2010 06 07 - LOINC Workshop
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Transcript of 2010 06 07 - LOINC Workshop
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©2010 Regenstrief Institute and James Case
James T. Case MS, DVM, PhD Health Program Specialist, SNOMED CT
National Library of Medicine
Laboratory LOINC Meeting – June 2010
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Acknowledgements • RELMA Development Team
• John Hook, Mark Fisher, Karen Ahmad, Craig Kelker
• Dan Vreeman
• Clem McDonald
• Kathy Mercer
• The Lab LOINC CommiFee
• Funding Support • NLM, Regenstrief InsJtute, NCI, CDC
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What will we cover today? • Overview of LOINC • Reviewing new RELMA features! • Installing RELMA • SeMng personal preferences • Loading a Local ObservaJon File (LMOF) • Searching for a LOINC Term • Preparing LMOF for Mapping • Review of Map Screen FuncJons • SeMng Search Limits • Mapping Local Terms to LOINC • Viewing LOINC Term Details • Proposing/SubmiMng New LOINC Terms • ExporJng/PrinJng Mapped Terms • Mapping your own LMOF data
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Why are we doing this? Goals of Health Information Standards
• Interoperability – the ability to exchange informaJon between organizaJons
• Comparability – the ability to ascertain the equivalence of data from different sources
• Data Quality – the measurement of accessibility, completeness, accuracy and precision (and more)
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Levels of Interoperability • Basic – allows data to be exchanged between computer systems • Word processing documents, text messages
• Func7onal – describes the standard syntax (format) of the data • Document templates, forms, data structures • Message standards
• Seman7c – requires use of standard vocabularies within the data
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Comparability • Meaning of the data is consistent when shared among different parJes • Erysipelas – Human skin disease; Streptococcus Grp A • Erysipelas – Animal SepJcemia/dermaJJs; Erysipelothrix rhusiopathiae
• Common terminology required • Should work in the background
• Not just words • Codes – uniquely idenJfies terms • ClassificaJon – groups related terms • Vocabulary – specialized, precise terms that remove ambiguity
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Potential Uses of Health Data are Constrained by Data Quality Factors
• Data quality issues • Different for client communicaJons vs. analysis
• O]en constrained by external forces • E.g. criteria for diagnosis o]en differs from the criteria for reporJng
• UnidirecJonal effect of data consolidaJon • Detailed → General • General → Detailed
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The Problem “In aFempJng to arrive at the truth, I have applied everywhere for informaJon, but in scarcely an instance have I been able to obtain hospital records fit for any purpose of comparison. If they could be obtained, they would enable us to decide many other quesJons… They would show [subscribers] how their money was being spent [and] what amount of good was really being done with it…”
Florence Nightingale - Notes on a Hospital, 1873
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Test comparisons
Lab A Test Name: Lyme Disease Serology
Measures: B. burgdorferi Ab IgG
Method: ELISA
Scale: quan7ta7ve
e.g.: Titer 1:40
Lab B Test Name: Lyme Disease An7body
Measures: B. burgdorferi Ab IgM
Method: Immune blot
Scale: qualita7ve
e.g.: Posi7ve
What you see in the order list
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Why LOINC? “Within one laboratory, local jargon terms
may be used which are usually well understood between colleagues, but
would not be sufficiently widely known for communicaJon with the outside world.”
U. Forsum et al., Pure Appl. Chem 72:555-‐745, 2000 Proper3es and Units in the Clinical Laboratory Sciences Part VII. Proper3es and Units in Clinical Microbiology
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LOINC® 101
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5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
5193-‐8 LOINC Code
Hepa77s B virus surface Ab
ACnc
Pt
Ser
Qn
EIA
Component
Property Measured
Timing
System
Scale
Method
There are six major LOINC axes
Anatomy of a LOINC Term
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What is NOT part of a LOINC Name?
• The instrument used in tesJng • Specific details about the specimen • Priority (e.g. STAT) • Where tesJng was done • Who did the test • Test interpretaJon • Anything that is not an intrinsic part of the name of the result
• Other things that are carried in; • The OBR or OBX segment • An HL7 Version 3 ObservaJon Object
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The substance or enJty that is measured, evaluated, or observed
Component/Analyte
-‐ Sodium -‐ Glucose -‐ Brucella sp. organism -‐ Influenza A Virus anJgen -‐ Cytomegalovirus Virus anJbody -‐ Lipids.Total
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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Component/Analyte Structure
• Formal name of Analyte (e.g. Calcium) • Must specify any “subanalyte”
• e.g. Coronavirus Ag • May have a subclass – separated by “.”
• e.g. Calcium.Free
• Challenge -‐ e.g, 1H post 100 gm Glucose PO • Two subparts separated by “post” • <Jme delay> post <challenge type>
• Adjustments/correcJons • E.g. Adjusted to pH 7.4
Analyte Name^Challenge^Adjustments
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• Mass: ObservaJons reported with mass (milligrams, grams, etc.) in the numerator of their units of measure
• Substance: ObservaJons reported with moles or milliequivalents in the numerator of their units of measure
• Cataly7c ac7vity: ObservaJons that report enzymaJc acJvity
• Arbitrary: Results that report arbitrary units in the numerator of their units of measure
• Number: Counts
Property
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
The characterisJc or aFribute of the analyte that is measured, evaluated, or observed
the most difficult LOINC axis
Major Categories
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• MCnc – mass concentraJon (mass/unit vol)
• MCnt – mass content (mass/unit mass) • NCnc – number concentraJon (number/unit vol)
• TmStp – Jme • CCnc – catalyJc concentraJon (acJvity) • Prid – presence or idenJty • Imp – impression/interpretaJon • Find – subjecJve or objecJve observaJon • Type – “Kind-‐of”
Property
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
the most difficult LOINC axis
Combine Major Categories with Subtypes for Full Property
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Common Issues with LOINC Properties
• FracJon = Part/whole • Number fracJon (NFr): % Eosinophils • Substance fracJon (SFr): % HGB which is A2
• RaJo = Measures mulJple analytes from the same system (specimen) • Mass concentraJon raJo -‐ MCrto
• e.g., BUN/Creat in urine specimen
• Substance raJo-‐SCrto • Urea/CreaJnine expressed as mmol/L (SI units)
• RelaJve RaJo = Measures from different systems • RelRto – mulJple of the median • RlTm – Jme from actual and normal control
FracJon (proporJon) vs. RaJo a/a+b vs. a/b
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• Pt -‐ at a point in Jme
• 12H -‐ a twelve hour collecJon • 24H -‐ a twenty four hour collecJon
Timing*
*non-‐Pt Jmings are usually associated with RaJo Property
The interval of Jme over which the observaJon or measurement was made
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• Ser -‐ Serum • Bld -‐ Whole blood (RBC) • Ur-‐ Urine • BldA -‐ Arterial blood • Liver -‐ Liver • Flu – Body Fluid, unspecified
• Gast – Gastric fluid/contents • Food – Food or feedstuff • Tiss – Tissue • XXX – To be specified in
another part of the message
System The system (context) or specimen type upon which
the observaJon was made.
Super System Second subpart (^). When not included, “paJent” is the default. Used to indicated blood product unit (BPU), a bone
marrow donor, or a fetus.
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• Qn -‐ quanJtaJve • ConJnuous numeric (real, integer, raJo) • OpJonal operator (>, ≥, ≤, <)
• When assay detecJon limits are exceeded
• Ord -‐ ordinal • a ranked set of possible values (1+, 2+, 3+)
• Nom -‐ nominal • an unranked collecJon of possible values • a taxonomy (e.g list of bacteria)
• Nar -‐ narraJve • free text narraJve (e.g., visit note)
Scale
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Scale (Special) • OrdQn – Ordinal or QuanJtaJve
• Primarily used for anJmicrobial observaJons e.g. MIC reported as resistant, intermediate, suscepJble or as the mm diameter of the inhibiJon zone
• Use is discouraged
• MulJ – structured text “globs” • e.g. chromatography output • Use is discouraged
• Doc – Clinical documents • Set – Clinical aFachments (headers)
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Method • Methods only needed if interpretaJon affected
• Different normal ranges • Test SensiJvity
• Listed only at the generic level • AggluJnaJon • Immunoassay • Probe with target amplificaJon
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Mapping Terms to LOINC Things to Remember
• The thing ordered is not always the thing measured: • Blood Culture – live organism(s) idenJfied • VDRL – Treponema pallidum Ab • Urinalysis – lots of different things
• The quesJon (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl) • You are mapping the quesJon, not the answer!
• You must know the specifics of the component being tested for (what is this test actually measuring?)
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What is in LOINC? Content
• Term structures • SubmiFed units, Example UCUM units
• aiming toward preferred units sorJng • Synonyms • Answer lists for categorical variables (Some)
• Text descripJons – links to info sources about individual tests • Panel structures • Foreign language translaJons
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Regenstrief LOINC Mapping Assistant
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Purpose of Tutorial
• “Eliminate” need to read the User’s Manual • Become familiar with RELMA features • Provide some insight into mapping Jps/pi}alls • Help begin the mapping process for your insJtuJon
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• Manual and automated mapping assistant • Same free use as LOINC (see license)
• Comes with the LOINC files and indexes
• Now migrated to MS .NET environment.
• RELMA tools transform local words in local file • User creates file of local term/name and codes
• Assigns LOINC term to local test/baFery code
• Context sensiJve hierarchies for local use.
RELMA Functions
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New in This Version (Rel. 4.4)
• New LOINC status values • Ac7ve (current) -‐ LOINC term is in acJve use • Trial (new) -‐ LOINC term is under development, so it may change.
• Discouraged (new) -‐ LOINC retained for backward compaJbility; should not be used for new mappings.
• Deprecated (current) -‐ LOINC has been deprecated; replace all mappings to replacement term LOINC.
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New in This Version (Rel. 4.4) • "Part Search" -‐ new tab on mapping form
• lets you search for common LOINC Parts using Google-‐like query syntax (Lucene).
• Ability to select the type of LOINC details display from the right-‐click menu: • View Details – Simple • View Details – Comprehensive • View Details – Custom (When viewing Parts, selecJng any of these performs the idenJcal
"View Details" acJon for Parts.)
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New in This Version (Rel. 4.4) • "View Panel Children“ -‐ context menu
• displays children of a selected LOINC panel in a grid on a new form.
• all normal right-‐click acJons on the LOINCs in this grid are available.
• Custom Export • export all row
• only the selected rows.
• The mapping screen now lets you type in the local term file entry # so you can go to that term directly.
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New in This Version (Rel. 4.4) • LOINC and Part grid (flat) search results now preserve their sort order between searches when you use the Sort Grid right-‐click acJon. • For example, if you search LOINC for OPIATES, "Sort Grid" ascending by the Component, then search for MORPHINE, the search results for MORPHINE will be sorted by Component.
• The View All Working Set Terms screen now has an "Export Local Term File" buFon.
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New in This Version (Rel. 4.4) • Upon compleJon of a text or HL7 import, a summary will appear showing the results. A]er user confirmaJon of the results, the process to idenJfy unrecognizable concepts (baFery, test, or units) will start automaJcally, showing words that RELMA cannot use for synonyms.
• The Custom Display now gives you finer-‐grained control over what LOINC Part informaJon you see.
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New in This Version (Rel. 4.4)
• Search result grids/trees now display an example UCUM units column, located just before the example units column.
• Search result grids/trees now display the HL7 CDA document secJon column, located just a]er the Order/ObservaJon column.
• New shortcuts • Ctrl-‐E – Export • Ctrl-‐P – Print
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LOINC Web Site
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What’s available to download?
• RELMA -‐ mapping and browsing tool • HL7 message converter-‐ Makes a database suitable for mapping
• HL7 lint (finds bad messages) • LOINC database and spreadsheets • LOINC User guide; RELMA User Guide • Tools to assist language translaJons by part • Tools for building databases to map from HL7 messages
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RELMA Highlights • Browseable Hierarchies • Display search results in tree view • Enhanced “details” view of terms/parts
• References • DescripJons • Sample units
• Empirically-‐derived common test list
• Special features for panels/forms
• Enhanced export/copy-‐paste opJons
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For a given test: • User can select LOINC records containing:
• A set of words connected by ANDs or Ors • AddiJonal keyed in words • A parJcular category of test (e.g. microbiology) • Wild cards of ? and * • Selected classes, systems, components, • Any intersecJon of the above
Notes: RELMA assumes exact match on word unless user adds terminal “*” to indicate wild card.
This is being migrated to Lucene searching in future releases
RELMA Mapping Window Search Logic
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RELMA Logic
Not → #<word A>
Or → <word A> | <word B >
And → <word B> <word A>
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Additional RELMA Features
• User Specified Search Limits
• Selectable trees for: • Class • MulJaxial (component/system)
• System (specimen)
• Component
• Method
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Installing RELMA®
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Installation Steps • Make sure you have enough free disk space!
• 2Gb is recommended
• From CD -‐ Start – Run – D:\RELMA\Setup
• Specify installaJon directory • Life will be easier if you accept the default
• Two database files installed • RELMA.MDB – LOINC Terms Database • LMOF3.MDB – Local Master ObservaJon File
• Two sample files included • Run from Start – (All) Programs – Regenstrief – RELMA
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File Locations New for this version!
• Database and Ancillary Files • Windows XP = C:\Documents and SeMngs\All Users\Documents\RELMA\
• Windows Vista = C:\Users\Public\Documents\RELMA\ • Windows 7 = C:\Users\Public\Documents\RELMA\
• Sample files • Windows XP = C:\Documents and SeMngs\All Users\Documents\RELMA\Samples\
• Windows Vista = C:\Users\Public\Documents\RELMA\Samples\
• Windows 7 = C:\Users\Public\Documents\RELMA\Samples\
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Running RELMA® Version 4.4
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Copyright Screen
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Main Menu/Welcome Screen
Click File, Set Preferred Language
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Select Linguistic Variant(s)
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LOINC Terms with Spanish Linguistic Variant
Spanish!
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Setting User Preferences
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Select User Preferences From the File Menu
Set User Preferences
...or from Welcome Screen
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Set User Preference Dialog
Startup Screen Preference
New File Locations: Now stored in All Users/Documents
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User Map Screen Preferences
Click Map Screen Tab
Include/Exclude Battery Terms
Add comments on Mappings
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Importing Local Terms into RELMA
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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
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Constructing a Local Dataset Create extract of your test catalog with:
• BaFery/Panel Code • BaFery/Panel DescripJon or Name • *Local Code • *Test DescripJon or Name
• Include Method if Important • Units • Example Values • Laboratory SecJon
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Creating Delimited ASCII File • RELMA can’t parse free text
• Need to create separate fields
• Can use any of these delimiters • Tab, Semicolon, Comma, Space • Can define your own
• Fields can be in any order • Minimum required fields
• Local Code • Local DescripJon • Units (highly recommended)
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Entering New Local Terms into RELMA
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Manual Enter/Edit
View/Add/Edit Local Terms
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Edit Term Dialog
Edit\Add\Delete Terms Export (New function)
Print Preview List Text alignment option
Search Terms by Keyword
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Export Local Term File
Delimiters supported: Tab, comma, bar (|)
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Add Local Term
Click to Add to Current Working File
MICRO!
BUBPLAG!
BUBONIC PLAGUE – RRT PCR!
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Search Local Term File
Hematocrit
Enter Keyword from any Field
Return to Full List
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Print Preview Local Term File
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Steps to Import Local Terms
1. Click Import Local Terms BuFon from Main Menu a) File>Import Local Terms from Delimited File
2. Locate your local terms text file a) E.g. WinXP Sample files loaded into C:\Documents and
SeMngs\All Users\Shared Documents\RELMA 3. Name your Working Set
a) LMOF database can contain mulJple work sets 4. Define default secJon (OpJonal) 5. IdenJfy file delimiter 6. Assign fields to LMOF aFributes
a) Ignore fields you don’t need b) Combine fields if needed
7. Check “Case-‐sensiJve” if needed 8. Click Import.
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Local Term File Options
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Example Tab-Delimited File
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Importing Local Files
Select Import Local Terms from Delimited File
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Navigate to File Location
Select File and Click Open Sample eiles stored in RELMA Directory
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Open File in RELMA
Name your working set. RELMA allows multiple sets in
LMOF database
Select your delimiter
Import Button
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Open File in RELMA
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Fields Segregated
Assign LMOF Attribute
Choose eield name
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Ready to Import
Minimum assignments
Now you can click the Import button!
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Post-Processing of Local File New Feature!
• A]er import, RELMA Searches for terms (words) that it does not recognize
• Stored in a file for future reconciliaJon
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Change Local Term File
Select the Working Set
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Alternative Pragmatic Way • Use large set of HL7 messages • AutomaJcally make dataset of:
• OBR ID • OBR descripJon • OBX ID • OBX descripJon • Sample of results with
• Real values • Units • Abnormal flags • Normal ranges
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Generate Local term eile from HL7 messages
Select Import Terms from HL7 File
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Select File to Import
Select HL7 File
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Specify HL7 File Name and Sample Size
Name the Local Term File (working set)
Select which codes to store
Select the number of sample values
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HL7 Messages Data Statistics
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New Terms added to LMOF
New Battery Code
Click on “Edit Test to see Sample Data
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Sample Results for Observation New Test Code
Sample Values from Messages
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Lenny L’OINC says: “Load the Sample Files Into RELMA now!”
• Import the two sample files provided • Import_Sample_OBR.txt
• Contains baFery code and descripJon
• Import_Sample_OBX.txt • Contains test code and descripJon
• Create 2 working sets • Load your personal data set
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Cleaning your data
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Preparing your Data for Mapping
• Improve mapping success by: • Expanding abbreviaJons • Standardizing colloquial terms • Ignoring “administraJve” terms • Standardizing Jme references
• Can be done prior to imporJng • BeFer to use tools built into RELMA
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RELMA Cleaning Tools Use this tool to edit unknown terms
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Review Unknown Local Terms
May Re-Scan File for Unknown Terms
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Replace Local Terms
Assign LMOF Attribute Replacement Options
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RELMA Cleaning Tools Use this tool to make global substitutions
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Term Substitution
Save this global substitution for only this working set
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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.
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Searching for LOINC Terms
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Simplieied Search Only Tool
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Search Window
Enter Search Terms
Limit to Specieic Units Limit to Common
Tests
“Common Tests” relative frequency
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Context Menu
Right click to bring up context menu
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Mapping Local Terms
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Mapping Local Terms
• Select your Working Set to Map • File>Change Local term File
• Select “Map Local Terms to LOINC” from Welcome Screen
• Select the subset of terms to work with: • All • Mapped • Unmapped
• Set your Search Limits
• Set Search Limits BuFon
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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
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Mapping Screen
View or edit local term
Quick select button list
Custom Grid Coneiguration
New function! Enter local term number
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Coneigure Grid
Reorder grid elements
Select elements to display
Reset Default Coneiguration Visually resize elements
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Quick choice buttons
Viewing LOINC term detail
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View Local Term Details
Select level of detail to display
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New Feature – select detail level
New function! Select level of detail to display
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Standard Mapping Screen
Begin a search (or hit “enter”)
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Initial Mapping Results
Click to show words used in search
EEK! What’ll I do?!
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Initial Mapping Results
Use term checkbox
Number of LOINC terms containing
keyword
Battery terms included in search
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Revised Mapping Results
Number of matching
records found
Match units selected by default
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Re-revised Mapping Results
Number of matching
records found Match units unselected
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Standard Mapping Screen
Clear all input eields
CANINE DISTEMPER VIRUS IF
Enter keywords here
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Ad hoc term search
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Standard Mapping Screen
Navigate through the local terms
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Tabbed Access to Functions
Navigate to Functions from Mapping Page
Switch between Grid and Tree Views
New function! Parts Search
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Tree View
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Tree View • Results displayed hierarchically
• Defined by the mulJ-‐axial hierarchy in search restricJons (covered later)
• Map to a term in tree by clicking Map buFon or double clicking term • Only rows that have LOINC Codes
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Tree View
Cannot map to terms
representing LOINC parts
Can map to terms with LOINC Codes
Tree Navigation Buttons
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Assigning a LOINC Map
Highlight correct term
Click “Map” Button (or doubleclick)
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Adding Mapping Comments
If comments option is selected, prompt appears
Check with Frank in Chemistry
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Assigning a LOINC Map
LOINC Term Assigned
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View LOINC Term Details
View details for a specieic LOINC Term
Right clicking on a LOINC term brings up a Task Menu
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View Panel Children (New Function!)
Select View Panel Children from context menu
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Panel Children
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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
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Coneigure Export Options
Output Options
Include column headers Save Coneiguration
and/or Export
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Excel Export Format
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More on Searching Mapping Screen
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Using Wildcards in Searches • Substring search supported by default
• “Gluc” yields any terms with “gluc” in the component/analyte
• “*” replaces any number of characters • GLUC* • *COSE • GLU*SE
• “?” replaces a single character • GLUCOS? • ?LUCOSE • GLUC?SE
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Other Search Qualieiers
• “#” represents the “NOT” operator • #GLUCOSE – terms without the Word Glucose
• “|” is the “OR” operator • GLUCOSE | LACTOSE
• Can have mulJple “OR”s per box • Can Mix OR and NOT and Wildcards
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Search Qualieiers
Includes Glucuronidase, Glucosidase,
Glucosylceramidase, etc.
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Combining Search Terms
Reduced number of terms
Exclude Glucosidase
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Limiting Searches
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Setting Search Limits
• Narrows search to specific subset of LOINC terms • Reduces number of candidate terms
• Limits can be applied to all components
• Component aFribute can be further restricted by number of words
• Tree structure allows for hierarchical constraints
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General Search Constraints
• Controls features including: • Limit to LOINC terms compaJble with submiFed units • Forced match with any specimen contained in name • Methodless terms only • Limit to components/analytes with N or fewer words in their name
• Pop up search Jming staJsJcs a]er each search
• Use carefully or search may not be successful (Note parallel control switches at boFom of screen)
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Setting Search Limits
Click Hierarchy & Search Limits Tab
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Setting search limits
Can also set most of them by toggling buFons at the boFom of the screen
Toggle Buttons
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Search Constraints
Predeeined, general search constraints
Attribute trees
Local Unit Constraint: Now defaults to “ON”
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Terms Consistent with Units
Only terms consistent with mmol/L appear
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Setting Search Limits
Specimen constraints
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Terms Consistent with Specimen
CSF
Enter default Specimen
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Terms Consistent with Specimen
Only CSF Terms are returned
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Setting Search Limits
Methodless Terms Restriction
Override Methodless Terms Restriction
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Limit to Methodless Terms
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Limit to Methodless Terms
Only Methodless Terms Appear
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More on Methodless Terms • Some LOINC categories do not have methodless terms
• Checking methodless only will remove these from view on results grid
• Checking addiJonal box allows these to be seen
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Methodless Only Unchecked
All terms returned
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Methodless Only Checked
Only Methodless terms returned
Differ in one or more components
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Conditional Methodless
More terms returned
No methodless term; all shown
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Setting Search Limits
Limit to Lab Tests Only (No Clinical LOINC Terms)
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Setting Search Limits
Limit to lab tests that comprise 99.8% of INPC volume
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Setting Search Limits
Limit Number of Words in the Component Attribute
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Limit Number of Component Words
Without Limit Applied: 838 terms returned
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Limit Number of Component Words
With Limit Applied: 69 terms returned
Restriction appears on Toggle Bar
(cannot toggle off)
Component limited to 1 word
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Setting Search Limits
Include Deprecated or Discouraged LOINC Codes with Returned Terms
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Include Deprecated LOINC Terms
Deprecated LOINC Terms appear as Strikethrough Text with a “Do Not”
Symbol
-‐ You cannot map to deprecated LOINC terms -‐ You are warned before mapping to discouraged LOINC terms
Discouraged LOINC Terms appear as an inverted triangle
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Favor Property Restriction
Favor one type of property over others
All other components being equal MCnc
only will be displayed
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Order/Observation Restriction
Order or Observation preference
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LOINC Hierarchies – Class Tree
Three top-level branches
Tree Navigation Buttons
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Before Class Restriction
Large number of candidate terms
Most terms have class of “CHAL”
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Search Trees
chal
Restrict eligible tests to non-challenge
chemistry tests only
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Following Class Restriction
Only Non-Challenge Chemistry tests returned
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Improvements to Trees
Continued reorganization to provide a Specimen
hierarchy
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Improved Hierarchy for Component
Show the LOINC Codes associated with these
components
Click on details for more information about the
selection
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Details Screen LOINC Part
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Show Associated LOINCs
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Details Screen LOINC Term
Detailed Information on LOINC Parts
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Tree Export Tools
Coneigure Export Format
Export according to Coneiguration
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Tree Export Coneiguration
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RELMA - Tree Features
• All trees operate the same way • Shows terms spelled out • Can expand and collapse parts or all of tree. • Tree is string searchable • Search can be based on one or more branches of a tree with or without other criteria
• Use “Clear Most Limits” buFon on Mapping Screen to remove all tree selecJons
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New Feature! LOINC Part Search
• Same look as term search • Uses “Google-‐like” query language
• Extremely fast
• Include and exclude criteria • ParJal string matching (using wildcards)
• Demo • Campylobacter fetus, not DNA
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Navigating through the Mapping Process
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• Limit effort to one lab secJon at a Jme and focus experJse
• Chemistry and hematology will be easiest • Consider prioriJzing by frequency
LOINC Mapping Tactics
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Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.
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More LOINC Mapping Tactics • Try using method-‐less terms first
• Specific methods can be transmiFed in: • OBX–17 (v2.x), ObservaJon.methodCode (v3.0)
• Examine local units or real results to verify correct properJes • ProperJes are rarely disJnguishable in tests
• You don’t have to do it all at one siMng • Use the “Unmapped” funcJon to return where you le] off
• With every release -‐ Update previous mappings to idenJfy deprecated terms
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Common Mapping Issues
• Locally Defined Test Name Ambiguity • Reuse of local test code
• “Analyte-‐free” Local Test Names • Incongruent Value sets (Scale ambiguity) • Result vs. InterpretaJon • Available LOINC Terms too Specific • Available LOINC Terms too General • Panel vs. Discrete Test
• Common in Microbiology
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Using your Mapped Terms
• Print results of LOINC Mapping • Export to File
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Coneigure Export Format
Context Sensitive Export Coneiguration
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LMOF Export Coneiguration
Select Fields to Export
Select Export Format
Save Coneiguration and Export
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Print Mapped Terms from View/Add/Edit Menu
May highlight terms to be printed
Click Print button to Preview output
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Formatted Report Output
Click Print button to output formatted report
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Custom Export Coneiguration
Select the Fields you wish to Export
Select the Format you wish to Export
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Excel™ Export
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Intelligent Mapper
• Run in batch mode to find N-‐ closest terms • Can then use this output to do final mapping • Again units are VERY important • Can pick all limits available to regular mapping • With Radiology can use CPT to help • Intelligent Mapper Radiology References
• Vreeman DJ, McDonald CJ. A Comparison of Intelligent Mapper and Document Similarity Scores for Mapping Local Radiology Terms to LOINC. Proc AMIA Symp. 2006;809-‐813.
• Vreeman DJ and McDonald CJ. Automated Mapping of Local Radiology Terms to LOINC. Proc AMIA Symp. 2005;769-‐773.
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Picking the Intelligent Mapper
Begin by einding qualifying candidates based on local
eile attributes
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Intelligent Mapper Start Screen
Max search time per local term
May Apply Hierarchy Restrictions Prior to Run
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Intelligent Mapper - Mapping Screen
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Exporting Mapped Terms
Export Terms to Delimited File
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Export Terms Dialog
Check Fields you wish to export
Select Delimiter
Select Term Set
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Other RELMA® Features
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Panels, Forms and Survey Review
Review Panels, Forms and Surveys
Review Panels, Forms and Surveys
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Government Forms
Form Name
Component LOINC terms
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Laboratory panels
Expand category to see panels
Double-click panel name to see
components
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Expanded Panel Detail
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Expanded Clinical Panel
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Clinical Panels
Find where a term has been used
35089-2, 35090-0
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LOINC Term Panel Usage
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Other Survey Instruments
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HIPAA Attachments
View Various HIPAA Attachments
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HIPPA Attachment Tree
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Expanded Attachment Data
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Context Specieic Hierarchies • Allows local definiJon of LOINC code hierarchies
• Template data base is provided with RELMA • CONTEXT_SPECIFIC_HIERARCHY_TEMPLATE.mdb
• Does not support .accdb format
• Hierarchies can be displayed (only) in RELMA
• Codes and terms may come from mulJple code systems
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Access Context-Specieic Hierarchies
Select Context Specieic Hierarchies
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Select Directory
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Context Specieic Hierarchies
Locally deeined aggregation
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Can’t eind the term you want?
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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
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Proposing New LOINC Terms
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Proposing New Terms • Make sure the term is really needed
• Think of other names for the same concept • Avoid detailed methods or localizaJons • Is the disJncJon really important?
• Supply sufficient annotaJon to jusJfy the new term • Package inserts, sample reports (email to Regenstrief) • The more the beFer!
• Construct new terms within RELMA • File>Propose a LOINC
• Linked to the “trees” to allow browsing
• Can review and submit them to LOINC from within RELMA
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Propose new LOINC terms
Select Propose a LOINC
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Propose new LOINC terms
Required eields Navigate through proposed terms
Create new term, save current term
or Exit form
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Preview Proposed Terms
Review your new terms
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Preview Proposed Terms
All proposed terms fully editable
Choose whether to send or postpone
X
X
X
X
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Use Existing Terms as Template
Select your closest match
Click the Propose Term button
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Use Existing Terms as Template
All required components eilled in
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Using LOINC and SNOMED Together
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Where do LOINC and SNOMED Fit?
• LOINC represents the quesJon: • Is there any Botulism toxin in my specimen? (33708-‐9)
• Organisms idenJfied in specimen? (634-‐6)
• SNOMED represents the answer: • NegaJve (SCTID 260385009) • E. coli O157:H7 (SCTID 103429008)
Remember:
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Where do LOINC and SNOMED Fit?
• In an HL7 message, LOINC may be used: • In OBR-‐4 (Universal Service IdenJfier)
• In OBX-‐3 (ObservaJon IdenJfier
• SNOMED may be used: • In OBX-‐5 (where nominal values are needed)
• Almost anyplace else in an HL7 message where coded values are needed
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The code is from SNOMED
The code is from LOINC
OBX-5: Data A code for L.
monocytogenes
A code that identieies the data type in OBX-5 as a
coded element
OBX: With a Coded Value
OBX-3:A code that identieies the data in
OBX-5 (Listeria culture)
OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT
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HL7 2.5 Example (ER-7 format) MSH|^~\&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01|
LABGL1199510221838581| P| 2.3||| NE| NE
PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^ Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090
OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult ^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^
UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN
OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837
OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility Panel^ LN||| 199812300934||||||||Bacterial isolate| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN
OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate ^SCT|||||| F||| 199812300934|| CA20837
OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934|| CA20837
OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F||| 199812300934|| CA20837
First Order OBR (Culture and ID)
First Result (Culture and ID) First Result
(Culture and ID) Second Result(s)
OBXs
First Result Value (SNOMED)
First Result Description OBX (LOINC)
Second Order OBR (Susceptibility)
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Q and A Session
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Exercise Map your own data