2014 06 04 - Laboratory LOINC and RELMA Workshop

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 2014
Acknowledgements
LOINC Development Team
Clem McDonald, Dan Vreeman, Jami Deckard,
David Baorto, Kelly Malott
RELMA Development Team
John Hook, Anandhi Sowmyan, James Dennis,
Katy Holck
LOINC Committee
Supporters: NLM, Regenstrief Institute,
Regenstrief Foundation
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
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)
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
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

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
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
Test comparisons
Lab A
Test Name: Lyme Disease Serology
Measures: B. burgdorferi Ab IgG
Method: ELISA
Scale: quantitative
e.g.: Titer 1:40

Lab B
Test Name: Lyme Disease Antibody
Measures: B. burgdorferi Ab IgM
Method: Immune blot
Scale: qualitative
e.g.: Positive

LOINC Code = 5062-5 LOINC Code = 6321-4
What you see in the order list
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
LOINC
101
Emphasis on Laboratory
LOINC
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
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
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
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
<time delay>post<challenge type>

Adjusted to pH 7.4
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
Threshold: Results that represent the relation between a value and some
established limit or cut-off
Number: Counts
Property
The characteristic or attribute of the analyte that is
measured, evaluated, or observed
the most difficult LOINC axis
Major Categories
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
the most difficult LOINC axis
Combine Major Categories with Subtypes for Full Property
Common Property Issues
Fraction = Part/Whole
NFr: % Eosinophils / leukocytes
SFr: % HGB which is A2

Ratio = multiple analytes from same system
MCrto: BUN/Creatinine in serum

Relative Ratio = measures from different system
RelRto: Albumin.pericard fld/Albumin.SerPl
Fraction versus Ratio
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 organisms now represented as
PR (presence)
For nominal results, property is still PRID
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
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
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
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
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)
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
Hierarchies
LOINC Class
One for each LOINC axis
Multi-axial
Component | System
Separate download

Mapping Terms to LOINC
Things to Remember
The thing ordered is not always the thing measured:
Blood Culture live organism(s) identified
VDRL Treponema pallidum Ab
Urinalysis lots of different things
You must know the specifics of the component being
tested for (what is this test actually measuring?)
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
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

RELMA

Regenstrief LOINC Mapping Assistant
Download of latest version
The latest version of the installation file
may be downloaded from:
https://iu.box.com/relma65
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
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
New in This Version (Rel. 6.5)
Exciting news! The ability to send a new term request
directly to Regenstrief directly from RELMA.
Ability to attach files such as package inserts and other
documentation.
Original functionality retained
New installer technology that should result in minimal
screen changes during the install.
Detail pages have been enhanced with hyperlinks.
All LOINC numbers, LOINC part numbers and LOINC Answer
list numbers are displayed as hyperlinks.
Answer string "LA" codes are now displayed in the list
of answers in the answer search screen.
LOINC Web Site
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

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
Installing RELMA
Installation Steps
Requires Windows (or VM on a Mac)
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
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\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\Public
Documents\RELMA\Samples\

Running RELMA
Version 6.5
Copyright Screen
Join the LOINC Community
LOINC crowdsourcing
Main Menu/Welcome Screen
Set Preferred Language
Click File, Set Preferred
Language
Select Linguistic Variant(s)
Selecting a translation may
require indexes to be built
LOINC Terms with Spanish Linguistic Variant
All Spanish!
Setting User Preferences
Select User Preferences
From the File Menu
Set User Preferences
...or from Welcome Screen
Set User Preference Dialog
Startup Screen Preference
New File Locations:
(See prior slide for location)
New Submissions tab
User Map Screen Preferences
Click Map Screen Tab
Include/Exclude Battery Terms
Add comments on Mappings
Auto create search terms
User Detail Pages Preferences
Download detail pages from LOINC.org
Request Submission Preference
Preferred method of request submission
Importing Local
Terms into RELMA
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
Constructing a Local Dataset
Create 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
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)
Entering New Local Terms
into RELMA
Manual Enter/Edit
View/Add/Edit Local Terms
Edit Term Dialog
Edit\Add\Delete Terms
Export Terms
Print Preview List
Text alignment option
User assigned tags
Export Local Term File
Delimiters supported:
Tab, comma, bar (|)
Export to Microsoft Excel
or Text File
Add Local Term
Click to Add to Current
Working File
MICRO
BUBPLAG
BUBONIC PLAGUE RRT PCR
Search Local Term File
Enter Keyword from any
Field
Calcium
Return to Full List
Tags panel only appears if
tags have been assigned
Using tags to filter local terms
Print preview local term
file
Configure output prior to
viewing and printing
Print Preview Local Term File
Only prints selected rows
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 file
3. Name your Working Set (Mandatory)
a) LMOF database can contain multiple work sets
4. Define default section (Optional)
5. Identify file delimiter
6. Assign fields to LMOF attributes
a) Ignore fields you dont need
b) Combine fields if needed
7. Check Case-sensitive if needed
8. Click Import.
Example Tab-Delimited File
Importing Local Files
Select Import Local Terms
from Delimited File or
Excel Spreadsheet
Navigate to File Location
Select File and Click Open
Sample files stored in
RELMA Directory
Open File in RELMA
Name your working set.
RELMA allows multiple sets in
LMOF database
Select your delimiter
Import Button
Fields Segregated
Assign LMOF Attribute
Assign working set name
Working set import
LOINC Workshop OBR
Ready to Import
Minimum assignments
Now you can click the
Import button!
Post-Processing of Local File
After import, RELMA Searches for terms
(words) that it does not recognize
Stored in a file for future reconciliation
Importing Excel file

Excel files now appear
along with text files
Excel format for import

Local Term File Options
Change Local Term File
Select the Working Set
Current mapping status
Can delete local term set; not
the active one
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

Generate Local term file from HL7 messages
Select Import Terms from
HL7 File
Select File to Import
Select HL7 File
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
HL7 Messages Data Statistics
New Terms added to LMOF
New Battery Code
Click on Edit Term to see
Sample Data
Sample Results for Observation
New Test Code
Sample Values from
Messages
Lenny LOINC says:
Load the Sample Files
Into RELMA now!
Import the two sample 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
Cleaning your data
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
RELMA Cleaning Tools
Use this tool to edit
unknown terms
Only available if no
language variant selected
Review Unknown Local Terms
May Re-Scan File for
Unknown Terms
Replace Local Terms
Assign LMOF Attribute Replacement Options
RELMA Cleaning Tools
Use this tool to make
global substitutions
Term Substitution
Save this global substitution
for only this working set
Lenny LOINC says:
Begin to clean your
data now!
Using the OBR sample file or
your own data, take 15-20
minutes to clean up these
unrecognized terms
Searching for LOINC Terms
Comprehensive Search
Only Tool
Search Window
Enter Search Terms
Limit to
Specific Units
Use different
logic
Help File
Restrict Limits
Search Window
Common Tests selected
Common Tests rank
RELMA Search Helpfile
Context Menu
Right click to bring
up context menu
Changed search function Max words
Large number of
results
Keyword
ComponentWordCount
restricts word count
Restricting to Common
labs refines further
Mapping Local Terms
Mapping Local Terms
Select your Working Set to Map
File>Select Local Term File to Process
Select Map Local Terms to LOINC from
Welcome Screen
Select the subset of terms to work with:
All
Mapped
Unmapped
Set your Search Limits
Set Search Limits Button
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

Mapping Screen
View or edit local term
Quick select button list
Custom Grid Configuration
Enter local term number
User assigned tags
Configure Grid
Reorder grid elements
Select elements to display
Reset Default Configuration
Visually resize elements
Quick choice buttons
Viewing LOINC term detail
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
Details Text Size
Select text size
Select detail display level
Select level of detail to
display
Standard Mapping Screen
Begin a search
(or hit enter)
EEK! Whatll
I do?!
Click to
show words
used in
search
Initial Mapping Results
Use term
checkbox
Number of LOINC
terms containing
keyword
Battery terms
included in
search
Revised Mapping Results
Number of
matching
records found
Re-revised Mapping Results
Number of
matching
records found
Match units
selected
Clear all
input fields
Enter keywords here
CANINE DISTEMPER VIRUS IF
Navigate through
the local terms
Tabbed Access to Functions
Navigate to Functions
from Mapping Page
Switch between Grid and
Tree Views
Tree View
Tree View
Results displayed hierarchically
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
Tree View
Cannot map to
terms
representing
LOINC parts
Can map to terms
with LOINC Codes
Tree Navigation
Buttons
Assigning a LOINC Map
Highlight correct
term
Click Map Button
(or doubleclick)
Adding Mapping Comments
If comments
option is selected,
prompt appears
Check with Frank in Chemistry
Assigning a LOINC Map
LOINC Term
Assigned
View Panel Children
Select View Panel Children
from context menu
Panel Children
Configure Export Options
Output Options
Include
column headers
Save Configuration
and/or Export
Excel Export Format
More on Searching
Search Screen
Basic Search Syntax

Special
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
Search Qualifiers
Includes Glucuronidase,
Glucosidase,
Glucosylceramidase, etc.
Detailed help available
Combining Search Terms
Reduced number of terms
Exclude Glucosidase
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
Applying advanced search
91 terms
33 terms
19 terms
8 terms
Limiting Searches
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
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)

Click Hierarchy & Search
Limits Tab
Setting search limits
Can also set most of them by toggling
buttons at the bottom of the screen
Toggle Buttons
Search Constraints
Expanded predefined,
general search constraints
Attribute trees
Limit to LOINC terms
consistent with local units
Terms Consistent with Units
Only terms consistent
with mmol/L appear
Specimen
constraints
Terms Consistent with Specimen
CSF
Enter default
Specimen
Terms Consistent with Specimen
Only CSF Terms are
returned
Exclude laterality
Exclude laterality
Laterality terms
Restrict to
common orders
Restriction to common orders
Large number of
candidates
Common orders
rank
Methodless Terms
Restriction
Override Methodless Terms
Restriction
Limit to Methodless Terms
Both method and
method-less terms
Limit to Methodless Terms
Only Methodless
Terms Appear
More on Methodless Terms
Some LOINC categories do not have
methodless terms
Checking methodless only will remove these
from view on results grid
Checking additional box allows these to be
seen
Methodless Only Unchecked
All terms returned
Methodless Only Checked
Only Methodless
terms returned
Differ in one or
more components
Conditional Methodless
More terms
returned
No method-less
term; all shown
Include Trial, Deprecated or
Discouraged LOINC Codes with
Returned Terms
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
Favor Property Restriction
Favor one type of
property over others
All other components
being equal MCnc
only will be displayed
Order/Observation Restriction
Order or Observation
preference
LOINC Hierarchies Class Tree
Three top-level
branches
Tree Navigation
Buttons
Before Class Restriction
Large number of
candidate terms
Many terms have class
of CHAL
Search Trees
Restrict eligible tests
to non-challenge
chemistry tests only
Following Class Restriction
Only Non-Challenge
Chemistry tests
returned
System Hierarchy
Component Hierarchy
Show the LOINC Codes
associated with these
components
Click on details for more
information about the
selection
Details Screen LOINC Part
Show Associated LOINCs
LOINC Term Details Screen
Tree Export Tools
Configure Export Format
Export according to
Configuration
Tree Export Configuration
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
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)
Demo
Campylobacter fetus, not Ab
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
Answer List Search
Answer Lists associated with
LOINC term
Navigating through the
Mapping Process
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
Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term
Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.
More LOINC Mapping Tactics
Try using method-less terms 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
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
Using your Mapped Terms
Print results of LOINC Mapping
Export to File
Configure Export Format
Context Sensitive Export
Configuration
LMOF Export Configuration
Select Fields to Export
Select Export Format
Save Configuration and
Export
Print Mapped Terms from View/Add/Edit Menu
May highlight terms to be
printed
Click Print button to Preview
output
Formatted Report Output
Click Print button to output
formatted report
Excel Export
Lab Auto Mapper
Run in batch mode to 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
Picking the Lab Auto Mapper
Lab Auto Mapper Start Screen
Maximum number of terms
to return
Can restrict search to
common tests
Lab Auto Mapper Start Screen
Terms used for
mapping
Local test code
Lab Auto Mapper - Mapping Screen
Exporting Mapped Terms
Export Terms to
Delimited File
Export Terms Dialog
Check Fields you
wish to export
Select Delimiter
Select Term Set
Direct export to
Excel
Select file location
Other RELMA

Features
Panels, Forms and Survey Review
Review Panels, Forms and
Surveys
Review Panels, Forms and
Surveys
Laboratory Panels
Expand category to
see panels
Double-click
panel test to see
components
Expanded Panel Detail
Government Panels
Form Category
Panel Codes
Government Panel Children
Expanded Clinical Panel
Clinical Panels
Find where a term has
been used
35089-2, 35090-0
LOINC Term Panel Usage
Other Survey Instruments
HIPAA Attachments
View Various HIPAA
Attachments
HIPPA Attachment Tree
Expanded Attachment Data
Cant find the
term you
want?
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
Proposing New LOINC Terms
Proposing New Terms
Make sure the term is really needed
Think of other names for the same concept
Avoid detailed methods or 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
Propose new LOINC terms
Select Propose a
new LOINC
Required fields in
red

Navigate through
proposed terms
Create new term,
save current term
or Exit form
Preview Proposed Terms
Review your new
terms
Review Proposed Terms
All proposed terms
fully editable
Choose whether to
send or postpone
X
X
X
James T. Case DVM, PhD
NIH/NLM
James.case@mail.nih.gov
301-555-1314
301-555-1315
New! Direct
submission via web
Submit Proposed Terms
Add additional
information, if
necessary
Add attachments
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
Use Existing Terms as Template
Select your closest
match
Click the Propose
Term button
Use Existing Terms as Template
All required
components filled in
Using LOINC and SNOMED
Together
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:
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
The code is
from SNOMED
The code is
from LOINC

OBX-5: Data
A 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
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)
Q and A Session
Exercise
Map your own data

2014 06 04 - Laboratory LOINC and RELMA Workshop

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2014 06 04 - Laboratory LOINC and RELMA Workshop

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2014 Regenstrief Institute and James Case

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