2011 06 06 - loinc workshop and tutorial
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©2011 Regenstrief Institute and James Case
Using RELMA Or…In Search of the Missing LOINC
James T. Case MS, DVM, PhD Health Program Specialist, SNOMED CT
National Library of Medicine
Laboratory LOINC Meeting – June 2011
©2011 Regenstrief Institute and James Case
Acknowledgements • RELMA Development Team
• John Hook, Karen Ahmad, Mark Fisher, Craig Kelker
• Dan Vreeman • Clem McDonald • Kathy Mercer • The Lab LOINC CommiFee • Funding Support
• NLM, Regenstrief InsJtute, NCI, CDC
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
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)
©2011 Regenstrief Institute and James Case
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 standardized content (vocabularies) within the data structure
©2011 Regenstrief Institute and James Case
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
• Words are not enough • Codes – uniquely idenJfy terms • Vocabulary – specialized, precise terms that remove ambiguity
• Ontology – describes nature of enJJes and their relaJons • ClassificaJon – groups related terms
©2011 Regenstrief Institute and James Case
Potential Uses of Health Data are Constrained by Data Quality Factors • Data quality issues
• Different for client/paJent communicaJons vs. clinical decision support vs. epidemiological 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
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
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
LOINC Code = 5062-‐5 LOINC Code = 6321-‐4
What you see in the order list
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
LOINC® 101 Emphasis on Laboratory
LOINC
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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
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
• 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
©2011 Regenstrief Institute and James Case
• 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
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
• 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
©2011 Regenstrief Institute and James Case
• 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. (e.g. Serum^BPU)
©2011 Regenstrief Institute and James Case
• 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 in other contexts • MulJ – structured text “globs”
• e.g. chromatography output • Use is discouraged
• Doc – Clinical documents • Set – Clinical aFachments (headers)
©2011 Regenstrief Institute and James Case
Method • Methods only needed if interpretaJon affected
• Different normal ranges • Test SensiJvity/Specificity
• Generally listed only at the generic level • AggluJnaJon (limited subtypes) • Immunoassay • Probe with target amplificaJon
©2011 Regenstrief Institute and James Case
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?)
©2011 Regenstrief Institute and James Case
What is in LOINC? Content
• Term structures • SubmiFed units, Example UCUM units
• aiming toward preferred units sorJng • Synonyms • Answer lists (increasing number) • Text descripJons – links to info sources about individual tests • Panel structures • Foreign language translaJons
©2011 Regenstrief Institute and James Case
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 insight into mapping Jps/pi}alls • Help begin the mapping process for your insJtuJon
©2011 Regenstrief Institute and James Case
• LOINC files and indexes • Manual and automated mapping funcJons • 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/baFery code • “Common tests” subset to speed mapping • Context sensiJve hierarchies for local use. • Flexible “Google-‐like” search funcJons
RELMA Functions
©2011 Regenstrief Institute and James Case
New in This Version (Rel. 5.2) • Searches now have opJon to use “Auto Mapper” methods
• Select "Use Auto Mapper Search" checkbox. • Revised screen for reviewing Terms Mapped to Deprecated/
Discouraged LOINCs • The "Replacement LOINC" secJon gives the user access to all the replacement LOINC codes.
• The Comment field has been added. (RaJonal for replacement term)
• Added navigaJon buFons. • Lucene proximity and fuzzy searches are now supported on
the mapping and simple search screens. • Lucene score is displayed on the mapping and the simple
search screens.
©2011 Regenstrief Institute and James Case
• Column headers on screens are the same as Lucene field names. • Example: [ ExUnits:mg ] -‐"ExUnits" = example units.
• Double-‐clicking displays the details for selected row.
• LOINC Part quoJents (e.g. "CreaJne kinase.MB/CreaJne kinase.total“) displayed in the Part secJon of details screen.
New in This Version (Rel. 5.2)
©2011 Regenstrief Institute and James Case
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 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
• New guidance documents for mappers
32
©2011 Regenstrief Institute and James Case
RELMA Highlights • Browse-‐able hierarchies of LOINC parts • 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
©2011 Regenstrief Institute and James Case
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>:\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
©2011 Regenstrief Institute and James Case
File Locations • 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\
©2011 Regenstrief Institute and James Case
Running RELMA® Version 5.2
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Copyright Screen
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Main Menu/Welcome Screen
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Set Preferred Language
Click File, Set Preferred Language
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Select Linguistic Variant(s)
Selecting a translation may require indexes to be built
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LOINC Terms with Spanish Linguistic Variant
All 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: (See prior slide for location)
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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
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
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)
©2011 Regenstrief Institute and James Case
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 Terms
Print Preview List Text alignment option
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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
Enter Keyword from any Field Return to Full List
Calcium
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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.
©2011 Regenstrief Institute and James Case
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 jiles 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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Fields Segregated
Assign LMOF Attribute
Choose jield name
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Ready to Import
Minimum assignments
Now you can click the Import button!
©2011 Regenstrief Institute and James Case
Post-‐Processing of Local File
• A\er import, RELMA Searches for terms (words) that it does not recognize
• Stored in a file for future reconciliaJon
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Local Term File Options
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Change Local Term File
Select the Working Set
Current mapping status
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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
©2011 Regenstrief Institute and James Case
Generate Local term jile 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
Skip import of sample values
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 Term” 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
©2011 Regenstrief Institute and James Case
Cleaning your data
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
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.
©2011 Regenstrief Institute and James Case
Searching for LOINC Terms
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Simplijied Search Only Tool
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Search Window
Enter Search Terms Limit to
Specijic Units Limit to Common
Tests
Use Automapper logic
Help File
“Common Tests” rank Restrict to “Common Tests”
New! Lucene score indicates relevance of search result
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New RELMA Helpjile
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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>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 BuFon
©2011 Regenstrief Institute and James Case
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
Mapping Screen View or edit local term
Quick select button list
Custom Grid Conjiguration
Enter local term number
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Conjigure Grid
Reorder grid elements
Select elements to display
Reset Default Conjiguration 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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View Local Term Details Select text size
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Select detail display level
Select level of detail to display
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Standard Mapping Screen
Begin a search (or hit “enter”)
EEK! What’ll I do?!
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Standard Mapping Screen
Click to show words used in search
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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 jields
Enter keywords here
CANINE DISTEMPER VIRUS IF
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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
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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
©2011 Regenstrief Institute and James Case
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 specijic LOINC Term
Right clicking on a LOINC term brings up a Task Menu
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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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View Panel Children
Select View Panel Children from context menu
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Panel Children
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Conjigure Export Options
Output Options Include
column headers Save Conjiguration and/or Export
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Excel Export Format
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More on Searching Mapping Screen
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Basic Search Syntax Special Character(s)
Example Defini7on
“ “ Influenza “virus A” Linked terms must appear together
AND Morphine AND Opiates
Both terms must appear in the search result term
OR Influenza OR Parainfluenza
Either or both terms must appear in the search result term
NOT Influenza NOT equine Excludes terms with the word following the NOT. Cannot be used alone.
? Gluc?se (glucose,glucase)
SubsJtutes a single character in the string. Cannot be used as the first character; cannot be used in “phrases”
* Gluc*se (glucose, glucuronidase, etc.)
SubsJtute mulJple characters in the string. Cannot be used as the first character; cannot be used in “phrases”
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Search Qualijiers
Includes Glucuronidase, Glucosidase,
Glucosylceramidase, etc.
Detailed help available
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Combining Search Terms
Reduced number of terms
Exclude Glucosidase
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Advanced Search Syntax based on Google-‐like search syntax
Parameter Descrip7on
+ 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 mulJple terms in a single field
~ Fuzzy search (e.g. Hemo�ilus~)
“ “~ Proximity search for mulJple terms (e.g. “funcJon panel”~1)
{}, [] Upper and lower bounds; {} exclusive, [] inclusive
\ Special character escape
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Applying advanced search
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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
©2011 Regenstrief Institute and James Case
General Search Constraints • Controls features including:
• Limit to LOINC terms compaJble with submiFed 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 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
Predejined, general search constraints
Attribute trees
Local Unit Constraint: Default is “ON”
New! Type toggle boxes
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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
©2011 Regenstrief Institute and James Case
Limit to Methodless Terms
Only 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 from view on results grid
• Checking addiJonal box allows these to be seen
©2011 Regenstrief Institute and James Case
Methodless Only Unchecked
All terms returned
©2011 Regenstrief Institute and James Case
Methodless Only Checked
Only Methodless terms returned
Differ in one or more components
©2011 Regenstrief Institute and James Case
Conditional Methodless
More terms returned
No methodless term; all shown
©2011 Regenstrief Institute and James Case
Setting Search Limits
Limit to Lab Tests Only (No Clinical LOINC Terms)
©2011 Regenstrief Institute and James Case
Setting Search Limits
Limit to common lab tests
©2011 Regenstrief Institute and James Case
Setting Search Limits
Limit Number of Words in the Component Attribute
©2011 Regenstrief Institute and James Case
Limit Number of Component Words
Without Limit Applied: 792 terms returned
©2011 Regenstrief Institute and James Case
Limit Number of Component Words
With Limit Applied: 57 terms returned
Restriction appears on Toggle Bar
(cannot toggle off)
Component limited to 1 word
©2011 Regenstrief Institute and James Case
Setting Search Limits
Include Trial, Deprecated or Discouraged LOINC Codes with
Returned Terms
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
Favor Property Restriction
Favor one type of property over others
All other components being equal MCnc
only will be displayed
©2011 Regenstrief Institute and James Case
Order/Observation Restriction
Order or Observation preference
©2011 Regenstrief Institute and James Case
LOINC Hierarchies – Class Tree
Three top-‐level branches
Tree Navigation Buttons
©2011 Regenstrief Institute and James Case
Before Class Restriction
Large number of candidate terms
Most terms have class of “CHAL”
©2011 Regenstrief Institute and James Case
Search Trees
+Non +Chem
Restrict eligible tests to non-‐challenge
chemistry tests only
©2011 Regenstrief Institute and James Case
Following Class Restriction
Only Non-‐Challenge Chemistry tests
returned
©2011 Regenstrief Institute and James Case
Improvements to Trees
Continued reorganization to provide a Specimen
hierarchy
©2011 Regenstrief Institute and James Case
Improved Hierarchy for Component
Show the LOINC Codes associated with these
components
Click on details for more information about the
selection
©2011 Regenstrief Institute and James Case
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 LOINC Parts
©2011 Regenstrief Institute and James Case
Tree Export Tools
Conjigure Export Format
Export according to Conjiguration
©2011 Regenstrief Institute and James Case
Tree Export Conjiguration
©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 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
©2011 Regenstrief Institute and James Case
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 Ab
©2011 Regenstrief Institute and James Case
Navigating through the Mapping Process
©2011 Regenstrief Institute and James Case
• Limit effort to one lab secJon at a Jme and focus experJse
• Chemistry and hematology will be easiest • For manufactured assays, use package insert as source informaJon
• Sample results give clue to property and scale • Consider prioriJzing by frequency of use
LOINC Mapping Tactics
©2011 Regenstrief Institute and James Case
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
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 property and scale • ProperJes are rarely disJnguishable in test names
• 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
©2011 Regenstrief Institute and James Case
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. InterpretaJon • Available LOINC Terms too Specific/General • Panel vs. Discrete Test
• Common in Microbiology
©2011 Regenstrief Institute and James Case
Using your Mapped Terms
• Print results of LOINC Mapping • Export to File
©2011 Regenstrief Institute and James Case
Conjigure Export Format
Context Sensitive Export Conjiguration
©2011 Regenstrief Institute and James Case
LMOF Export Conjiguration
Select Fields to Export
Select Export Format
Save Conjiguration and Export
©2011 Regenstrief Institute and James Case
Print Mapped Terms from View/Add/Edit Menu
May highlight terms to be printed
Click Print button to Preview output
©2011 Regenstrief Institute and James Case
Formatted Report Output
Click Print button to output formatted report
©2011 Regenstrief Institute and James Case
Custom Export Conjiguration
Select the Fields you wish to Export
Select the Format you wish to Export
©2011 Regenstrief Institute and James Case
Excel™ Export
©2011 Regenstrief Institute and James Case
New and Improved 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
Picking the Lab Auto Mapper
©2011 Regenstrief Institute and James Case
Lab Auto Mapper Start Screen
Maximum number of terms to return
Can restrict search to common tests
©2011 Regenstrief Institute and James Case
Lab Auto Mapper Start Screen
Local terms used for mapping
Local test code
©2011 Regenstrief Institute and James Case
Lab Auto Mapper -‐ Mapping Screen
©2011 Regenstrief Institute and James Case
Exporting Mapped Terms
Export Terms to Delimited File
©2011 Regenstrief Institute and James Case
Export Terms Dialog
Check Fields you wish to export
Select Delimiter
Select Term Set
©2011 Regenstrief Institute and James Case
Other RELMA® Features
©2011 Regenstrief Institute and James Case
Panels, Forms and Survey Review
Review Panels, Forms and Surveys
Review Panels, Forms and Surveys
©2011 Regenstrief Institute and James Case
Government Forms
Form Name
Component LOINC terms
©2011 Regenstrief Institute and James Case
Laboratory Panels
Expand category to see panels
Double-‐click panel name to see
components
©2011 Regenstrief Institute and James Case
Expanded Panel Detail
©2011 Regenstrief Institute and James Case
Expanded Clinical Panel
©2011 Regenstrief Institute and James Case
Clinical Panels
Find where a term has been used
35089-2, 35090-0
©2011 Regenstrief Institute and James Case
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 Institute and James Case
HIPPA Attachment Tree
©2011 Regenstrief Institute and James Case
Expanded Attachment Data
©2011 Regenstrief Institute and James Case
Can’t jind 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 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
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 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 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
Propose new LOINC terms
Select Propose a new LOINC
©2011 Regenstrief Institute and James Case
Required jields in red
Navigate through proposed terms
Create new term, save current term
or Exit form
©2011 Regenstrief Institute and James Case
Preview Proposed Terms
Review your new terms
©2011 Regenstrief Institute and James Case
Review Proposed Terms
All proposed terms fully editable
Choose whether to send or postpone
X
X X
James T. Case DVM, PhD
NIH/NLM
James.case@mail.nih.gov
301-555-1314
301-555-1315
©2011 Regenstrief Institute and James Case
Submitting New Terms • Must supply name, organizaJon, phone and email of submiFer
• Must select at least one proposed term to send
• “Configure export” does not affect submission output
• Email resulJng file to Regenstrief
©2011 Regenstrief Institute and James Case
Use Existing Terms as Template
Select your closest match
Click the Propose Term button
©2011 Regenstrief Institute and James Case
Use Existing Terms as Template
All required components jilled in
©2011 Regenstrief Institute and James Case
Using LOINC and SNOMED Together
©2011 Regenstrief Institute and James Case
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:
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
The code is from SNOMED
The code is from LOINC
OBX-‐5: Data A code for L.
monocytogenes
A code that identijies the data type in OBX-‐5 as a
coded element
OBX: With a Coded Value
OBX-‐3:A code that identijies the data in
OBX-‐5 (Listeria culture)
OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT
©2011 Regenstrief Institute and James Case
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)
©2011 Regenstrief Institute and James Case
Q and A Session
©2011 Regenstrief Institute and James Case
Exercise Map your own data
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