ©2011 Regenstrief Institute and James Case
  115. 115. Adding Mapping CommentsCheck with Frank in Chemistry If comments option is selected, prompt appears ©2011 Regenstrief Institute and James Case
  116. 116. Assigning a LOINC Map LOINC Term Assigned ©2011 Regenstrief Institute and James Case
  117. 117. View LOINC Term Details View details for a specific LOINC Term Right clicking on a LOINCterm brings up a Task Menu ©2011 Regenstrief Institute and James Case
  118. 118. LOINC Term Details Can scroll down a single formatted page Can scroll throughChange to expanded returned subset of details view terms Change text size ©2011 Regenstrief Institute and James Case
  119. 119. View Panel ChildrenSelect View Panel Children from context menu ©2011 Regenstrief Institute and James Case
  120. 120. Panel Children ©2011 Regenstrief Institute and James Case
  121. 121. Configure Export Options Output Options IncludeSave Configuration column headers and/or Export ©2011 Regenstrief Institute and James Case
  122. 122. Excel Export Format ©2011 Regenstrief Institute and James Case
  123. 123. More on Searching Mapping Screen ©2011 Regenstrief Institute and James Case
  124. 124. Basic Search SyntaxSpecial Example DefinitionCharacter(s)“ “ Influenza “virus A” Linked terms must appear togetherAND Morphine AND Both terms must appear in the search result Opiates termOR Influenza OR Either or both terms must appear in the Parainfluenza search result termNOT Influenza NOT equine Excludes terms with the word following the NOT. Cannot be used alone.? Gluc?se Substitutes a single character in the string. (glucose,glucase) Cannot be used as the first character; cannot be used in “phrases”* Gluc*se Substitute multiple characters in the string. (glucose, Cannot be used as the first character; cannot glucuronidase, etc.) be used in “phrases” ©2011 Regenstrief Institute and James Case
  125. 125. Search Qualifiers Detailed help available Includes Glucuronidase, Glucosidase, Glucosylceramidase, etc. ©2011 Regenstrief Institute and James Case
  126. 126. Combining Search Terms Exclude Glucosidase Reduced number of terms ©2011 Regenstrief Institute and James Case
  127. 127. Advanced Search Syntax based on Google-like search syntaxParameter Description+ Term must be included in search- Term must be excluded from the search() Group terms for subquery (i.e. A OR B; A AND B)Fieldname: Limit term search to the associated field (e.g. Component: glucose)Fieldname:() Group multiple terms in a single field~ Fuzzy search (e.g. Hemofhilus~)“ “~ Proximity search for multiple terms (e.g. “function panel”~1){}, [] Upper and lower bounds; {} exclusive, [] inclusive Special character escape ©2011 Regenstrief Institute and James Case
  128. 128. Applying advanced search ©2011 Regenstrief Institute and James Case
  129. 129. Limiting Searches ©2011 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 attribute can be further restricted by number of words• Tree structure allows for hierarchical constraints ©2011 Regenstrief Institute and James Case
  131. 131. General Search Constraints• Controls features including: • Limit to LOINC terms compatible with submitted units • Forced match with any specimen contained in name • Method-less terms only • Limit to components/analytes with N or fewer words in their name • Pop up search timing statistics after each search• Use carefully or search may not be successful (Note parallel control switches at bottom of screen) ©2011 Regenstrief Institute and James Case
  132. 132. Setting Search LimitsClick Hierarchy & Search Limits Tab ©2011 Regenstrief Institute and James Case
  133. 133. Setting search limitsCan also set most of them by toggling buttons at the bottom of the screen Toggle Buttons ©2011 Regenstrief Institute and James Case
  134. 134. Search Constraints Attribute trees Local Unit Constraint: Default is “ON” Type toggle boxesPredefined, general search constraints ©2011 Regenstrief Institute and James Case
  135. 135. Terms Consistent with Units New! - Status saved betweenediting sessions Only terms consistent with mmol/L appear ©2011 Regenstrief Institute and James Case
  136. 136. Setting Search Limits Specimen constraints ©2011 Regenstrief Institute and James Case
  137. 137. Terms Consistent with Specimen CSF Enter default Specimen ©2011 Regenstrief Institute and James Case
  138. 138. Terms Consistent with SpecimenOnly CSF Terms are returned ©2011 Regenstrief Institute and James Case
  139. 139. Setting Search Limits New! - Exclude laterality ©2011 Regenstrief Institute and James Case
  140. 140. Exclude laterality Laterality terms ©2011 Regenstrief Institute and James Case
  141. 141. Setting Search Limits New! - Restrict to common orders ©2011 Regenstrief Institute and James Case
  142. 142. Restriction to common orders Large number of New! Common candidates orders rank ©2011 Regenstrief Institute and James Case
  143. 143. Setting Search LimitsMethodless Terms Override Methodless Terms Restriction Restriction ©2011 Regenstrief Institute and James Case
  144. 144. Limit to Methodless TermsBoth method andmethod-less terms ©2011 Regenstrief Institute and James Case
  145. 145. Limit to Methodless TermsOnly Methodless Terms Appear ©2011 Regenstrief Institute and James Case
  146. 146. More on Methodless Terms• Some LOINC categories do not have methodless terms• Checking methodless only will remove these from view on results grid• Checking additional box allows these to be seen ©2011 Regenstrief Institute and James Case
  147. 147. Methodless Only Unchecked All terms returned ©2011 Regenstrief Institute and James Case
  148. 148. Methodless Only Checked Only Methodless terms returned Differ in one ormore components ©2011 Regenstrief Institute and James Case
  149. 149. Conditional Methodless More terms returnedNo method-lessterm; all shown ©2011 Regenstrief Institute and James Case
  150. 150. Setting Search Limits Limit to Lab Tests Only (No Clinical LOINC Terms) ©2011 Regenstrief Institute and James Case
  151. 151. Setting Search Limits Limit to common lab tests ©2011 Regenstrief Institute and James Case
  152. 152. Setting Search LimitsLimit Number of Words in the Component Attribute ©2011 Regenstrief Institute and James Case
  153. 153. Limit Number of Component Words Without Limit Applied: 850 terms returned ©2011 Regenstrief Institute and James Case
  154. 154. Limit Number of Component Words Restriction appears on Toggle Bar (cannot toggle off)Component limited to 1 word With Limit Applied: 68 terms returned ©2011 Regenstrief Institute and James Case
  155. 155. Setting Search Limits Include Trial, Deprecated or Discouraged LOINC Codes with Returned Terms ©2011 Regenstrief Institute and James Case
  156. 156. 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 ©2011 Regenstrief Institute and James Case
  157. 157. Favor Property Restriction Favor one type ofproperty over others All other components being equal MCnc only will be displayed ©2011 Regenstrief Institute and James Case
  158. 158. Order/Observation RestrictionOrder or Observation preference ©2011 Regenstrief Institute and James Case
  159. 159. LOINC Hierarchies – Class Tree Three top-level branches Tree Navigation Buttons ©2011 Regenstrief Institute and James Case
  160. 160. Before Class Restriction Many terms have class of “CHAL” Large number of candidate terms ©2011 Regenstrief Institute and James Case
  161. 161. Search Trees+Chem* +non Restrict eligible tests to non-challenge chemistry tests only ©2011 Regenstrief Institute and James Case
  162. 162. Following Class Restriction Only Non-Challenge Chemistry tests returned ©2011 Regenstrief Institute and James Case
  163. 163. System Hierarchy ©2011 Regenstrief Institute and James Case
  164. 164. Component Hierarchy Click on details for more information about the selection Show the LOINC Codes associated with these components ©2011 Regenstrief Institute and James Case
  165. 165. Details Screen LOINC Part ©2011 Regenstrief Institute and James Case
  166. 166. Show Associated LOINCs ©2011 Regenstrief Institute and James Case
  167. 167. LOINC Term Details Screen Detailed Information on LOINC Parts ©2011 Regenstrief Institute and James Case
  168. 168. Tree Export ToolsExport according to Configuration Configure Export Format ©2011 Regenstrief Institute and James Case
  169. 169. Tree Export Configuration ©2011 Regenstrief Institute and James Case
  170. 170. 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” button on Mapping Screen to remove all tree selections ©2011 Regenstrief Institute and James Case
  171. 171. LOINC Part Search• Same look as term search• Uses “Google-like” query language • Extremely fast • Include and exclude criteria • Partial string matching (using wildcards)• Demo • Campylobacter fetus, not Ab ©2011 Regenstrief Institute and James Case
  172. 172. Navigating through the Mapping Process ©2011 Regenstrief Institute and James Case
  173. 173. LOINC Mapping Tactics• Limit effort to one lab section at a time and focus expertise• Chemistry and hematology will be easiest• For manufactured assays, use package insert as source information• Sample results give clue to property and scale• Consider prioritizing by frequency of use ©2011 Regenstrief Institute and James Case
  174. 174. Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775. ©2011 Regenstrief Institute and James Case
  175. 175. More LOINC Mapping Tactics• Try using method-less terms first • Specific methods can be transmitted in: • OBX–17 (v2.x), Observation.methodCode (v3.0)• Examine local units or real results to verify correct property and scale • Properties are rarely distinguishable in test names• You don’t have to do it all at one sitting • Use the “Unmapped” function to return where you left off• With every release - Update previous mappings to identify deprecated terms ©2011 Regenstrief Institute and James Case
  176. 176. Common Mapping Issues• Locally Defined Test Name Ambiguity • Reuse of local test code• “Analyte-free” Local Test Names • (Miscellaneous serology)• Incongruent Value sets (Scale ambiguity)• Result vs. Interpretation• Available LOINC Terms too Specific/General• Panel vs. Discrete Test • Common in Microbiology ©2011 Regenstrief Institute and James Case
  177. 177. Using your Mapped Terms• Print results of LOINC Mapping• Export to File ©2011 Regenstrief Institute and James Case
  178. 178. Configure Export FormatContext Sensitive Export Configuration ©2011 Regenstrief Institute and James Case
  179. 179. LMOF Export ConfigurationSelect Export Format Select Fields to Export Save Configuration and Export ©2011 Regenstrief Institute and James Case
  180. 180. Print Mapped Terms from View/Add/Edit Menu Click Print button to PreviewMay highlight terms to be output printed ©2011 Regenstrief Institute and James Case
  181. 181. Formatted Report OutputClick Print button to output formatted report ©2011 Regenstrief Institute and James Case
  182. 182. Custom Export Configuration Select the Format you wish to Export Select the Fields you wish to Export ©2011 Regenstrief Institute and James Case
  183. 183. Excel™ Export ©2011 Regenstrief Institute and James Case
  184. 184. Lab Auto 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 ©2011 Regenstrief Institute and James Case
  185. 185. Picking the Lab Auto Mapper ©2011 Regenstrief Institute and James Case
  186. 186. Lab Auto Mapper Start Screen Can restrict search to Maximum number of terms common tests to return ©2011 Regenstrief Institute and James Case
  187. 187. Lab Auto Mapper Start Screen Local test code Local terms used for mapping ©2011 Regenstrief Institute and James Case
  188. 188. Lab Auto Mapper - Mapping Screen ©2011 Regenstrief Institute and James Case
  189. 189. Exporting Mapped Terms Export Terms to Delimited File ©2011 Regenstrief Institute and James Case
  190. 190. Export Terms DialogSelect Term Set Select DelimiterCheck Fields you wish to export ©2011 Regenstrief Institute and James Case
  191. 191. Other RELMA® Features ©2011 Regenstrief Institute and James Case
  192. 192. Panels, Forms and Survey Review Review Panels, Forms and Surveys Review Panels, Forms and Surveys ©2011 Regenstrief Institute and James Case
  193. 193. Government Forms Component LOINC terms Form Name ©2011 Regenstrief Institute and James Case
  194. 194. Laboratory Panels Expand category to see panels Double-click panel name to see components ©2011 Regenstrief Institute and James Case
  195. 195. Expanded Panel Detail ©2011 Regenstrief Institute and James Case
  196. 196. Expanded Clinical Panel ©2011 Regenstrief Institute and James Case
  197. 197. Clinical Panels35089-2, 35090-0 Find where a term has been used ©2011 Regenstrief Institute and James Case
  198. 198. LOINC Term Panel Usage ©2011 Regenstrief Institute and James Case
  199. 199. Other Survey Instruments ©2011 Regenstrief Institute and James Case
  200. 200. HIPAA Attachments View Various HIPAA Attachments ©2011 Regenstrief Institute and James Case
  201. 201. HIPPA Attachment Tree ©2011 Regenstrief Institute and James Case
  202. 202. Expanded Attachment Data ©2011 Regenstrief Institute and James Case
  203. 203. Can’t find the term you want? ©2011 Regenstrief Institute and James Case
  204. 204. 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 ©2011 Regenstrief Institute and James Case
  205. 205. Proposing New LOINC Terms ©2011 Regenstrief Institute and James Case
  206. 206. Proposing New Terms• Make sure the term is really needed • Think of other names for the same concept • Avoid detailed methods or localizations • Is the distinction really important?• Supply sufficient annotation to justify the new term • Package inserts, sample reports (email to Regenstrief) • The more the better!• Construct new terms within RELMA • File>Propose a new LOINC • Linked to the “trees” to allow browsing• Can review and submit them to LOINC from within RELMA ©2011 Regenstrief Institute and James Case
  207. 207. Propose new LOINC terms Select Propose a new LOINC ©2011 Regenstrief Institute and James Case
  208. 208. Advanced/Simple toggle Required fields in Navigate through Create new term, red proposed terms save current term or Exit form ©2011 Regenstrief Institute and James Case
  209. 209. Preview Proposed Terms Review your new terms ©2011 Regenstrief Institute and James Case
  210. 210. Review Proposed Terms James T. Case DVM, PhD 301-555-1314 NIH/NLM 301-555-1315 James.case@mail.nih.govXXX Choose whether to send or postpone All proposed terms fully editable ©2011 Regenstrief Institute and James Case
  211. 211. Submitting New Terms• Must supply name, organization, phone and email of submitter• Must select at least one proposed term to send• “Configure export” does not affect submission output• Email resulting file to Regenstrief ©2011 Regenstrief Institute and James Case
  212. 212. Use Existing Terms as Template Click the Propose Term button Select your closest match ©2011 Regenstrief Institute and James Case
  213. 213. Use Existing Terms as Template All required components filled in ©2011 Regenstrief Institute and James Case
  214. 214. Using LOINC and SNOMED Together ©2011 Regenstrief Institute and James Case
  215. 215. Where do LOINC and SNOMED Fit?Remember:• LOINC represents the question: • Is there any Botulism toxin in my specimen? (33708-9) • Organisms identified in specimen? (634-6)• SNOMED represents the answer: • Negative (SCTID 260385009) • E. coli O157:H7 (SCTID 103429008) ©2011 Regenstrief Institute and James Case
  216. 216. Where do LOINC and SNOMED Fit?• In an HL7 message, LOINC may be used: • In OBR-4 (Universal Service Identifier) • In OBX-3 (Observation Identifier• SNOMED may be used: • In OBX-5 (where nominal values are needed) • Almost anyplace else in an HL7 message where coded values are needed ©2011 Regenstrief Institute and James Case
  217. 217. OBX: With a Coded Value A code that identifies the data type in The code is The code is OBX-5 as a from LOINC from SNOMED coded elementOBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT OBX-3:A code that identifies the data in OBX-5: Data OBX-5 A code for L. (Listeria culture) monocytogenes ©2011 Regenstrief Institute and James Case
  218. 218. HL7 2.5 Example (ER-7 format)MSH|^~&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01| LABGL1199510221838581| P| 2.3||| NE| NE First Order OBRPID||| 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|| 773789090 First Result Value (SNOMED)OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult Second Order OBR^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN (Susceptibility)OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility Second Result(s) First Result First Result Description Panel^ LN||| 199812300934||||||||Bacterial isolate| IN2973^ Schadow^ OBXs Gunther^^^^ OBX (LOINC) (Culture and ID)MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPINOBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate ^SCT|||||| F||| 199812300934|| CA20837OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934|| CA20837OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F||| 199812300934|| CA20837 ©2011 Regenstrief Institute and James Case
  219. 219. Q and A Session ©2011 Regenstrief Institute and James Case
  220. 220. ExerciseMap your own data ©2011 Regenstrief Institute and James Case

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