2015 06 03 - LOINC Workshop
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Transcript of 2015 06 03 - LOINC Workshop
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2014 Regenstrief Institute and James Case
Using RELMA OrIn Search of the Missing LOINC
James T. Case MS, DVM, PhD, FHL7, FACMI Health Program Specialist, SNOMED CT National Library of Medicine Laboratory LOINC Meeting June 2015
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2014 Regenstrief Institute and James Case
The views and opinions expressed do not necessarily state or reect those of the U.S. Government, and they may not be used for adver?sing or product endorsement purposes.
Disclaimer
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2014 Regenstrief Institute and James Case
Acknowledgements LOINC Development Team
Clem McDonald, Dan Vreeman, Jami Deckard, David Baorto, Katy Holck, Swapna Abhyankar, Theresa Pritchard, Rachel Fuhr, Sara Armson
RELMA Development Team John Hook, Anandhi Sowmyan, James Dennis
LOINC CommiLee Supporters
NLM, Regenstrief InsJtute, Regenstrief FoundaJon, APTA, RSNA, the LOINC Premium Members and Donors
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2014 Regenstrief Institute and James Case
What will we cover today? Overview of LOINC Reviewing new RELMA features! Installing RELMA SeNng personal preferences Loading a Local ObservaJon File (LMOF) Searching for a LOINC Term Preparing LMOF for Mapping Review of Map Screen FuncJons SeNng Search Limits Mapping Local Terms to LOINC Viewing LOINC Term Details Proposing/SubmiNng New LOINC Terms ExporJng/PrinJng Mapped Terms Mapping your own LMOF data
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2014 Regenstrief Institute and James Case
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2014 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 dierent 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
Func?onal describes the standard syntax (format) of the data Document templates, forms, data structures Message standards
Seman?c requires use of standardized content (vocabularies) within the data structure
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Comparability Meaning of the data is consistent when shared among dierent 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 ClassicaJon groups related terms by category
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Potential Uses of Health Data are Constrained by Data Quality Factors Data quality issues
Dierent for client/paJent communicaJons 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 reporJng
UnidirecJonal eect of data consolidaJon Detailed General General Detailed
This is a problem even when standard
terminologies are used
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The Problem In a_empJng to arrive at the truth, I have applied everywhere for informaJon, 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 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: quan?ta?ve e.g.: Titer 1:40
Lab B Test Name: Lyme Disease An?body Measures: B. burgdorferi Ab IgM Method: Immune blot Scale: qualita?ve e.g.: Posi?ve
LOINC Code = 5062-5 LOINC Code = 6321-4
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 suciently 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 Emphasis on Laboratory
LOINC
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5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
5193-8 LOINC Code
Hepa??s 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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NOT part of a LOINC Name Reason for the test (why it was ordered or the disease it
diagnoses)
TesJng instrument Specic details about the specimen Priority (e.g. STAT) Where tesJng was done Who did the test Test interpretaJon Pricing or cost Anything not part of naming the test Things from other elds in an HL7 arJfact
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The substance or enJty that is measured, evaluated, or observed
Component/Analyte
- Sodium - Glucose - Brucella sp. organism - Inuenza 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 Structure Analyte Name^Challenge^Adjustments
Formal analyte name Specify subanalytes May have subclasses
Challenge Two parts separated by post
Adjustments
Calcium Coronavirus Ag Calcium.ionized
1H post 100 g Glucose PO
post
Adjusted to pH 7.4
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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
Cataly?c ac?vity: ObservaJons that report enzymaJc acJvity Arbitrary: Results that report arbitrary units in the numerator of their units
of measure (slowly being reJred) Threshold: Results that represent the relaJon between a value and some
established limit or cut-o Number: Counts
Property
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
The characterisJc or a_ribute of the analyte that is measured, evaluated, or observed
the most dicult LOINC axis
Major Categories
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MCnc mass concentraJon (mass/unit vol; e.g. mg/dL) MCnt mass content (mass/unit mass; e.g. mg/Kg) NCnc number concentraJon (number/unit vol; e.g. num/mL) TmStp Jme CCnc catalyJc concentraJon (acJvity; e.g. kat/L) 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 dicult LOINC axis
Combine Major Categories with Subtypes for Full Property
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Common Property Issues
Frac?on = Part/Whole NFr: % Eosinophils / leukocytes SFr: % HGB which is A2
Ra?o = mulJple analytes from same system
MCrto: BUN/CreaJnine in serum Rela?ve Ra?o = measures from dierent system
RelRto: Albumin.pericard d/Albumin.SerPl
Fraction versus Ratio
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Important property changes ACNC was always a placeholder
For P/N results, changed to Threshold AddiJonal migraJons occurring gradually LOINC IDs being retained
Flavors of Threshold Property ThrSCnc Threshold Substance ConcentraJon ThrMCnc Threshold Mass ConcentraJon ThrACnc Threshold Arbitrary ConcentraJon
PR vs PRID Presence or absence of an analyte now represented as PR (presence)
For nominal results, property is sJll PRID
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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 Rate Property
The interval of Jme over which the observaJon or measurement was made
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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System The system (context) or specimen type upon
which the observation was made.
Ser Ser/Plas Bld Ur Flu Tiss XXX
serum serum or plasma whole blood urine body fluid tissue specified elsewhere
photo via AlishaV
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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System Structure
Super System PaJent is the default Used to indicate
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:
System^Super System
photo via Xurble
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Scale Qn Ord Nom Nar
Quantitative continuous numeric can have operators ()
Ordinal Ranked set (1+, 2+, 3+)
Nominal unranked collection Taxonomy (e.g. bacteria)
Narrative
photo via puuikibeach
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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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 a_achments (headers)
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Method Only needed if interpretaJon aected
Dierent normal ranges Test sensiJvity/specicity
Generally listed at the generic level AggluJnaJon Enzyme Immunoassay Probe with target amplicaJon
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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Hierarchies LOINC Class
one per term arbitrarily assigned
One for each LOINC axis MulJ-axial
Component | System Separate download
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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) idenJed VDRL Treponema pallidum Ab Urinalysis lots of dierent things
You must know the specics of the component being tested for (what actually being measured?)
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!
Need to get the observaJon/result boundary correct. Sample values help substanJally
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What is in LOINC? Content
Term structures Submi_ed 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
And much more
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RELMA Regenstrief LOINC Mapping Assistant
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Download of latest version
The latest version of the installaJon le may be downloaded from:
h_ps://iu.box.com/relma69
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Purpose of Tutorial Eliminate need to read the Users Manual Become familiar with RELMA features Provide some insight into mapping Jps/piyalls Help begin the mapping process for your insJtuJon
Hang with some really cool folks
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LOINC les and indexes Manual and automated mapping funcJons 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 sensiJve hierarchies for local use. Flexible Google-like search funcJons
RELMA Functions
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New in This Version (Rel. 6.9) End of support for Windows XP.
Microso\ ends support or XP in April 2014. No longer tesJng RELMA on Windows XP. The December 2015 release (version 6.12) of RELMA will not run on Windows XP.
Proxy support. Congure it in the Windows Internet OpJons applet. (see RELMA manual for details)
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New in This Version (Rel. 6.9) New search restricJons added (See "Advanced Search Syntax" secJon of the user guide ): "PanelType
Allows limitaJon of search results to a panel type categories. "LForms"
True/false restricJon - indicates if LOINC code can be viewed in LForms data widget tool.
"AssociatedObservaJons Contains one or more LOINC codes that point to an addiJonal list of terms associated with an observaJon.
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New in This Version (Rel. 6.9) "Export full panel structure to Excel" opJon available on Search tab grid and the grid on the Mapping tab.
New column added to search grids - "LForms". A hyperlink that opens your default browser to the specied URL. Not all rows will have this eld populated.
"Panels, Forms & Surveys" screen has been completely restructured.
"Associated observaJon" terms displayed on comprehensive detail pages when available.
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LOINC Web Site
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Whats available to download? RELMA - mapping and browsing tool
HL7 message converter- Makes a database suitable for mapping
LOINC database and spreadsheets Accessory les (panels, forms, top 2000, etc.) LOINC User guide; RELMA User Guide Tools to assist language translaJons by part Tools for building databases to map from HL7 messages
Guidance documents for mappers
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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 Empirically-derived common order list Special features for panels/forms Enhanced export/copy-paste opJons
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Installing RELMA
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Installation Steps Requires Windows (or VM on a Mac) Make sure you have enough free disk space!
2Gb is recommended
From CD - Start Run :\RELMA\Setup Specify installaJon directory
Life will be easier if you accept the default
Two database les installed RELMA.MDB LOINC Terms Database LMOF3.MDB Local Master ObservaJon File
Two sample les included Run from Start (All) Programs Regenstrief RELMA
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File Locations Database and Ancillary Files
Windows Vista = C:\Users\Public\Documents\RELMA\ Windows 7, 8 = C:\Users\Public\Public Documents\RELMA\
Sample les Windows Vista = C:\Users\Public\Documents\RELMA\Samples\ Windows 7, 8 = C:\Users\Public\Public Documents\RELMA\Samples\
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Running RELMA Version 6.9
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Copyright Screen
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Join the LOINC Community
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LOINC crowdsourcing
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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
File Locations: (See prior slide for location)
Local Term Backup Tab
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User Map Screen Preferences Click Map Screen Tab
Include/Exclude Battery Terms
Add comments on Mappings
Auto create search terms
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User Detail Pages Preferences
Download detail pages from LOINC.org
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Request Submission Preference
Preferred method of request submission
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Local Backup Preferences
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Importing Local Terms into RELMA
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5 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)
Import Excel le 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:
Ba_ery/Panel Code Ba_ery/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 cant parse free text
Need to create separate elds Can use any of these delimiters
Tab, Semicolon, Comma, Space Can dene your own
Fields can be in any order Minimum required elds
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 Terms
Print Preview List Text alignment option
User assigned tags
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Export Local Term File
Delimiters supported: Tab, comma, semicolon, bar (|)
Export to Microsoft Excel or Text File
Export assigned tags
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Add Local Term
Click to Add to Current Working File
MICRO
BUBPLAGBUBONIC PLAGUE RRT PCR
Add tags
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Search Local Term File
Enter Keyword from any Field
Calcium
Return to Full List
Tags panel only appears if tags have been assigned
Open or close tag list
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Using tags to gilter local terms
Print preview local term gile
Congigure output prior to viewing and printing
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Print Preview Local Term File
Only prints selected rows
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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 (Mandatory)
a) LMOF database can contain mulJple work sets 4. Dene default secJon (OpJonal) 5. IdenJfy le delimiter 6. Assign elds to LMOF a_ributes
a) Ignore elds you dont need b) Combine elds if needed
7. Check Case-sensiJve if needed 8. Click Import.
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Example Tab-Delimited File
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Importing Local Files
Select Import Local Terms from Delimited File or Excel Spreadsheet
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Navigate to File Location Select File and Click Open Sample giles 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
Assign working set name
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Working set import LOINC Workshop OBR
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Ready to Import
Minimum assignments
Now you can click the Import button!
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Import tags
You can include tags in your import le that allow you to categorize your local terms
Fields in import funcJon allow assignment of Tag with
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Local term gile with added tags
Tag terms
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Assign tag values
Tag with gield assignment
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Tagged local terms
Imported tags
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Post-Processing of Local File
A\er import, RELMA Searches for terms (words) that it does not recognize
Stored in a le for future reconciliaJon
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Importing Excel gile
Excel giles now appear along with text giles
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Excel format for import
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Local Term File Options
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Change Local Term File
Select the Working Set
Current mapping status
Can delete local term set; not the active one
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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 ags Normal ranges
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Generate Local term gile 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 LOINC says: Load the Sample Files Into RELMA now!
Import the two sample les provided Import_Sample_OBR.txt
Contains ba_ery code and descripJon
Sample_HL7.HL7 Contains test code and descripJon and sample values
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 Be_er to use tools built into RELMA
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RELMA Cleaning Tools Use this tool to edit unknown terms
Only available if no language variant selected
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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 LOINC says: Begin to clean your
data now!
Using the OBR sample le or your own data, take 15-20 minutes to clean up these unrecognized terms
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Searching for LOINC Terms
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Comprehensive Search Only Tool
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Search Window
Enter Search Terms
Limit to Specigic Units
Use different logic
Help File
Restrict Limits
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Search Window
Common Tests selected Common Tests rank
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RELMA Search Helpgile
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Context Menu
Right click to bring up context menu
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Changed search function Max words
Large number of results
Keyword ComponentWordCount restricts word count Restricting to Common
labs regines further
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Search function - Answerlist
Large number of results
Restricting to terms that have answer lists
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Answerlist details
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New advanced search syntax Paneltype
Classies LOINC panel term in categories
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New advanced search syntax LForms
This true/false eld indicates whether or not the LOINC term is available for viewing in the LForms data widget tool.
Restricting to terms that have answer lists
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Lforms widget demo
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New advanced search syntax AssociatedObservations
AddiJonal terms that are related to a order term.
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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 Bu_on
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Standard Mapping Window Features
Customizable grid View details of LOINC term New! Add searchable tags to local 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 Congiguration
Enter local term number
User assigned tags
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Congigure Grid
Reorder grid elements
Select elements to display
Reset Default Congiguration 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
Can scroll through returned subset of
terms
Change text size
Can scroll down a single formatted page
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Details Text Size 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! Whatll 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
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Re-revised Mapping Results
Number of matching
records found Match units selected
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Standard Mapping Screen
Clear all input gields
Enter keywords here
CANINE DISTEMPER VIRUS IF
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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
Dened by the mulJ-axial hierarchy in search restricJons (covered later)
Map to a term in tree by clicking Map bu_on or double clicking term Only to 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 Panel Children
Select View Panel Children from context menu
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Panel Children
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Congigure Export Options
Output Options Include
column headers Save Congiguration and/or Export
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Excel Export Format
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Linked answer lists
Adds answer list IDs to the answer tab of a panel export
Allows linkage using the AnswerlistID with the LOINC codes and the answer to see which answers go with a specic LOINC
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2014 Regenstrief Institute and James Case
Search for a panel
Search for panel or LOINC code
Find the panels associated
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2014 Regenstrief Institute and James Case
Get panel details and export
Export the full panel structure
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2014 Regenstrief Institute and James Case
Detailed answer data
Answer tab
LOINC code AnswerListID Answer String
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2014 Regenstrief Institute and James Case
More on Searching Search Screen
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2014 Regenstrief Institute and James Case
Basic Search Syntax Special Character(s)
Example Deni?on
Inuenza virus A Linked terms must appear together
AND Morphine AND Opiates
Both terms must appear in the search result term
OR Inuenza OR Parainuenza
Either or both terms must appear in the search result term
NOT Inuenza 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 rst character; cannot be used in phrases
* Gluc*se (glucose, glucuronidase, etc.)
SubsJtute mulJple characters in the string. Cannot be used as the rst character; cannot be used in phrases
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2014 Regenstrief Institute and James Case
Search Qualigiers
Includes Glucuronidase, Glucosidase,
Glucosylceramidase, etc.
Detailed help available
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2014 Regenstrief Institute and James Case
Combining Search Terms
Reduced number of terms
Exclude Glucosidase
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2014 Regenstrief Institute and James Case
Advanced Search Syntax based on Google-like search syntax
Parameter Descrip?on
+ 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 eld (e.g. Component: glucose)
Fieldname:() Group mulJple terms in a single eld
~ Fuzzy search (e.g. Hemoilus~)
~ Proximity search for mulJple terms (e.g. funcJon panel~1)
{}, [] Upper and lower bounds; {} exclusive, [] inclusive
\ Special character escape
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2014 Regenstrief Institute and James Case
Applying advanced search
91 terms
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2014 Regenstrief Institute and James Case
Applying advanced search
33 terms
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2014 Regenstrief Institute and James Case
Applying advanced search
19 terms
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2014 Regenstrief Institute and James Case
Applying advanced search
8 terms
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2014 Regenstrief Institute and James Case
Limiting Searches
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2014 Regenstrief Institute and James Case
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
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2014 Regenstrief Institute and James Case
General Search Constraints Controls features including:
Limit to LOINC terms compaJble with submi_ed units Forced match with any specimen contained in name Method-less terms only Restrict by class type Remove lateralized terms
Use carefully or search may not be successful (Note parallel control switches at bo_om of screen)
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Setting Search Limits
Click Hierarchy & Search Limits Tab
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2014 Regenstrief Institute and James Case
Setting search limits Can also set most of them by toggling bu_ons
at the bo_om of the screen
Toggle Buttons
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2014 Regenstrief Institute and James Case
Search Constraints
Expanded predegined, general search constraints
Attribute trees
Limit to LOINC terms consistent with local units
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2014 Regenstrief Institute and James Case
Terms Consistent with Units
Only terms consistent with mmol/L appear
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2014 Regenstrief Institute and James Case
Setting Search Limits
Specimen constraints
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2014 Regenstrief Institute and James Case
Terms Consistent with Specimen
CSF
Enter default Specimen
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2014 Regenstrief Institute and James Case
Terms Consistent with Specimen
Only CSF Terms are returned
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2014 Regenstrief Institute and James Case
Setting Search Limits
Exclude laterality
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2014 Regenstrief Institute and James Case
Exclude laterality
Laterality terms
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2014 Regenstrief Institute and James Case
Setting Search Limits
Restrict to common orders
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2014 Regenstrief Institute and James Case
Restriction to common orders
Large number of candidates Common orders
rank
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2014 Regenstrief Institute and James Case
Setting Search Limits
Methodless Terms Restriction
Override Methodless Terms Restriction
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2014 Regenstrief Institute and James Case
Limit to Methodless Terms
Both method and method-less terms
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2014 Regenstrief Institute and James Case
Limit to Methodless Terms
Only Methodless Terms Appear
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2014 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
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2014 Regenstrief Institute and James Case
Methodless Only Unchecked
All terms returned
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2014 Regenstrief Institute and James Case
Methodless Only Checked
Only Methodless terms returned
Differ in one or more components
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Conditional Methodless
More terms returned
No method-less term; all shown
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2014 Regenstrief Institute and James Case
Setting Search Limits
Include Trial, 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
The map button is grayed out if one of these terms is selected
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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2014 Regenstrief Institute and James Case
Before Class Restriction
Large number of candidate terms
Many terms have class of CHAL
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2014 Regenstrief Institute and James Case
Search Trees
Restrict eligible tests to non-challenge
chemistry tests only
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2014 Regenstrief Institute and James Case
Following Class Restriction
Only Non-Challenge Chemistry tests
returned
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2014 Regenstrief Institute and James Case
System Hierarchy
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2014 Regenstrief Institute and James Case
Component Hierarchy
Show the LOINC Codes associated with these
components
Click on details for more information about the
selection
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2014 Regenstrief Institute and James Case
Details Screen LOINC Part
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2014 Regenstrief Institute and James Case
Show Associated LOINCs
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LOINC Term Details Screen
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Tree Export Tools
Congigure Export Format
Export according to Congiguration
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2014 Regenstrief Institute and James Case
Tree Export Congiguration
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2014 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 bu_on on Mapping Screen to remove all tree selecJons
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2014 Regenstrief Institute and James Case
LOINC Part Search Same look as term search Uses same Google-like query language
Extremely fast Include and exclude criteria ParJal string matching (using wildcards)
LOINC CLASS values may now be search using "ClassList:" eld
Demo Campylobacter fetus, not Ab
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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
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2014 Regenstrief Institute and James Case
Answer List Search
Answer Lists associated with LOINC term New! Revised and expanded answer list export options
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Navigating through the Mapping Process
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Limit eort 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
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2014 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.
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2014 Regenstrief Institute and James Case
More LOINC Mapping Tactics Try using method-less terms rst
Specic methods can be transmi_ed in: OBX17 (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 dont have to do it all at one siNng Use the Unmapped funcJon to return where you le\ o
With every release - Update previous mappings to idenJfy deprecated terms
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2014 Regenstrief Institute and James Case
Common Mapping Issues
Locally Dened Test Name Ambiguity Reuse of local test code
Analyte-free Local Test Names (Miscellaneous serology, PCR)
Incongruent Value sets (Scale ambiguity) Result vs. InterpretaJon Available LOINC Terms too Specic/General Panel vs. Discrete Test
Common in Microbiology
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2014 Regenstrief Institute and James Case
Using your Mapped Terms
Print results of LOINC Mapping Export to File
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Congigure Export Format
Context Sensitive Export Congiguration
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2014 Regenstrief Institute and James Case
LMOF Export Congiguration
Select Fields to Export
Select Export Format
Save Congiguration and Export
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2014 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
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Formatted Report Output
Click Print button to output formatted report
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2014 Regenstrief Institute and James Case
Excel Export
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2014 Regenstrief Institute and James Case
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
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2014 Regenstrief Institute and James Case
Picking the Lab Auto Mapper
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2014 Regenstrief Institute and James Case
Lab Auto Mapper Start Screen
Maximum number of terms to return
Can restrict search to common tests
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Lab Auto Mapper Start Screen
Terms used for mapping
Local test code
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2014 Regenstrief Institute and James Case
Lab Auto 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
Direct export to Excel
Select gile location
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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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Panels, forms and surveys revised display
Expand category to see panels
Double-click panel test 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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HIPAA Attachments
View Various HIPAA Attachments
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HIPPA Attachment Tree
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Expanded Attachment Data
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Cant gind the term you want?
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2014 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 dont make sense
E.g. Method-less tests plus Method tree set to EIA Did not nd 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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2014 Regenstrief Institute and James Case
Proposing New LOINC Terms
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2014 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 sucient annotaJon to jusJfy the new term Package inserts, sample reports (email to Regenstrief) The more the be_er!
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
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2014 Regenstrief Institute and James Case
Propose new LOINC terms
Select Propose a new LOINC
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2014 Regenstrief Institute and James Case
Required gields in red
Navigate through proposed terms
Create new term, save current term
or Exit form
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2014 Regenstrief Institute and James Case
Preview Proposed Terms
Review your new terms
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2014 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
301-555-1314
301-555-1315
Direct submission via web
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2014 Regenstrief Institute and James Case
Submit Proposed Terms
Add additional information, if
necessary Add attachments
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2014 Regenstrief Institute and James Case
Submitting New Terms Must supply name, organizaJon, phone and email of submi_er
Must select at least one proposed term to send
Congure export does not aect submission output
Email resulJng le to Regenstrief
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2014 Regenstrief Institute and James Case
Use Existing Terms as Template
Select your closest match
Click the Propose Term button
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2014 Regenstrief Institute and James Case
Use Existing Terms as Template
All required components gilled in
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2014 Regenstrief Institute and James Case
Using LOINC and SNOMED Together
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2014 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 idenJed in specimen? (634-6)
SNOMED represents the answer: NegaJve (SCTID 260385009) E. coli O157:H7 (SCTID 103429008)
Remember:
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2014 Regenstrief Institute and James Case
Where do LOINC and SNOMED Fit? In an HL7 message, LOINC may be used:
In OBR-4 (Universal Service IdenJer) In OBX-3 (ObservaJon IdenJer
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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2014 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 identigies the data type in OBX-5 as a
coded element
OBX: With a Coded Value
OBX-3:A code that identigies the data in
OBX-5 (Listeria culture)
OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT
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2014 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)
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2014 Regenstrief Institute and James Case
Q and A Session
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2014 Regenstrief Institute and James Case
Exercise Map your own data