2012 06 08 - Laboratory LOINC and RELMA Workshop

Using
RELMA
OrIn Search of the Missing LOINC
Laboratory LOINC Meeting June 2012
James T. Case MS, DVM, PhD, FHL7

Health Program Specialist, SNOMED CT National Library of Medicine
2012 Regenstrief Institute and James Case
Acknowledgements
LOINC Development Team
Clem McDonald, Dan Vreemen, Kathy Mercer, Jaci Phillips, Kelly Mallot, David Baorto
RELMA Development Team LOINC Commi7ee Supporters:
John Hook, Anandhi Sowmyan, James Dennis
NLM, Regenstrief (including the Indiana Center of Excellence in Public Health InformaKcs), Regenstrief FoundaKon
What will we cover today?

Overview of LOINC Reviewing new RELMA features! Installing RELMA SePng personal preferences Loading a Local ObservaKon File (LMOF) Searching for a LOINC Term Preparing LMOF for Mapping Review of Map Screen FuncKons SePng Search Limits Mapping Local Terms to LOINC Viewing LOINC Term Details Proposing/SubmiPng New LOINC Terms ExporKng/PrinKng Mapped Terms Mapping your own LMOF data
Why are we doing this?

Goals of Health Information Standards
Interoperability the ability to exchange informaKon between organizaKons Comparability the ability to ascertain the equivalence of data from dierent sources Data Quality the measurement of accessibility, completeness, accuracy and precision (and more)
Levels of Interoperability
Basic allows data to be exchanged between computer systems
Word processing documents, text messages
FuncConal describes the standard syntax (format) of the data

Document templates, forms, data structures Message standards
SemanCc requires use of standardized content (vocabularies) within the data structure
Comparability
Meaning of the data is consistent when shared among dierent parKes

Erysipelas Human skin disease; Streptococcus Grp A Erysipelas Animal SepKcemia/dermaKKs; Erysipelothrix rhusiopathiae Should work in the background
Common terminology required
Words are not enough

Codes uniquely idenKfy terms Vocabulary specialized, precise terms that remove ambiguity Ontology describes nature of enKKes and their relaKons ClassicaKon groups related terms
Potential Uses of Health Data are Constrained by Data Quality Factors

Data quality issues
Dierent for client/paKent communicaKons vs. clinical decision support vs. epidemiological analysis O\en constrained by external forces
e.g. criteria for diagnosis o\en diers from the criteria for reporKng
UnidirecKonal eect of data consolidaKon

Detailed General General Detailed

The Problem
In a_empKng to arrive at the truth, I have applied everywhere for informaKon, but in scarcely an instance have I been able to obtain hospital records t for any purpose of comparison. If they could be obtained, they would enable us to decide many other quesKons 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
Test comparisons
What you see in the order list
Lab A
Test Name: Lyme Disease Serology Measures: B. burgdorferi Ab IgG Method: ELISA Scale: quanCtaCve e.g.: Titer 1:40
Lab B
Test Name: Lyme Disease AnCbody Measures: B. burgdorferi Ab IgM Method: Immune blot Scale: qualitaCve e.g.: PosiCve
LOINC Code = 5062-5
LOINC Code = 6321-4
Why LOINC?
Within one laboratory, local jargon terms may be used which are usually well understood between colleagues, but would not be suciently widely known for communicaKon 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
101 LOINC
Emphasis on Laboratory LOINC
Anatomy of a LOINC Term

5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA LOINC Code Component Property Measured Timing System Scale Method 5193-8 HepaCCs B virus surface Ab ACnc Pt Ser Qn EIA
There are six major LOINC axes

What is NOT part of a LOINC Name?

The instrument used in tesKng Specic details about the specimen Priority (e.g. STAT) Where tesKng was done Who did the test Test interpretaKon 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 ObservaKon Object

Component/Analyte
The substance or enKty that is measured, evaluated, or observed
- Sodium
- Glucose - Brucella sp. organism - Inuenza A Virus anKgen - Cytomegalovirus Virus anKbody - Lipids.Total
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
Component/Analyte Structure
Analyte Name^ChallengeÂdjustments
Formal name of Analyte (e.g. Calcium)

Must specify any subanalyte
May have a subclass separated by .

e.g. Calcium.Free
e.g. Coronavirus Ag
Challenge - e.g, 1H post 100 gm Glucose PO

Adjustments/correcKons
E.g. Adjusted to pH 7.4
Two subparts separated by post <Kme delay> post <challenge type>
Property
the most dicult LOINC axis
The characterisKc or a_ribute of the analyte that is measured, evaluated, or observed

Major Categories Mass: ObservaKons reported with mass (milligrams, grams, etc.) in the numerator of their units of measure Substance: ObservaKons reported with moles or milliequivalents in the numerator of their units of measure CatalyCc acCvity: ObservaKons that report enzymaKc acKvity 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 2012 Regenstrief Institute and James Case
Property
the most dicult LOINC axis
Combine Major Categories with Subtypes for Full Property MCnc mass concentraKon (mass/unit vol) MCnt mass content (mass/unit mass) NCnc number concentraKon (number/unit vol) TmStp Kme CCnc catalyKc concentraKon (acKvity) Prid presence or idenKty Imp impression/interpretaKon Find subjecKve or objecKve observaKon Type Kind-of
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA 2012 Regenstrief Institute and James Case
Common Issues with LOINC Properties

FracKon (proporKon) vs. RaKo a/a+b vs. a/b FracKon = Part/whole

Number fracKon (NFr): % Eosinophils Substance fracKon (SFr): % HGB which is A2
RaKo = Measures mulKple analytes from the same system (specimen)

Mass concentraKon raKo - MCrto
e.g., BUN/Creat in urine specimen Urea/CreaKnine expressed as mmol/L (SI units)
Substance raKo-SCrto
RelaKve RaKo = Measures from dierent systems

RelRto Lithium.saliva/Lithium.serum RlTm Kme from actual and normal control MoM MulKple of the Median
Timing*
The interval of Kme over which the observaKon or measurement was made
Pt - at a point in Kme 12H - a twelve hour collecKon 24H - a twenty four hour collecKon
*non-Pt Kmings are usually associated with Rate Property

System
The system (context) or specimen type upon which the observaKon was made. Ser - Serum Bld - Whole blood (RBC) Ur- Urine BldA - Arterial blood Liver - Liver Flu Body Fluid, unspecied Gast Gastric uid/ contents Food Food or feedstu Tiss Tissue XXX To be specied in another part of the message
System Structure
System^Super System
Super System
PaKent 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:
Scale
Qn - QuanKtaKve

ConKnuous numeric (real, integer, raKo) OpKonal operator (>, , , <)
When assay detecKon limits are exceeded
Ord - Ordinal
a ranked set of possible values (1+, 2+, 3+) an unranked collecKon of possible values a taxonomy (e.g list of bacteria) free text narraKve (e.g., visit note)
Nom - Nominal

Nar - NarraKve
Scale (Special)
OrdQn Ordinal or QuanKtaKve
Primarily used for anKmicrobial observaKons e.g. MIC reported as resistant, intermediate, suscepKble or as the mm diameter of the inhibiKon zone Use is discouraged in other contexts e.g. chromatography output Use is discouraged
MulK structured text globs

Doc Clinical documents Set Clinical a_achments (headers)

Method
Methods only needed if interpretaKon aected

Dierent normal ranges Test SensiKvity/Specicity AggluKnaKon (limited subtypes) Immunoassay Probe with target amplicaKon
Generally listed only at the generic level

Hierarchies
LOINC Class Each LOINC axis MulK-axial
Component | System Separate download
Mapping Terms to LOINC

Things to Remember
The thing ordered is not always the thing measured:

Blood Culture live organism(s) idenKed VDRL Treponema pallidum Ab Urinalysis lots of dierent things
The quesKon (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl)
You are mapping the quesKon, not the answer!
You must know the specics of the component being tested for (what is this test actually measuring?)
What is in LOINC? Content

Term structures Submi_ed units, Example UCUM units
aiming toward preferred units sorKng
Synonyms Answer lists (increasing number) Text descripKons links to info sources about individual tests

Panel structures Foreign language translaKons
Regenstrief LOINC Mapping Assistant
RELMA
Purpose of Tutorial
Eliminate need to read the Users Manual Become familiar with RELMA features Provide some insight into mapping Kps/pi}alls Help begin the mapping process for your insKtuKon Hang with some really cool folks
RELMA Functions
LOINC les and indexes Manual and automated mapping funcKons Same free use as LOINC (see license) RELMA tools transform local words in local le
User creates le of local term/name and codes
Assigns LOINC term to local test/ba_ery code Common tests subset to speed mapping Context sensiKve hierarchies for local use. Flexible Google-like search funcKons
New in This Version (Rel. 5.7)

Search and mapping screen redesigned to be cleaner and more intuiKve. Answer lists may be searched and displayed via Answer List Search tab on the Mapping screen. The details screen displays:

LOINC Part ID and text values in the answer list Answer list ID LOINCs that use the answer list
Right-click on an Answer List Search result to access "Find LOINCs that use this answer list" acKon.

The grids on the "Edit Term in Local Term File" form now have context sensiKve (i.e. right-click) menus with persistent Custom Export sePngs. ImporKng HL7 or delimited les requires a new name for the local term le.
Prevent accidental import into wrong local term le.

Support for ltering results on SI version of the Top 2000+ "common" lab results.
h_p://loinc.org/usage
"Clear Limits" on the Mapping Screen now clears all limits including units.
Formerly labeled "Clear Most Limits
New warning: RELMA ignores units it does not recognize or if searching without a units restricKon.

RELMA automaKcally trims local term le names of leading or trailing spaces upon loading. New PDF output opKon for "Report Local Terms and Their LOINC Mappings...". PrinKng without using Custom Export prints only selected rows.
LOINC Web Site
Whats available to download?

RELMA - mapping and browsing tool

HL7 message converter- Makes a database suitable for mapping HL7 lint (nds bad messages)
LOINC database and spreadsheets LOINC User guide; RELMA User Guide Tools to assist language translaKons by part Tools for building databases to map from HL7 messages New guidance documents for mappers
37
RELMA Highlights
Browse-able hierarchies of LOINC parts Display search results in tree view Enhanced details view of terms/parts

References DescripKons Sample units
Empirically-derived common test list Empirically-derived common order list Special features for panels/forms Enhanced export/copy-paste opKons
Installing RELMA
Make sure you have enough free disk space!
Installation Steps
2Gb is recommended
From CD - Start Run <drive>:\RELMA\Setup Specify installaKon directory
Life will be easier if you accept the default RELMA.MDB LOINC Terms Database LMOF3.MDB Local Master ObservaKon File
Two database les installed

Two sample les included Run from Start (All) Programs Regenstrief RELMA
File Locations
Database and Ancillary Files

Windows XP = C:\Documents and SePngs\All Users \Documents\RELMA\ Windows Vista = C:\Users\Public\Documents\RELMA\ Windows 7 = C:\Users\Public\Documents\RELMA\ Windows XP = C:\Documents and SePngs\All Users \Documents\RELMA\Samples\ Windows Vista = C:\Users\Public\Documents\RELMA \Samples\ Windows 7 = C:\Users\Public\Documents\RELMA \Samples\
Sample les

Running RELMA
Version 5.7
Copyright Screen
Main Menu/Welcome Screen
Set Preferred Language

Click File, Set Preferred Language
Select Linguistic Variant(s)

Selecting a translation may require indexes to be built
LOINC Terms with Spanish Linguistic Variant
All Spanish!
Setting User Preferences
Set User Preferences

Select User Preferences From the File Menu ...or from Welcome Screen
Set User Preference Dialog
New File Locations: (See prior slide for location) Startup Screen Preference
User Map Screen Preferences

Click Map Screen Tab Auto create search terms Include/Exclude Battery Terms Add comments on Mappings
Importing Local Terms into RELMA
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 le 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
Constructing a Local Dataset

Create extract of your test catalog with:

Ba_ery/Panel Code Ba_ery/Panel DescripKon or Name *Local Code *Test DescripKon or Name
Units Example Values Laboratory SecKon
Include Method if Important
Creating Delimited ASCII File

RELMA cant parse free text
Need to create separate elds Tab, Semicolon, Comma, Space Can dene your own
Can use any of these delimiters

Fields can be in any order Minimum required elds

Local Code Local DescripKon Units (highly recommended)

Entering New Local Terms into RELMA
Manual Enter/Edit
View/Add/Edit Local Terms
Edit Term Dialog
Edit\Add\Delete Terms Export Terms
Text alignment option
Print Preview List
Export Local Term File
Delimiters supported: Tab, comma, bar (|)
Add Local Term

MICRO!
BUBPLAG! BUBONIC PLAGUE RRT PCR!
Click to Add to Current Working File
Search Local Term File

Calcium
Enter Keyword from any Return to Full List Field
Print Preview Local Term File

New! Only prints selected rows
Steps to Import Local Terms

1. Click Import Local Terms Bu_on from Main Menu
a) File>Import Local Terms from Delimited File
2. Locate your local terms text le
3. Name your Working Set (New! Now mandatory)

a) LMOF database can contain mulKple work sets
a) E.g. WinXP Sample les loaded into C:\Documents and SePngs\All Users\Shared Documents\RELMA
4. Dene default secKon (OpKonal) 5. IdenKfy le delimiter 6. Assign elds to LMOF a_ributes
a) b)
7. Check Case-sensiKve if needed 8. Click Import.

Ignore elds you dont need Combine elds if needed
Example Tab-Delimited File
Importing Local Files

Select Import Local Terms from Delimited File
Navigate to File Location

Select File iles stored ipen Sample j and Click O n RELMA Directory
Open File in RELMA

Name your working set. RELMA allows multiple sets in LMOF database
Select your delimiter
Import Button
Fields Segregated
Assign working set name
Assign LMOF Attribute
Working set import

LOINC Workshop OBR"
Ready to Import
Minimum assignments
Now you can click the Import button!
Post-Processing of Local File

A\er import, RELMA Searches for terms (words) that it does not recognize Stored in a le for future reconciliaKon
Local Term File Options
Change Local Term File

Select the Working Set Current mapping status
Alternative Pragmatic Way

Use large set of HL7 messages AutomaKcally make dataset of:

OBR ID OBR descripKon OBX ID OBX descripKon Sample of results with

Real values Units Abnormal ags Normal ranges

Generate Local term jile from HL7 messages

Select Import Terms from HL7 File
Select File to Import
Select HL7 File
Specify HL7 File Name and Sample Size
Skip import of sample values Name the Local Term File (working set) Select which codes to store Select the number of sample values
HL7 Messages Data Statistics
New Terms added to LMOF
Click on Edit Term to see Sample Data New Battery Code
Sample Results for Observation

New Test Code
Sample Values from Messages
Lenny LOINC says: Load the Sample Files Into RELMA now! Import the two sample les provided
Import_Sample_OBR.txt
Import_Sample_OBX.txt
Contains ba_ery code and descripKon Contains test code and descripKon
Create 2 working sets Load your personal data set

Cleaning your data
Preparing your Data for Mapping Improve mapping success by:

Expanding abbreviaKons Standardizing colloquial terms Ignoring administraKve terms Standardizing Kme references
Can be done prior to imporKng Be_er to use tools built into RELMA
RELMA Cleaning Tools

Use this tool to edit unknown terms
Review Unknown Local Terms

May Re-Scan File for Unknown Terms
Replace Local Terms
Assign LMOF Attribute Replacement Options
RELMA Cleaning Tools

Use this tool to make global substitutions
Term Substitution
Save this global substitution for only this working set

Lenny LOINC says: Begin to clean your data now!
Using the OBR or OBX sample les, take 15-20 minutes to clean up these unrecognized terms
You may use your own data if you wish.
Searching for LOINC Terms
Even more simplijied Search Only Tool
Search Window
Help File
Enter Search Terms
Limit to Specijic Units Restrict to Common Limits
Use different logic
Search Window
hematocrit bld qn
Common Tests selected
Common Tests rank
RELMA Search Helpjile
Context Menu
Right click to bring up context menu
Mapping Local Terms
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
Bu_on
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
Mapping Screen
View or edit local term
Enter local term number
Quick select button list
Custom Grid Conjiguration
Conjigure Grid
Select elements to display Reorder grid elements
Visually resize elements Reset Default Conjiguration
Quick choice buttons
Viewing LOINC term detail
View Local Term Details

Can scroll down a single formatted page Select level of detail to display
Can scroll through returned subset of terms
Change text size
View Local Term Details

Select text size
Select detail display level
Select level of detail to display
Standard Mapping Screen
Begin a search (or hit enter)
EEK! Whatll I do?!
Click to show words used in search

Initial Mapping Results
Use term checkbox
Number of LOINC terms containing keyword
Battery terms included in search
Revised Mapping Results
Number of matching records found
Re-revised Mapping Results
Match units selected
Number of matching records found
CANINE DISTEMPER VIRUS IF
Enter keywords here Clear all input jields
Ad hoc term search
Navigate through the local terms
Tabbed Access to Functions
Navigate to Functions from Mapping Page
Switch between Grid and Tree Views
Tree View
Tree View
Results displayed hierarchically
Dened by the mulK-axial hierarchy in search restricKons (covered later)
Map to a term in tree by clicking Map bu_on or double clicking term
Only to rows that have LOINC Codes
Tree View
Can map to terms with LOINC Codes Tree Navigation Buttons Cannot map to terms representing LOINC parts
Assigning a LOINC Map
Click Map Button Highlight correct term

(or doubleclick)
Adding Mapping Comments
If comments option is selected, prompt appears
Check with Frank in Chemistry
Assigning a LOINC Map
LOINC Term Assigned
View Panel Children
Select View Panel Children from context menu

Panel Children
Conjigure Export Options
Output Options Save Conjiguration and/or Export Include column headers
Excel Export Format
More on Searching Mapping Screen
Basic Search Syntax

Special Character(s) AND OR NOT ? Example Inuenza virus A Morphine AND Opiates Inuenza OR Parainuenza Inuenza NOT equine Gluc?se (glucose,glucase) Gluc*se (glucose, glucuronidase, etc.) DeniCon Linked terms must appear together Both terms must appear in the search result term Either or both terms must appear in the search result term Excludes terms with the word following the NOT. Cannot be used alone. SubsKtutes a single character in the string. Cannot be used as the rst character; cannot be used in phrases SubsKtute mulKple characters in the string. Cannot be used as the rst character; cannot be used in phrases
Search Qualijiers
Detailed help available Includes Glucuronidase, Glucosidase, Glucosylceramidase, etc.
Combining Search Terms
Exclude Glucosidase
Reduced number of terms
Advanced Search Syntax based on Google-like search syntax

Parameter + - ( ) Fieldname: Fieldname:() ~ ~ {}, [] \ DescripCon 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) Limit term search to the associated eld (e.g. Component: glucose) Group mulKple terms in a single eld Fuzzy search (e.g. Hemoilus~) Proximity search for mulKple terms (e.g. funcKon panel~1) Upper and lower bounds; {} exclusive, [] inclusive Special character escape
Applying advanced search
83 terms 33 terms 32 terms 14 terms

Limiting Searches
Setting Search Limits

Narrows search to specic subset of LOINC terms Reduces number of candidate terms Limits can be applied to all components Component a_ribute can be further restricted by number of words Tree structure allows for hierarchical constraints
General Search Constraints

Controls features including:

Limit to LOINC terms compaKble with submi_ed 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 Kming staKsKcs a\er each search (Note parallel control switches at bo_om of screen)
Use carefully or search may not be successful

Click Hierarchy & Search Limits Tab

Setting search limits

Can also set most of them by toggling bu_ons at the bo_om of the screen
Toggle Buttons
Search Constraints
Attribute trees
Limit to LOINC terms consistent with local units
Predejined, general search constraints Type toggle boxes
Terms Consistent with Units
Only terms consistent with mmol/L appear
Specimen constraints
Terms Consistent with Specimen
CSF
Enter default Specimen
Terms Consistent with Specimen
Only CSF Terms are returned

Exclude laterality
Exclude laterality
Laterality terms
Restrict to common orders
Restriction to common orders
Common orders rank
Large number of candidates
Methodless Terms Restriction
Override Methodless Terms Restriction
Limit to Methodless Terms
Both method and method-less terms

Limit to Methodless Terms
Only Methodless Terms Appear

More on Methodless Terms

Some LOINC categories do not have methodless terms Checking methodless only will remove these from view on results grid Checking addiKonal box allows these to be seen
Methodless Only Unchecked
All terms returned
Methodless Only Checked

Only Methodless terms returned
Differ in one or more components
Conditional Methodless
More terms returned
No method-less term; all shown
Limit Number of Words in the Component Attribute
Limit Number of Component Words
Without Limit Applied: 855 terms returned
Limit Number of Component Words

Restriction appears on Toggle Bar (cannot toggle off) Component limited to 1 word With Limit Applied: 68 terms returned
Include Trial, Deprecated or Discouraged LOINC Codes with Returned Terms

Include Deprecated LOINC Terms

-You cannot map to deprecated LOINC terms - The map button is grayed out if one of these terms is selected
Discouraged LOINC Terms appear as an inverted triangle Deprecated LOINC Terms appear as Strikethrough Text with a Do Not Symbol 2012 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
Order/Observation Restriction
Order or Observation preference
LOINC Hierarchies Class Tree
Three top-level branches Tree Navigation Buttons
Before Class Restriction

Many terms have class of CHAL
Large number of candidate terms

Search Trees
Restrict eligible tests to non-challenge chemistry tests only
Following Class Restriction
Only Non-Challenge Chemistry tests returned
System Hierarchy
Component Hierarchy
Click on details for more information about the selection
Show the LOINC Codes associated with these components
Details Screen LOINC Part
Show Associated LOINCs
LOINC Term Details Screen
Detailed Information on LOINC Parts
Tree Export Tools

Export according to Conjiguration
Conjigure Export Format
Tree Export Conjiguration
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 bu_on on Mapping Screen to remove all tree selecKons
LOINC Part Search

Same look as term search Uses Google-like query language

Extremely fast Include and exclude criteria ParKal string matching (using wildcards) Campylobacter fetus, not Ab
Demo
LOINC Answer List Search
Nominal LOINC terms are now required to be submi_ed with answer lists. Finding answer lists and the use of them can be done with Answer List Search tab
Answer List Search
Answer Lists associated with LOINC term
Navigating through the Mapping Process
LOINC Mapping Tactics

Limit eort to one lab secKon at a Kme and focus experKse Chemistry and hematology will be easiest For manufactured assays, use package insert as source informaKon Sample results give clue to property and scale Consider prioriKzing by frequency of use
Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.
More LOINC Mapping Tactics

Try using method-less terms rst
Specic methods can be transmi_ed in:
OBX17 (v2.x), ObservaKon.methodCode (v3.0)
Examine local units or real results to verify correct property and scale
ProperKes are rarely disKnguishable in test names Use the Unmapped funcKon to return where you le\ o
You dont have to do it all at one siPng
With every release - Update previous mappings to idenKfy deprecated terms

Common Mapping Issues

Locally Dened Test Name Ambiguity
Reuse of local test code (Miscellaneous serology, PCR)
Analyte-free Local Test Names
Incongruent Value sets (Scale ambiguity) Result vs. InterpretaKon Available LOINC Terms too Specic/General Panel vs. Discrete Test
Common in Microbiology
Using your Mapped Terms

Print results of LOINC Mapping Export to File
Conjigure Export Format
Context Sensitive Export Conjiguration
LMOF Export Conjiguration
Select Export Format
Select Fields to Export Save Conjiguration and Export
Print Mapped Terms from View/Add/Edit Menu
May highlight terms to be printed
Click Print button to Preview output
Formatted Report Output
Click Print button to output formatted report
Excel Export
Lab Auto Mapper

Run in batch mode to nd N- closest terms Can then use this output to do nal mapping Again units are VERY important Can pick all limits available to regular mapping
Picking the Lab Auto Mapper
Lab Auto Mapper Start Screen
Can restrict search to common tests
Maximum number of terms to return
Lab Auto Mapper Start Screen
Local test code
Terms used for mapping

Lab Auto Mapper - Mapping Screen
Exporting Mapped Terms
Export Terms to Delimited File
Export Terms Dialog

Select Term Set
Select Delimiter
Check Fields you wish to export

Other RELMA
Features
Panels, Forms and Survey Review

Review Panels, Forms and Surveys
Review Panels, Forms and Surveys
Government Forms
Component LOINC terms
Form Name
Laboratory Panels
Expand category to see panels
Double-click panel test to see components
Expanded Panel Detail
Expanded Clinical Panel
Clinical Panels
35089-2, 35090-0
Find where a term has been used
LOINC Term Panel Usage
Other Survey Instruments
HIPAA Attachments
View Various HIPAA Attachments
HIPPA Attachment Tree
Expanded Attachment Data
Cant jind the term you want?
Search Hints and Tips

Keywords with zero frequency are ignored
May need to rephrase use synonym Too many keywords in search uncheck some Limits applied that dont make sense
Some causes for no returned terms

E.g. Method-less tests plus Method tree set to EIA Local units not in RELMA
Did not nd and revise words not in RELMA
Units are GREAT discriminators You may have tests that need to be added to LOINC
Proposing New LOINC Terms
Proposing New Terms

Make sure the term is really needed

Think of other names for the same concept Avoid detailed methods or localizaKons Is the disKncKon really important? Package inserts, sample reports (email to Regenstrief) The more the be_er!
File>Propose a new LOINC
Supply sucient annotaKon to jusKfy the new term

Construct new terms within RELMA
Linked to the trees to allow browsing
Can review and submit them to LOINC from within RELMA

Propose new LOINC terms
Select Propose a new LOINC
Advanced/Simple toggle Required jields in red
Navigate through proposed terms
Create new term, save current term or Exit form
Preview Proposed Terms
Review your new terms
Review Proposed Terms

James T. Case DVM, PhD NIH/NLM 301-555-1314 301-555-1315 James.case@mail.nih.gov
X X X
Choose whether to send or postpone All proposed terms fully editable
Submitting New Terms

Must supply name, organizaKon, phone and email of submi_er Must select at least one proposed term to send Congure export does not aect submission output Email resulKng le to Regenstrief
Use Existing Terms as Template

Click the Propose Term button
Select your closest match
Use Existing Terms as Template
All required components jilled in
Using LOINC and SNOMED Together
Where do LOINC and SNOMED Fit? Remember:

LOINC represents the quesKon:

Is there any Botulism toxin in my specimen? (33708-9) Organisms idenKed in specimen? (634-6) NegaKve (SCTID 260385009) E. coli O157:H7 (SCTID 103429008)
SNOMED represents the answer:

Where do LOINC and SNOMED Fit?

In an HL7 message, LOINC may be used:

In OBR-4 (Universal Service IdenKer) In OBX-3 (ObservaKon IdenKer
SNOMED may be used:

In OBX-5 (where nominal values are needed) Almost anyplace else in an HL7 message where coded values are needed
OBX: With a Coded Value

A code that identijies the data type in OBX-5 as a coded element The code is from LOINC The code is from SNOMED
OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT
OBX-3:A code that

identijies the data in OBX-5 (Listeria culture)
OBX-5: Data A c for L. ode monocytogenes
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^^ First Order OBR Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090alue (Culture and ID) First Result V (SNOMED) OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult ^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^ Second Order OBR UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN (Susceptibility) 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 First Result Description Second Result(s) First LN||| Panelêsult 199812300934||||||||Bacterial isolate| IN2973^ Schadow^ OBX (LOINC) (Culture and ID) OBXs Gunther^^^^ MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006Întermediate ^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
Q and A Session
Exercise Map your own data

2012 06 08 - Laboratory LOINC and RELMA Workshop

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2012 06 08 - Laboratory LOINC and RELMA Workshop

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Using

James T. Case MS, DVM, PhD, FHL7

2012 Regenstrief Institute and James Case

RELMA Development Team LOINC Commi7ee Supporters:

John Hook, Anandhi Sowmyan, James Dennis

What will we cover today?

2012 Regenstrief Institute and James Case

Why are we doing this?

2012 Regenstrief Institute and James Case

Word processing documents, text messages

FuncConal describes the standard syntax (format) of the data

Document templates, forms, data structures Message standards

Common terminology required

Words are not enough

Potential Uses of Health Data are Constrained by Data Quality Factors

UnidirecKonal eect of data consolidaKon

Detailed General General Detailed

2012 Regenstrief Institute and James Case

LOINC Code = 5062-5

LOINC Code = 6321-4

2012 Regenstrief Institute and James Case

2012 Regenstrief Institute and James Case

Anatomy of a LOINC Term

There are six major LOINC axes

What is NOT part of a LOINC Name?

The OBR or OBX segment An HL7 Version 3 ObservaKon Object

Must specify any subanalyte

May have a subclass separated by .

Challenge - e.g, 1H post 100 gm Glucose PO

Two subparts separated by post <Kme delay> post <challenge type>

2012 Regenstrief Institute and James Case

The characterisKc or a_ribute of the analyte that is measured, evaluated, or observed

Common Issues with LOINC Properties

Number fracKon (NFr): % Eosinophils Substance fracKon (SFr): % HGB which is A2

RaKo = Measures mulKple analytes from the same system (specimen)

Mass concentraKon raKo - MCrto

e.g., BUN/Creat in urine specimen Urea/CreaKnine expressed as mmol/L (SI units)

RelaKve RaKo = Measures from dierent systems

*non-Pt Kmings are usually associated with Rate Property

2012 Regenstrief Institute and James Case

blood product unit bone marrow donor fetus

818-5:A Ag:ACnc:Pt:RBC^BPU:Ord: 54417-1:ABO+Rh group:Type:Pt:Bld^fetus:Nom:

2012 Regenstrief Institute and James Case

ConKnuous numeric (real, integer, raKo) OpKonal operator (>, , , <)

When assay detecKon limits are exceeded

MulK structured text globs

Doc Clinical documents Set Clinical a_achments (headers)

Generally listed only at the generic level

2012 Regenstrief Institute and James Case

2012 Regenstrief Institute and James Case

Mapping Terms to LOINC

You are mapping the quesKon, not the answer!

2012 Regenstrief Institute and James Case

What is in LOINC? Content

aiming toward preferred units sorKng

Panel structures Foreign language translaKons

2012 Regenstrief Institute and James Case

Regenstrief LOINC Mapping Assistant

2012 Regenstrief Institute and James Case

2012 Regenstrief Institute and James Case

User creates le of local term/name and codes

New in This Version (Rel. 5.7)

2012 Regenstrief Institute and James Case

New in This Version (Rel. 5.7)