2015 12 02 - loinc workshop - using relma
DESCRIPTION
LOINC and RELMA Workshop presented by Jim Case at the Laboratory LOINC Workshop and Committee MeetingTRANSCRIPT
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Using RELMA OrIn Search of the Missing LOINC
James T. Case MS, DVM, PhD, FHL7, FACMIHealth Program Specialist, SNOMED CT
National Library of Medicine
Laboratory LOINC Meeting December 2015
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The views and opinions expressed do not necessarily state or reflect those of the U.S. Government, and they may not be used for advertising or product endorsement purposes.
Disclaimer
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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 Committee Supporters
NLM, Regenstrief Institute, Regenstrief Foundation, APTA, RSNA, the LOINC Premium Members and Donors
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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
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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)
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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
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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 by category
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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
This is a problem even when standard
terminologies are used
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The ProblemIn 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
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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
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Why LOINC?Within one laboratory, local jargon terms
may be used which are usually well understood between colleagues, but
would not be sufficiently widely known for 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
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LOINC 101Emphasis on Laboratory
LOINC
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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
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NOT part of a LOINC Name Reason for the test (why it was ordered or the disease it
diagnoses)
Testing instrument Specific details about the specimen Priority (e.g. STAT) Where testing was done Who did the test Test interpretation Pricing or cost Anything not part of naming the test Things from other fields in an HL7 artifact
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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
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Component StructureAnalyte Name^Challenge^Adjustments
Formal analyte nameSpecify subanalytesMay have subclasses
ChallengeTwo parts separated by post
Adjustments
CalciumCoronavirus AgCalcium.ionized
1H post 100 g Glucose POpost
Adjusted to pH 7.4
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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 (slowly being retired) Threshold: Results that represent the relation between a value and some
established limit or cut-off 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
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MCnc mass concentration (mass/unit vol; e.g. mg/dL) MCnt mass content (mass/unit mass; e.g. mg/Kg) NCnc number concentration (number/unit vol; e.g. num/mL) TmStp time CCnc catalytic concentration (activity; e.g. kat/L) 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
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Common Property Issues
Fraction = Part/WholeNFr: % Eosinophils / leukocytesSFr: % HGB which is A2
Ratio = multiple analytes from same systemMCrto: BUN/Creatinine in serum
Relative Ratio = measures from different systemRelRto: Albumin.pericard fld/Albumin.SerPl
Fraction versus Ratio
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Important property changes ACNC was always a placeholder
For P/N results, changed to Threshold Additional migrations occurring gradually LOINC IDs being retained
Flavors of Threshold Property ThrSCnc Threshold Substance Concentration ThrMCnc Threshold Mass Concentration ThrACnc Threshold Arbitrary Concentration
PR vs PRID Presence or absence of an analyte now represented as
PR (presence) For nominal results, property is still PRID
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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
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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SystemThe system (context) or specimen type upon
which the observation was made.SerSer/PlasBldUrFluTissXXX
serumserum or plasmawhole blood urinebody fluidtissuespecified elsewhere
photo via AlishaV
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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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
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ScaleQn
Ord
Nom
Nar
Quantitativecontinuous numericcan have operators ()
OrdinalRanked set (1+, 2+, 3+)
Nominalunranked collectionTaxonomy (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 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)
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Method Only needed if interpretation affected
Different normal ranges Test sensitivity/specificity
Generally listed at the generic level
Agglutination Enzyme Immunoassay Probe with target amplification
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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HierarchiesLOINC Class
one per term arbitrarily assigned
One for each LOINC axisMulti-axial
Component | System Separate download
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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
You must know the specifics of the component being tested for (what actually being measured?)
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! Need to get the observation/result boundary correct.
Sample values help substantially
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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
And much more
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RELMARegenstrief LOINC Mapping Assistant
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Download of latest version
The latest version of the installation file may be downloaded from:
https://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 tips/pitfalls Help begin the mapping process for your
institution Hang with some really cool folks
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LOINC files and indexes Manual and automated mapping functions 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
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New in This Version Nuttin but big fixes
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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 files (panels, forms, top 2000, etc.) LOINC User guide; RELMA User Guide Tools to assist language translations 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 Descriptions Sample units
Empirically-derived common test list Empirically-derived common order list Special features for panels/forms Enhanced export/copy-paste options
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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 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
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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 files Windows Vista = C:\Users\Public\Documents\RELMA\Samples\ Windows 7, 8 = C:\Users\Public\Public
Documents\RELMA\Samples\
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Running RELMAVersion 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 PreferencesFrom 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 PreferencesClick 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 file from your local test catalog (good choice)
Import Excel file 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 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
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Creating Delimited ASCII File RELMA cant 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)
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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 TermsExport Terms
Print Preview ListText 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 filter local terms
Print preview local term file
Configure 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 Terms1. Click Import Local Terms Button from Main Menu
a) File>Import Local Terms from Delimited File2. Locate your local terms text file3. Name your Working Set (Mandatory)
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 dont needb) Combine fields if needed
7. Check Case-sensitive if needed8. 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 LocationSelect File and Click OpenSample files 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 importLOINC 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 file that allow you to categorize your local terms
Fields in import function allow assignment of Tag with
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Local term file with added tags
Tag terms
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Assign tag values
Tag with field assignment
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Tagged local terms
Imported tags
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Post-Processing of Local File
After import, RELMA Searches for terms (words) that it does not recognize
Stored in a file for future reconciliation
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Importing Excel file
Excel files now appear along with text files
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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 Automatically make dataset of:
OBR ID OBR description OBX ID OBX description Sample of results with
Real values Units Abnormal flags Normal ranges
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Generate Local term file 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 ObservationNew Test Code
Sample Values from Messages
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Lenny LOINC says:Load the Sample Files
Into RELMA now!
Import the two sample files provided
Import_Sample_OBR.txt Contains battery code and
description Sample_HL7.HL7
Contains test code and description 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 abbreviations Standardizing colloquial terms Ignoring administrative terms Standardizing time references
Can be done prior to importing Better to use tools built into RELMA
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RELMA Cleaning ToolsUse 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 AttributeReplacement Options
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RELMA Cleaning ToolsUse 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 file 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 Specific Units
Use different logic
Help File
Restrict Limits
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Search Window
Common Tests selectedCommon Tests rank
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RELMA Search Helpfile
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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 countRestricting to Common labs refines 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 syntaxPaneltype
Classifies LOINC panel term in categories
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New advanced search syntaxLForms
This true/false field 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 syntaxAssociatedObservations
Additional 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 Button
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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 Configuration
Enter local term number
User assigned tags
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Configure Grid
Reorder grid elements
Select elements to display
Reset Default ConfigurationVisually 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 SizeSelect 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 foundMatch units selected
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Standard Mapping Screen
Clear all input fields
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
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 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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Configure Export Options
Output OptionsInclude
column headersSave Configuration 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 specific LOINC
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Search for a panel
Search for panel or LOINC code
Find the panels associated
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Get panel details and export
Export the full panel structure
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Detailed answer data
Answer tab
LOINC code AnswerListID Answer String
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More on Searching Search Screen
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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
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Search Qualifiers
Includes Glucuronidase, Glucosidase,
Glucosylceramidase, etc.
Detailed help available
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Combining Search Terms
Reduced number of terms
Exclude Glucosidase
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Advanced Search Syntax based on Google-like search syntax
Parameter 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
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Applying advanced search
91 terms
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Applying advanced search
33 terms
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Applying advanced search
19 terms
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Applying advanced search
8 terms
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Limiting Searches
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Setting Search Limits
Narrows search to specific subset of LOINC terms Reduces number of candidate terms Limits can be applied to all components Component attribute can be further restricted by
number of words Tree structure allows for hierarchical constraints
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General Search Constraints Controls features including:
Limit to LOINC terms compatible with submitted 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 bottom of screen)
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Setting Search Limits
Click Hierarchy & Search Limits Tab
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Setting search limitsCan also set most of them by toggling buttons
at the bottom of the screen
Toggle Buttons
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Search Constraints
Expanded predefined, general search constraints
Attribute trees
Limit to LOINC terms consistent with local units
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Terms Consistent with Units
Only terms consistent with mmol/L appear
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Setting Search Limits
Specimen constraints
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Terms Consistent with Specimen
CSF
Enter default Specimen
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Terms Consistent with Specimen
Only CSF Terms are returned
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Setting Search Limits
Exclude laterality
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Exclude laterality
Laterality terms
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Setting Search Limits
Restrict to common orders
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Restriction to common orders
Large number of candidates Common orders
rank
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Setting Search Limits
Methodless Terms Restriction
Override Methodless Terms Restriction
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Limit to Methodless Terms
Both method and method-less terms
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Limit to Methodless Terms
Only Methodless Terms Appear
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More on Methodless Terms Some LOINC categories do not have
methodless terms Checking methodless only will remove these
from view on results grid Checking additional box allows these to be
seen
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Methodless Only Unchecked
All terms returned
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Methodless Only Checked
Only Methodless terms returned
Differ in one or more components
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Conditional Methodless
More terms returned
No method-less term; all shown
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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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Before Class Restriction
Large number of candidate terms
Many terms have class of CHAL
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Search Trees
Restrict eligible tests to non-challenge
chemistry tests only
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Following Class Restriction
Only Non-Challenge Chemistry tests returned
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System Hierarchy
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Component Hierarchy
Show the LOINC Codes associated with these
components
Click on details for more information about the
selection
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Details Screen LOINC Part
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Show Associated LOINCs
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LOINC Term Details Screen
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Tree Export Tools
Configure Export Format
Export according to Configuration
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Tree Export Configuration
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RELMA - Tree Features All trees operate the same way Shows terms spelled out Can expand and collapse parts or all of tree. Tree is string searchable Search can be based on one or more
branches of a tree with or without other criteria
Use Clear Most Limits button on Mapping Screen to remove all tree selections
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LOINC Part Search Same look as term search Uses same Google-like query language
Extremely fast Include and exclude criteria Partial string matching (using wildcards)
LOINC CLASS values may now be search using "ClassList:" field
Demo Campylobacter fetus, not Ab
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LOINC Answer List Search
Nominal LOINC terms are now required to be submitted with answer lists.
Finding answer lists and the use of them can be done with Answer List Search tab
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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 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
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Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.
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More LOINC Mapping Tactics Try using method-less terms first
Specific methods can be transmitted in: OBX17 (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 dont 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
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Common Mapping Issues
Locally Defined Test Name Ambiguity Reuse of local test code
Analyte-free Local Test Names (Miscellaneous serology, PCR)
Incongruent Value sets (Scale ambiguity) Result vs. Interpretation Available LOINC Terms too Specific/General Panel vs. Discrete Test
Common in Microbiology
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Using your Mapped Terms
Print results of LOINC Mapping Export to File
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Configure Export Format
Context Sensitive Export Configuration
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LMOF Export Configuration
Select Fields to Export
Select Export Format
Save Configuration and Export
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Print Mapped Terms from View/Add/Edit Menu
May highlight terms to be printed
Click Print button to Preview output
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Formatted Report Output
Click Print button to output formatted report
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Excel Export
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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
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Picking the Lab Auto Mapper
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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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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 file 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 find the term you
want?
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Search Hints and Tips Keywords with zero frequency are ignored
May need to rephrase use synonym Some causes for no returned terms
Too many keywords in search uncheck some Limits applied that dont make sense
E.g. Method-less tests plus Method tree set to EIA Did not find and revise words not in RELMA
Local units not in RELMA
Units are GREAT discriminators You may have tests that need to be added to
LOINC
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Proposing New LOINC Terms
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Proposing New Terms Make sure the term is really needed
Think of other names for the same concept Avoid detailed methods or 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
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Propose new LOINC terms
Select Propose a new LOINC
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Required fields in red
Navigate through proposed terms
Create new term, save current term
or Exit form
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Preview Proposed Terms
Review your new terms
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Review Proposed Terms
All proposed terms fully editable
Choose whether to send or postpone
X
XX
James T. Case DVM, PhD
NIH/NLM
301-555-1314
301-555-1315
Direct submission via web
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Submit Proposed Terms
Add additional information, if
necessaryAdd attachments
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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
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Use Existing Terms as Template
Select your closest match
Click the Propose Term button
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Use Existing Terms as Template
All required components filled in
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Using LOINC and SNOMED Together
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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:
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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
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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
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HL7 2.5 Example (ER-7 format)MSH|^~\&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01|
LABGL1199510221838581| P| 2.3||| NE| NE
PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090
OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult ^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^
UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN
OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837
OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility Panel^ LN||| 199812300934||||||||Bacterial isolate| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN
OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate ^SCT|||||| F||| 199812300934|| CA20837
OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934|| CA20837
OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F||| 199812300934|| CA20837
First Order OBR (Culture and ID)
First Result (Culture and ID)
First Result (Culture and ID)Second Result(s)
OBXs
First Result Value (SNOMED)
First Result Description OBX (LOINC)
Second Order OBR (Susceptibility)
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Q and A Session
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ExerciseMap your own data