©2011 Regenstrief Institute and James Case
Using RELMA Or…In Search of the Missing LOINC
James T. Case MS, DVM, PhDHealth Program Specialist, SNOMED CT
National Library of Medicine
Laboratory LOINC Meeting – December 2011
©2011 Regenstrief Institute and James Case
Acknowledgements• LOINC Development TeamClem Mcdonald, Dan Vreemen, Kathy Mercer, Jaci Phillips, Ian Pyle, David Baorto, Fran Brahmi
• RELMA Development TeamJohn Hook, Mark Fisher, Karen Ahmed, Anandhi Sowmyan, James Dennis
• LOINC Committee • Supporters: NLM, Regenstrief (including the Indiana Center of Excellence in Public Health Informatics), Regenstrief Foundation
©2011 Regenstrief Institute and James Case
What will we cover today?• Overview of LOINC• Reviewing new RELMA features!• Installing RELMA• Setting personal preferences• Loading a Local Observation File (LMOF)• Searching for a LOINC Term• Preparing LMOF for Mapping• Review of Map Screen Functions• Setting Search Limits• Mapping Local Terms to LOINC• Viewing LOINC Term Details• Proposing/Submitting New LOINC Terms• Exporting/Printing Mapped Terms• Mapping your own LMOF data
©2011 Regenstrief Institute and James Case
©2011 Regenstrief Institute and James Case
Why are we doing this?Goals of Health Information Standards
• Interoperability – the ability to exchange information between organizations
• Comparability – the ability to ascertain the equivalence of data from different sources
• Data Quality – the measurement of accessibility, completeness, accuracy and precision (and more)
©2011 Regenstrief Institute and James Case
Levels of Interoperability• Basic – allows data to be exchanged between
computer systems• Word processing documents, text messages
• Functional – describes the standard syntax (format) of the data• Document templates, forms, data structures• Message standards
• Semantic – requires use of standardized content (vocabularies) within the data structure
©2011 Regenstrief Institute and James Case
Comparability• Meaning of the data is consistent when shared
among different parties• Erysipelas – Human skin disease; Streptococcus Grp A• Erysipelas – Animal Septicemia/dermatitis; Erysipelothrix
rhusiopathiae• Common terminology required
• Should work in the background• Words are not enough
• Codes – uniquely identify terms• Vocabulary – specialized, precise terms that remove
ambiguity• Ontology – describes nature of entities and their relations• Classification – groups related terms
©2011 Regenstrief Institute and James Case
Potential Uses of Health Data are Constrained by Data Quality Factors• Data quality issues
• Different for client/patient communications vs. clinical decision support vs. epidemiological analysis
• Often constrained by external forces• e.g. criteria for diagnosis often differs from the criteria
for reporting
• Unidirectional effect of data consolidation• Detailed → General• General → Detailed
©2011 Regenstrief Institute and James Case
The Problem“In attempting to arrive at the truth, I have applied
everywhere for information, but in scarcely an instance have I been able to obtain hospital records fit for any purpose of comparison. If they could be obtained, they would enable us to decide many other questions… They would show [subscribers] how their money was being spent [and] what amount of good was really being done with it…”
Florence Nightingale - Notes on a Hospital, 1873
©2011 Regenstrief Institute and James Case
Test comparisons
Lab ATest Name: Lyme Disease SerologyMeasures: B. burgdorferi Ab IgGMethod: ELISAScale: quantitativee.g.: Titer 1:40
Lab BTest Name: Lyme Disease AntibodyMeasures: B. burgdorferi Ab IgMMethod: Immune blotScale: qualitativee.g.: Positive
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 communication with the outside world.”
U. Forsum et al., Pure Appl. Chem 72:555-745, 2000 Properties and Units in the Clinical Laboratory Sciences Part VII. Properties and Units in Clinical Microbiology
©2011 Regenstrief Institute and James Case
LOINC® 101Emphasis on Laboratory
LOINC
©2011 Regenstrief Institute and James Case
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
5193-8 LOINC Code
Hepatitis 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
©2011 Regenstrief Institute and James Case
What is NOT part of a LOINC Name?
• The instrument used in testing• Specific details about the specimen• Priority (e.g. STAT)• Where testing was done• Who did the test• Test interpretation• Anything that is not an intrinsic part of the name of
the result• Other things that are carried in;
• The OBR or OBX segment• An HL7 Version 3 Observation Object
©2011 Regenstrief Institute and James Case
The substance or entity that is measured, evaluated, or observed
Component/Analyte
- Sodium- Glucose- Brucella sp. organism- Influenza A Virus antigen- Cytomegalovirus Virus antibody- Lipids.Total
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
©2011 Regenstrief Institute and James Case
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”• <time delay> post <challenge type>
• Adjustments/corrections• E.g. Adjusted to pH 7.4
Analyte Name^Challenge^Adjustments
©2011 Regenstrief Institute and James Case
• Mass: Observations reported with mass (milligrams, grams, etc.) in the numerator of their units of measure
• Substance: Observations reported with moles or milliequivalents in the numerator of their units of measure
• Catalytic activity: Observations that report enzymatic activity • Arbitrary: Results that report arbitrary units in the numerator of
their units of measure• Number: Counts
Property
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
The characteristic or attribute of the analyte that is measured, evaluated, or observed
the most difficult LOINC axis
Major Categories
©2011 Regenstrief Institute and James Case
• MCnc – mass concentration (mass/unit vol)• MCnt – mass content (mass/unit mass)• NCnc – number concentration (number/unit vol)• TmStp – time• CCnc – catalytic concentration (activity)• Prid – presence or identity• Imp – impression/interpretation• Find – subjective or objective observation• Type – “Kind-of”
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
• Fraction = Part/whole• Number fraction (NFr): % Eosinophils• Substance fraction (SFr): % HGB which is A2
• Ratio = Measures multiple analytes from the same system (specimen)• Mass concentration ratio - MCrto
• e.g., BUN/Creat in urine specimen• Substance ratio-SCrto
• Urea/Creatinine expressed as mmol/L (SI units)
• Relative Ratio = Measures from different systems• RelRto• RlTm – time from actual and normal control
Fraction (proportion) vs. Ratioa/a+b vs. a/b
©2011 Regenstrief Institute and James Case
• Pt - at a point in time• 12H - a twelve hour collection• 24H - a twenty four hour collection
Timing*
*non-Pt timings are usually associated with Rate Property
The interval of time over which the observation 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
SystemThe system (context) or specimen type upon which
the observation was made.
©2011 Regenstrief Institute and James Case
System Structure
• Super System• Patient 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
©2011 Regenstrief Institute and James Case
• Qn - Quantitative • Continuous numeric (real, integer, ratio)• Optional operator (>, , , <)
• When assay detection limits are exceeded
• Ord - Ordinal • a ranked set of possible values (1+, 2+, 3+)
• Nom - Nominal • an unranked collection of possible values• a taxonomy (e.g list of bacteria)
• Nar - Narrative • free text narrative (e.g., visit note)
Scale
©2011 Regenstrief Institute and James Case
Scale (Special)• OrdQn – Ordinal or Quantitative
• Primarily used for antimicrobial observations e.g. MIC reported as resistant, intermediate, susceptible or as the mm diameter of the inhibition zone
• Use is discouraged in other contexts• Multi – structured text “globs”
• e.g. chromatography output• Use is discouraged
• Doc – Clinical documents• Set – Clinical attachments (headers)
©2011 Regenstrief Institute and James Case
Method• Methods only needed if interpretation affected
• Different normal ranges• Test Sensitivity/Specificity
• Generally listed only at the generic level• Agglutination (limited subtypes)• Immunoassay • Probe with target amplification
©2011 Regenstrief Institute and James Case
Hierarchies• LOINC ‘class’• Each LOINC axis• Multi-axial
• Component | System• Separate download
©2011 Regenstrief Institute and James Case
Mapping Terms to LOINCThings to Remember
• The thing ordered is not always the thing measured:• Blood Culture – live organism(s) identified• VDRL – Treponema pallidum Ab• Urinalysis – lots of different things
• The question (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl)• You are mapping the question, not the answer!
• You must know the specifics of the component being tested for (what is this test actually measuring?)
©2011 Regenstrief Institute and James Case
What is in LOINC?Content
• Term structures• Submitted units, Example UCUM units
• aiming toward preferred units sorting• Synonyms• Answer lists (increasing number)• Text descriptions – links to info sources
about individual tests • Panel structures• Foreign language translations
©2011 Regenstrief Institute and James Case
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 tips/pitfalls• Help begin the mapping process for your
institution
©2011 Regenstrief Institute and James Case
• LOINC files and indexes• Manual and automated mapping functions• Same free use as LOINC (see license)• RELMA tools transform local words in local file
• User creates file of local term/name and codes• Assigns LOINC term to local test/battery code• “Common tests” subset to speed mapping• Context sensitive hierarchies for local use.• Flexible “Google-like” search functions
RELMA Functions
©2011 Regenstrief Institute and James Case
New in This Version (Rel. 5.4) • Default - latest copy of LOINC details retrieved from the
loinc.org website. • Configurable from File -> User Preferences -> Details Pages ->
Get from Internet. • Build locally File -> User Preferences -> Details Pages -> Build
Locally.
• Common order rank displayed as "Common Order Rank" in the LOINC Details displays.
• New search restriction - "Exclude LOINCs containing 'left' or 'right'“. Bilateral LOINCs and LOINCs without laterality remain in the search results.
©2011 Regenstrief Institute and James Case
• "Terms consistent with local units" search restriction status is saved between editing sessions.
• Answer string descriptions displayed with answer string (configurable).
• Images are now displayed on Part details pages, if available.
• Obsolete LOINC fields deleted from the Details displays -- ANSWERLIST and DEFINITION_DESCRIPTION_HELP.
New in This Version (Rel. 5.4)
©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 translations by part• Tools for building databases to map from
HL7 messages• New guidance documents for mappers
35
©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• Descriptions• Sample units
• Empirically-derived common test list• Empirically-derived common order list• Special features for panels/forms• Enhanced export/copy-paste options
©2011 Regenstrief Institute and James Case
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 installation directory• Life will be easier if you accept the default
• Two database files installed• RELMA.MDB – LOINC Terms Database• LMOF3.MDB – Local Master Observation File
• Two sample files included • Run from Start – (All) Programs – Regenstrief – RELMA
©2011 Regenstrief Institute and James Case
File Locations
• Database and Ancillary Files• Windows XP = C:\Documents and Settings\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 Settings\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 5.4
©2011 Regenstrief Institute and James Case
Copyright Screen
©2011 Regenstrief Institute and James Case
Main Menu/Welcome Screen
©2011 Regenstrief Institute and James Case
Set Preferred Language
Click File, Set Preferred Language
©2011 Regenstrief Institute and James Case
Select Linguistic Variant(s)
Selecting a translation may require indexes to be built
©2011 Regenstrief Institute and James Case
LOINC Terms with Spanish Linguistic Variant
All Spanish!
©2011 Regenstrief Institute and James Case
Setting User Preferences
©2011 Regenstrief Institute and James Case
Select User PreferencesFrom the File Menu
Set User Preferences
...or from Welcome Screen
©2011 Regenstrief Institute and James Case
Set User Preference Dialog
Startup Screen Preference
New File Locations:(See prior slide for location)
©2011 Regenstrief Institute and James Case
User Map Screen Preferences
Click Map Screen Tab
Include/Exclude Battery Terms
Add comments on Mappings
Auto create search terms
©2011 Regenstrief Institute and James Case
Importing Local Terms into RELMA
©2011 Regenstrief Institute and James Case
4 Ways to Load LMOF Files• Direct entry into LMOF from within RELMA (painful)
• Handy for individual entries/edits
• 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 DatasetCreate extract of your test catalog with:
• Battery/Panel Code• Battery/Panel Description or Name• *Local Code • *Test Description or Name
• Include Method if Important• Units• Example Values• Laboratory Section
©2011 Regenstrief Institute and James Case
Creating Delimited ASCII File• RELMA can’t parse free text
• Need to create separate fields• Can use any of these delimiters
• Tab, Semicolon, Comma, Space• Can define your own
• Fields can be in any order• Minimum required fields
• Local Code• Local Description• Units (highly recommended)
©2011 Regenstrief Institute and James Case
Entering New Local Terms into RELMA
©2011 Regenstrief Institute and James Case
Manual Enter/Edit
View/Add/Edit Local Terms
©2011 Regenstrief Institute and James Case
Edit Term Dialog
Edit\Add\Delete TermsExport Terms
Print Preview ListText alignment option
©2011 Regenstrief Institute and James Case
Export Local Term File
Delimiters supported:Tab, comma, bar (|)
©2011 Regenstrief Institute and James Case
Add Local Term
Click to Add to Current Working File
MICRO
BUBPLAG
BUBONIC PLAGUE – RRT PCR
©2011 Regenstrief Institute and James Case
Search Local Term File
Enter Keyword from any Field
Calcium
Return to Full List
©2011 Regenstrief Institute and James Case
Print Preview Local Term File
©2011 Regenstrief Institute and James Case
Steps to Import Local Terms
1. Click Import Local Terms Button from Main Menu a) File>Import Local Terms from Delimited File
2. Locate your local terms text filea) E.g. WinXP Sample files loaded into C:\Documents and
Settings\All Users\Shared Documents\RELMA3. Name your Working Set
a) LMOF database can contain multiple work sets4. Define default section (Optional)5. Identify file delimiter 6. Assign fields to LMOF attributes
a) Ignore fields you don’t needb) Combine fields if needed
7. Check “Case-sensitive” if needed8. Click Import.
©2011 Regenstrief Institute and James Case
Example Tab-Delimited File
©2011 Regenstrief Institute and James Case
Importing Local Files
Select Import Local Terms from Delimited File…
©2011 Regenstrief Institute and James Case
Navigate to File Location
Select File and Click OpenSample files stored in RELMA Directory
©2011 Regenstrief Institute and James Case
Open File in RELMA
Name your working set. RELMA allows multiple sets in
LMOF database
Select your delimiter
Import Button
©2011 Regenstrief Institute and James Case
Fields Segregated
Assign LMOF Attribute
Choose field name
©2011 Regenstrief Institute and James Case
Ready to Import
Minimum assignments
Now you can click the Import button!
©2011 Regenstrief Institute and James Case
Post-Processing of Local File
• After import, RELMA Searches for terms (words) that it does not recognize
• Stored in a file for future reconciliation
©2011 Regenstrief Institute and James Case
Local Term File Options
©2011 Regenstrief Institute and James Case
Change Local Term File
Select the Working Set
Current mapping status
©2011 Regenstrief Institute and James Case
Alternative Pragmatic Way• Use large set of HL7 messages• Automatically make dataset of:
• OBR ID• OBR description• OBX ID• OBX description• Sample of results with
• Real values• Units• Abnormal flags• Normal ranges
©2011 Regenstrief Institute and James Case
Generate Local term file from HL7 messages
Select Import Terms from HL7 File
©2011 Regenstrief Institute and James Case
Select File to Import
Select HL7 File
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
HL7 Messages Data Statistics
©2011 Regenstrief Institute and James Case
New Terms added to LMOF
New Battery Code
Click on “Edit Term” to see Sample Data
©2011 Regenstrief Institute and James Case
Sample Results for ObservationNew Test Code
Sample Values from Messages
©2011 Regenstrief Institute and James Case
Lenny L’OINC says:“Load the Sample Files
Into RELMA now!”
• Import the two sample files provided• Import_Sample_OBR.txt
• Contains battery code and description
• Import_Sample_OBX.txt• Contains test code and
description• Create 2 working sets• Load your personal data set
©2011 Regenstrief Institute and James Case
Cleaning your data
©2011 Regenstrief Institute and James Case
Preparing your Data for Mapping
• Improve mapping success by:• Expanding abbreviations• Standardizing colloquial terms• Ignoring “administrative” terms• Standardizing time references
• Can be done prior to importing• Better to use tools built into RELMA
©2011 Regenstrief Institute and James Case
RELMA Cleaning ToolsUse this tool to edit
unknown terms
©2011 Regenstrief Institute and James Case
Review Unknown Local Terms
May Re-Scan File for Unknown Terms
©2011 Regenstrief Institute and James Case
Replace Local Terms
Assign LMOF AttributeReplacement Options
©2011 Regenstrief Institute and James Case
RELMA Cleaning ToolsUse this tool to make global substitutions
©2011 Regenstrief Institute and James Case
Term Substitution
Save this global substitution for only this working set
©2011 Regenstrief Institute and James Case
Lenny L’OINC says:“Begin to clean your
data now!”
• Using the OBR or OBX sample files, take 15-20 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
©2011 Regenstrief Institute and James Case
Simplified Search Only Tool
©2011 Regenstrief Institute and James Case
Search Window
Enter Search Terms
Limit to Specific Units
Use Automapper logic
Help File
Restrict to “Common Orders”
Restrict to “Common Results”
©2011 Regenstrief Institute and James Case
Search Window
Hematocrit bld qn
“Common Tests” rank
©2011 Regenstrief Institute and James Case
New RELMA Helpfile
©2011 Regenstrief Institute and James Case
Context Menu
Right click to bring up context menu
©2011 Regenstrief Institute and James Case
Mapping Local Terms
©2011 Regenstrief Institute and James Case
Mapping Local Terms
• Select your Working Set to Map• File>Select Local Term File to Process
• Select “Map Local Terms to LOINC” from Welcome Screen
• Select the subset of terms to work with:• All• Mapped• Unmapped
• Set your Search Limits• Set Search Limits Button
©2011 Regenstrief Institute and James Case
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 Configuration
Enter local term number
©2011 Regenstrief Institute and James Case
Configure Grid
Reorder grid elements
Select elements to display
Reset Default ConfigurationVisually resize elements
©2011 Regenstrief Institute and James Case
Quick choice buttons
Viewing LOINC term detail
©2011 Regenstrief Institute and James Case
View Local Term Details
Select level of detail to display
©2011 Regenstrief Institute and James Case
View Local Term DetailsSelect text size
©2011 Regenstrief Institute and James Case
Select detail display level
Select level of detail to display
©2011 Regenstrief Institute and James Case
Standard Mapping Screen
Begin a search(or hit “enter”)
EEK! What’ll I do?!
©2011 Regenstrief Institute and James Case
Standard Mapping Screen
Click to show words
used in search
©2011 Regenstrief Institute and James Case
Initial Mapping Results
Use term checkbox
Number of LOINC terms containing
keywordBattery terms
included in search
©2011 Regenstrief Institute and James Case
Revised Mapping Results
Number of matching
records found
Match units selected by
default
©2011 Regenstrief Institute and James Case
Re-revised Mapping Results
Number of matching
records foundMatch units unselected
©2011 Regenstrief Institute and James Case
Standard Mapping Screen
Clear all input fields
Enter keywords here
CANINE DISTEMPER VIRUS IF
©2011 Regenstrief Institute and James Case
Ad hoc term search
©2011 Regenstrief Institute and James Case
Standard Mapping Screen
Navigate through the local terms
©2011 Regenstrief Institute and James Case
Tabbed Access to Functions
Navigate to Functions from Mapping Page
Switch between Grid and Tree Views
©2011 Regenstrief Institute and James Case
Tree View
©2011 Regenstrief Institute and James Case
Tree View• Results displayed hierarchically
• Defined by the multi-axial hierarchy in search restrictions (covered later)
• Map to a term in tree by clicking Map button or double clicking term• Only rows that have LOINC Codes
©2011 Regenstrief Institute and James Case
Tree View
Cannot map to terms
representing LOINC parts
Can map to terms with LOINC Codes
Tree Navigation Buttons
©2011 Regenstrief Institute and James Case
Assigning a LOINC Map
Highlight correct term
Click “Map” Button (or doubleclick)
©2011 Regenstrief Institute and James Case
Adding Mapping Comments
If comments option is selected, prompt appears
Check with Frank in Chemistry
©2011 Regenstrief Institute and James Case
Assigning a LOINC Map
LOINC Term Assigned
©2011 Regenstrief Institute and James Case
View LOINC Term Details
View details for a specific LOINC Term
Right clicking on a LOINC term brings up a Task Menu
©2011 Regenstrief Institute and James Case
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
©2011 Regenstrief Institute and James Case
View Panel Children
Select View Panel Children from context menu
©2011 Regenstrief Institute and James Case
Panel Children
©2011 Regenstrief Institute and James Case
Configure Export Options
Output Options
Include column headersSave Configuration
and/or Export
©2011 Regenstrief Institute and James Case
Excel Export Format
©2011 Regenstrief Institute and James Case
More on Searching Mapping Screen
©2011 Regenstrief Institute and James Case
Basic Search SyntaxSpecial Character(s)
Example Definition
“ “ 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)
Substitutes a single character in the string. Cannot be used as the first character; cannot be used in “phrases”
* Gluc*se(glucose, glucuronidase, etc.)
Substitute multiple characters in the string. Cannot be used as the first character; cannot be used in “phrases”
©2011 Regenstrief Institute and James Case
Search Qualifiers
Includes Glucuronidase, Glucosidase,
Glucosylceramidase, etc.
Detailed help available
©2011 Regenstrief Institute and James Case
Combining Search Terms
Reduced number of terms
Exclude Glucosidase
©2011 Regenstrief Institute and James Case
Advanced Search Syntax based on Google-like search syntax
Parameter Description
+ Term must be included in search
- Term must be excluded from the search
( ) Group terms for subquery (i.e. A OR B; A AND B)
Fieldname: Limit term search to the associated field (e.g. Component: glucose)
Fieldname:() Group multiple terms in a single field
~ Fuzzy search (e.g. Hemofhilus~)
“ “~ Proximity search for multiple terms (e.g. “function panel”~1)
{}, [] Upper and lower bounds; {} exclusive, [] inclusive
\ Special character escape
©2011 Regenstrief Institute and James Case
Applying advanced search
©2011 Regenstrief Institute and James Case
Limiting Searches
©2011 Regenstrief Institute and James Case
Setting Search Limits
• Narrows search to specific subset of LOINC terms• Reduces number of candidate terms• Limits can be applied to all components• Component attribute can be further restricted by
number of words• Tree structure allows for hierarchical constraints
©2011 Regenstrief Institute and James Case
General Search Constraints• Controls features including:
• Limit to LOINC terms compatible with submitted units• Forced match with any specimen contained in name• Method-less terms only • Limit to components/analytes with N or fewer words in their
name• Pop up search timing statistics after each search
• Use carefully or search may not be successful(Note parallel control switches at bottom of screen)
©2011 Regenstrief Institute and James Case
Setting Search Limits
Click Hierarchy & Search Limits Tab
©2011 Regenstrief Institute and James Case
Setting search limitsCan also set most of them by toggling buttons
at the bottom of the screen
Toggle Buttons
©2011 Regenstrief Institute and James Case
Search Constraints
Predefined, general search constraints
Attribute trees
Local Unit Constraint:Default is “ON”
Type toggle boxes
©2011 Regenstrief Institute and James Case
Terms Consistent with Units
Only terms consistent with mmol/L appear
New! - Status saved between
editing sessions
©2011 Regenstrief Institute and James Case
Setting Search Limits
Specimen constraints
©2011 Regenstrief Institute and James Case
Terms Consistent with Specimen
CSF
Enter default Specimen
©2011 Regenstrief Institute and James Case
Terms Consistent with Specimen
Only CSF Terms are returned
©2011 Regenstrief Institute and James Case
Setting Search Limits
New! - Exclude laterality
©2011 Regenstrief Institute and James Case
Exclude laterality
Laterality terms
©2011 Regenstrief Institute and James Case
Setting Search Limits
New! - Restrict to common orders
©2011 Regenstrief Institute and James Case
Restriction to common orders
Large number of candidates New! Common
orders rank
©2011 Regenstrief Institute and James Case
Setting Search Limits
Methodless Terms Restriction
Override Methodless Terms Restriction
©2011 Regenstrief Institute and James Case
Limit to Methodless Terms
Both method and method-less 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 additional 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 method-less 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: 850 terms returned
©2011 Regenstrief Institute and James Case
Limit Number of Component Words
With Limit Applied: 68 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
Many terms have class of “CHAL”
©2011 Regenstrief Institute and James Case
Search Trees
Restrict eligible tests to non-challenge
chemistry tests only
+Chem* +non
©2011 Regenstrief Institute and James Case
Following Class Restriction
Only Non-Challenge Chemistry tests
returned
©2011 Regenstrief Institute and James Case
System Hierarchy
©2011 Regenstrief Institute and James Case
Component Hierarchy
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
Configure Export Format
Export according to Configuration
©2011 Regenstrief Institute and James Case
Tree Export Configuration
©2011 Regenstrief Institute and James Case
RELMA - Tree Features
• All trees operate the same way• Shows terms spelled out• Can expand and collapse parts or all of tree.• Tree is string searchable • Search can be based on one or more
branches of a tree with or without other criteria
• Use “Clear Most Limits” button on Mapping Screen to remove all tree selections
©2011 Regenstrief Institute and James Case
LOINC Part Search
• Same look as term search• Uses “Google-like” query language
• Extremely fast• Include and exclude criteria• Partial string matching (using wildcards)
• Demo• Campylobacter fetus, not Ab
©2011 Regenstrief Institute and James Case
Navigating through the Mapping Process
©2011 Regenstrief Institute and James Case
• Limit effort to one lab section at a time and focus expertise
• Chemistry and hematology will be easiest• For manufactured assays, use package insert as
source information• Sample results give clue to property and scale• Consider prioritizing by frequency of use
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 transmitted in:• OBX–17 (v2.x), Observation.methodCode (v3.0)
• Examine local units or real results to verify correct property and scale• Properties are rarely distinguishable in test names
• You don’t have to do it all at one sitting• Use the “Unmapped” function to return where you
left off• With every release - Update previous mappings
to identify deprecated terms
©2011 Regenstrief Institute and James Case
Common Mapping Issues
• Locally Defined Test Name Ambiguity• Reuse of local test code
• “Analyte-free” Local Test Names• (Miscellaneous serology)
• Incongruent Value sets (Scale ambiguity)• Result vs. Interpretation• Available LOINC Terms too Specific/General• Panel vs. Discrete Test
• Common in Microbiology
©2011 Regenstrief Institute and James Case
Using your Mapped Terms
• Print results of LOINC Mapping• Export to File
©2011 Regenstrief Institute and James Case
Configure Export Format
Context Sensitive Export Configuration
©2011 Regenstrief Institute and James Case
LMOF Export Configuration
Select Fields to Export
Select Export Format
Save Configuration 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 Configuration
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
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 find the term you
want?
©2011 Regenstrief Institute and James Case
Search Hints and Tips• Keywords with zero frequency are ignored
• May need to rephrase – use synonym• Some causes for 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 localizations• Is the distinction really important?
• Supply sufficient annotation to justify the new term• Package inserts, sample reports (email to Regenstrief)• The more the better!
• Construct new terms within RELMA• File>Propose a new LOINC• Linked to the “trees” to allow browsing
• Can review and submit them to LOINC from within RELMA
©2011 Regenstrief Institute and James Case
Propose new LOINC terms
Select Propose a new LOINC
©2011 Regenstrief Institute and James Case
Required fields in red
Navigate through proposed terms
Create new term, save current term
or Exit form
Advanced/Simple toggle
©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
301-555-1314
301-555-1315
©2011 Regenstrief Institute and James Case
Submitting New Terms• Must supply name, organization, phone and
email of submitter• Must select at least one proposed term to
send• “Configure export” does not affect
submission output• Email resulting file to Regenstrief
©2011 Regenstrief Institute and James Case
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 filled 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 question:• Is there any Botulism toxin in my specimen?
(33708-9)• Organisms identified in specimen? (634-6)
• SNOMED represents the answer:• Negative (SCTID 260385009)• E. coli O157:H7 (SCTID 103429008)
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 Identifier)• In OBX-3 (Observation Identifier
• SNOMED may be used:• In OBX-5 (where nominal values are needed)• Almost anyplace else in an HL7 message where
coded values are needed
©2011 Regenstrief Institute and James Case
The code isfrom SNOMED
The code isfrom LOINC
OBX-5: DataA code for L.
monocytogenes
A code that identifies the data type in OBX-5 as a
coded element
OBX: With a Coded Value
OBX-3:A code that identifies 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
ExerciseMap your own data