2015 06 03 - LOINC Workshop

Using
RELMA
OrIn Search of the Missing LOINC
Laboratory LOINC Meeting June 2015
James T. Case MS, DVM, PhD, FHL7, FACMI

Health Program Specialist, SNOMED CT
National Library of Medicine
2014 Regenstrief Institute and James Case
Disclaimer
The views and opinions expressed do
not necessarily state or reect those of
the U.S. Government, and they may
not be used for adver?sing or product
endorsement purposes.
Acknowledgements
LOINC Development Team
Clem McDonald, Dan Vreeman, Jami Deckard, David

Baorto, Katy Holck, Swapna Abhyankar, Theresa
Pritchard, Rachel Fuhr, Sara Armson
RELMA Development Team
John Hook, Anandhi Sowmyan, James Dennis
LOINC CommiLee
Supporters
NLM, Regenstrief InsJtute, Regenstrief FoundaJon,

APTA, RSNA, the LOINC Premium Members and Donors
What will we cover today?
Overview of LOINC
Reviewing new RELMA features!
Installing RELMA
SeNng personal preferences
Loading a Local ObservaJon File (LMOF)
Searching for a LOINC Term
Preparing LMOF for Mapping
Review of Map Screen FuncJons
SeNng Search Limits
Mapping Local Terms to LOINC
Viewing LOINC Term Details
Proposing/SubmiNng New LOINC Terms
ExporJng/PrinJng Mapped Terms
Mapping your own LMOF data
Why are we doing this?

Goals of Health Information Standards
Interoperability the ability to exchange

informaJon between organizaJons
Comparability the ability to ascertain the
equivalence of data from dierent sources
Data Quality the measurement of
accessibility, completeness, accuracy and
precision (and more)
Levels of Interoperability
Basic allows data to be exchanged between
computer systems
Word processing documents, text messages
Func?onal describes the standard syntax

(format) of the data
Document templates, forms, data structures

Message standards
Seman?c requires use of standardized

content (vocabularies) within the data
structure
Comparability
Meaning of the data is consistent when shared
among dierent parJes
Erysipelas Human skin disease; Streptococcus Grp A

Erysipelas Animal SepJcemia/dermaJJs; Erysipelothrix
rhusiopathiae
Common terminology required
Should work in the background
Words are not enough
Codes uniquely idenJfy terms

Vocabulary specialized, precise terms that remove
ambiguity
Ontology describes nature of enJJes and their relaJons
ClassicaJon groups related terms by category
Potential Uses of Health Data are

Constrained by Data Quality Factors
Data quality issues
Dierent for client/paJent communicaJons vs.

clinical decision support vs. epidemiological
analysis
O\en constrained by external forces
e.g. criteria for diagnosis o\en diers from the criteria

for reporJng
UnidirecJonal eect of data consolidaJon
Detailed General
General Detailed
This is a problem even

when standard
terminologies are used
The Problem
In a_empJng to arrive at the truth, I have applied
everywhere for informaJon, but in scarcely an
instance have I been able to obtain hospital
records t for any purpose of comparison. If they
could be obtained, they would enable us to
decide many other quesJons They would show
[subscribers] how their money was being spent
[and] what amount of good was really being done
with it
Florence Nightingale - Notes on a Hospital, 1873
Test comparisons
What you see in the order list
Lab A
Lab B
Test Name: Lyme Disease Serology

Measures: B. burgdorferi Ab IgG
Method: ELISA
Scale: quan?ta?ve
e.g.: Titer 1:40
Test Name: Lyme Disease An?body

Measures: B. burgdorferi Ab IgM
Method: Immune blot
Scale: qualita?ve
e.g.: Posi?ve
LOINC Code = 5062-5
LOINC Code = 6321-4
Why LOINC?
Within one laboratory, local jargon terms
may be used which are usually well
understood between colleagues, but
would not be suciently widely known for
communicaJon with the outside world.

U. Forsum et al., Pure Appl. Chem 72:555-745, 2000 Proper3es and Units in the Clinical
Laboratory Sciences Part VII. Proper3es and Units in Clinical Microbiology

LOINC 101
Emphasis on Laboratory
LOINC
Anatomy of a LOINC Term

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

NOT part of a LOINC Name

Reason for the test (why it was ordered or the disease it
diagnoses)
TesJng instrument
Specic details about the specimen
Priority (e.g. STAT)
Where tesJng was done
Who did the test
Test interpretaJon
Pricing or cost
Anything not part of naming the test
Things from other elds in an HL7 arJfact
Component/Analyte
The substance or enJty that is measured,
evaluated, or observed
- Sodium
- Glucose
- Brucella sp. organism
- Inuenza A Virus anJgen
- Cytomegalovirus Virus anJbody
- Lipids.Total
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
Component Structure
Analyte Name^Challenge^Adjustments
Formal analyte name
Calcium
Specify subanalytes
May have subclasses
1H post 100 g Glucose PO
Challenge
Two parts separated
by post
Adjustments
Coronavirus Ag
Calcium.ionized
<time delay>post<challenge type>
Adjusted to pH 7.4
Property
the most dicult LOINC axis
The characterisJc or a_ribute of the analyte that is

measured, evaluated, or observed
Major Categories
Mass: ObservaJons reported with mass (milligrams, grams, etc.) in the

numerator of their units of measure
Substance: ObservaJons reported with moles or milliequivalents in the
numerator of their units of measure
Cataly?c ac?vity: ObservaJons that report enzymaJc acJvity
Arbitrary: Results that report arbitrary units in the numerator of their units
of measure (slowly being reJred)
Threshold: Results that represent the relaJon between a value and some
established limit or cut-o
Number: Counts
5193-8:Hepatitis B2014
virus
surface Ab:ACnc:Pt:Ser:Qn:EIA
Regenstrief Institute and James Case
Property
the most dicult LOINC axis
Combine Major Categories with Subtypes for Full Property
MCnc mass concentraJon (mass/unit vol; e.g. mg/dL)

MCnt mass content (mass/unit mass; e.g. mg/Kg)
NCnc number concentraJon (number/unit vol; e.g. num/mL)
TmStp Jme
CCnc catalyJc concentraJon (acJvity; e.g. kat/L)
Prid presence or idenJty
Imp impression/interpretaJon
Find subjecJve or objecJve observaJon
Type Kind-of
virus
Common Property Issues

Fraction versus Ratio
Frac?on = Part/Whole
NFr: % Eosinophils / leukocytes
SFr: % HGB which is A2

Ra?o = mulJple analytes from same system
MCrto: BUN/CreaJnine in serum

Rela?ve Ra?o = measures from dierent system
RelRto: Albumin.pericard d/Albumin.SerPl
Important property changes

ACNC was always a placeholder
For P/N results, changed to Threshold

AddiJonal migraJons occurring gradually
LOINC IDs being retained
Flavors of Threshold Property
ThrSCnc Threshold Substance ConcentraJon

ThrMCnc Threshold Mass ConcentraJon
ThrACnc Threshold Arbitrary ConcentraJon
PR vs PRID
Presence or absence of an analyte now represented as

PR (presence)
For nominal results, property is sJll PRID
Timing*
The interval of Jme over which the observaJon or
measurement was made
Pt - at a point in Jme
12H - a twelve hour collecJon
24H - a twenty four hour collecJon
*non-Pt Jmings are usually associated with Rate Property

virus
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
virus
System Structure
System^Super System
Super System
PaJent is the default

Used to indicate
blood product unit

bone marrow donor
fetus
818-5:A Ag:ACnc:Pt:RBC^BPU:Ord:
54417-1:ABO+Rh group:Type:Pt:Bld^fetus:Nom:
photo via Xurble
Scale
Qn
Quantitative
continuous numeric
can have operators (<,>)
Ord
Ordinal
Ranked set (1+, 2+, 3+)
Nom Nominal
photo via puuikibeach
unranked collection
Taxonomy (e.g. bacteria)
Nar
Narrative
virus
Scale (Special)
OrdQn Ordinal or QuanJtaJve
Primarily used for anJmicrobial observaJons e.g.

MIC reported as resistant, intermediate, suscepJble
or as the mm diameter of the inhibiJon zone
Use is discouraged in other contexts
MulJ structured text globs
e.g. chromatography output

Use is discouraged
Doc Clinical documents

Set Clinical a_achments (headers)
Method
Only needed if interpretaJon aected
Dierent normal ranges

Test sensiJvity/specicity
Generally listed at the generic

level
AggluJnaJon
Enzyme Immunoassay
Probe with target amplicaJon
virus
Hierarchies
LOINC Class
one per term
arbitrarily assigned
One for each LOINC axis

MulJ-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) idenJed

VDRL Treponema pallidum Ab
Urinalysis lots of dierent things
You must know the specics of the component being

tested for (what actually being measured?)
The quesJon (what am I measuring? e.g. Glucose) is
not the answer (e.g. 90 mg/dl)
You are mapping the quesJon, not the answer!
Need to get the observaJon/result boundary correct.
Sample values help substanJally

What is in LOINC?
Content
Term structures
Submi_ed units, Example UCUM units
aiming toward preferred units sorJng
Synonyms
Answer lists (increasing number)
Text descripJons links to info sources
about individual tests
Panel structures
Foreign language translaJons
And much more


RELMA
Regenstrief LOINC Mapping Assistant
Download of latest version

The latest version of the installaJon le
may be downloaded from:
h_ps://iu.box.com/relma69
Purpose of Tutorial
Eliminate need to read the Users Manual
Become familiar with RELMA features
Provide some insight into mapping Jps/piyalls
Help begin the mapping process for your
insJtuJon
Hang with some really cool folks
RELMA Functions
LOINC les and indexes
Manual and automated mapping funcJons
RELMA tools transform local words in local le
User creates le of local term/name and codes
Assigns LOINC term to local test/ba_ery code

Common tests subset to speed mapping
Context sensiJve hierarchies for local use.
Flexible Google-like search funcJons
New in This Version (Rel. 6.9)

End of support for Windows XP.
Microso\ ends support or XP in April 2014.

No longer tesJng RELMA on Windows XP.
The December 2015 release (version 6.12) of RELMA will not
run on Windows XP.
Proxy support.
Congure it in the Windows Internet OpJons applet. (see

RELMA manual for details)

New search restricJons added (See "Advanced Search
Syntax" secJon of the user guide ):
"PanelType
"LForms"
Allows limitaJon of search results to a panel type categories.
True/false restricJon - indicates if LOINC code can be viewed in

LForms data widget tool.
"AssociatedObservaJons
Contains one or more LOINC codes that point to an addiJonal list of

terms associated with an observaJon.

"Export full panel structure to Excel" opJon
available on Search tab grid and the grid on the
Mapping tab.
New column added to search grids - "LForms".
A hyperlink that opens your default browser to the specied

URL. Not all rows will have this eld populated.
"Panels, Forms & Surveys" screen has been completely

restructured.
"Associated observaJon" terms displayed on
comprehensive detail pages when available.
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 les (panels, forms, top 2000, etc.)
LOINC User guide; RELMA User Guide
Tools to assist language translaJons by part
Tools for building databases to map from HL7
messages
Guidance documents for mappers

RELMA Highlights
Browse-able hierarchies of LOINC parts
Display search results in tree view
Enhanced details view of terms/parts
References
DescripJons
Sample units
Empirically-derived common test list

Empirically-derived common order list
Special features for panels/forms
Enhanced export/copy-paste opJons
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 installaJon directory
Life will be easier if you accept the default
Two database les installed
RELMA.MDB LOINC Terms Database

LMOF3.MDB Local Master ObservaJon File
Two sample les included

Run from Start (All) Programs Regenstrief RELMA
File Locations
Database and Ancillary Files
Windows Vista = C:\Users\Public\Documents\RELMA\

Windows 7, 8 = C:\Users\Public\Public Documents\RELMA\
Sample les
Windows Vista = C:\Users\Public\Documents\RELMA\Samples\

Windows 7, 8 = C:\Users\Public\Public Documents\RELMA
\Samples\
Running RELMA
Version 6.9
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
Set User Preferences

Select User Preferences
From the File Menu
...or from Welcome Screen
Set User Preference Dialog

Local Term Backup Tab
File Locations:
(See prior slide for location)
Startup Screen Preference
User Map Screen Preferences

Click Map Screen Tab
Auto create search terms
Include/Exclude Battery
Terms
Add comments on Mappings
User Detail Pages Preferences

Download detail pages from LOINC.org
Request Submission Preference

Preferred method of request
submission
Local Backup Preferences
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 le from your local test

catalog (good choice)
Import Excel le
Load directly from HL7 v2.x messages
Pulls data from OBR and OBX segments

Stores NTE segment data
Constructing a Local Dataset

Create extract of your test catalog with:
Ba_ery/Panel Code
Ba_ery/Panel DescripJon or Name
*Local Code
*Test DescripJon or Name
Include Method if Important
Units
Example Values
Laboratory SecJon
Creating Delimited ASCII File

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

Can dene your own
Fields can be in any order

Minimum required elds
Local Code
Local DescripJon
Units (highly recommended)
Entering New Local Terms

into RELMA
Manual Enter/Edit
View/Add/Edit Local Terms
Edit Term Dialog
Edit\Add\Delete Terms
Export Terms
User assigned tags
Text alignment option
Print Preview List
Export Local Term File
Export to Microsoft Excel

or Text File
Export assigned tags
Delimiters supported:
Tab, comma, semicolon, bar (|)
Add Local Term

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

Calcium
Tags panel only appears if

tags have been assigned
Enter Keyword from any
Open or close tag list
Field
Return to Full List
Using tags to gilter local terms
Congigure output prior to

viewing and printing
Print preview local term

gile
Print Preview Local Term File

Only prints selected rows
Steps to Import Local Terms

1. Click Import Local Terms Bu_on from Main Menu
a) File>Import Local Terms from Delimited File
2. Locate your local terms text le

3. Name your Working Set (Mandatory)
a) LMOF database can contain mulJple work sets
4. Dene default secJon (OpJonal)

5. IdenJfy le delimiter
6. Assign elds to LMOF a_ributes
a)
b)
Ignore elds you dont need

Combine elds if needed
7. Check Case-sensiJve 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 iO
Sample
giles
stored
n pen
RELMA Directory
Open File in RELMA

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

LOINC Workshop OBR
Ready to Import
Minimum assignments
Now you can click the

Import button!
Import tags
You can include tags in your import le
that allow you to categorize your local
terms
Fields in import funcJon allow assignment
of Tag with
Local term gile with added tags
Tag terms
Assign tag values
Tag with gield

assignment
Tagged local terms
Imported tags
Post-Processing of Local File

A\er import, RELMA Searches for terms
(words) that it does not recognize
Stored in a le for future reconciliaJon
Importing Excel gile
Excel giles now appear

along with text giles
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
AutomaJcally make dataset of:
OBR ID
OBR descripJon
OBX ID
OBX descripJon
Sample of results with
Real values
Units
Abnormal ags
Normal ranges
Generate Local term gile from HL7 messages
Select Import Terms from

HL7 File
Select File to Import
Select HL7 File
Specify HL7 File Name and Sample Size
Skip import of
sample values
Name the Local Term
File (working set)
Select the number of

sample values
Select which codes to store
HL7 Messages Data Statistics
New Terms added to LMOF
Click on Edit Term to see

Sample Data
New Battery Code
Sample Results for Observation

New Test Code
Sample Values from

Messages
Lenny LOINC says:

Load the Sample Files
Into RELMA now!
Import the two sample les
provided
Import_Sample_OBR.txt
Contains ba_ery code and

descripJon
Sample_HL7.HL7
Contains test code and

descripJon and sample values
Create 2 working sets

Load your personal data set
Cleaning your data
Preparing your Data for Mapping

Improve mapping success by:
Expanding abbreviaJons
Standardizing colloquial terms
Ignoring administraJve terms
Standardizing Jme references
Can be done prior to imporJng

Be_er to use tools built into RELMA
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
Replacement
LMOF AOptions
ttribute
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 le or

your own data, take 15-20
minutes to clean up these
unrecognized terms
Searching for LOINC Terms
Comprehensive Search
Only Tool
Search Window
Help File
Enter Search
Terms
Limit to
Specigic Units
Use different
logic
Restrict Limits
Search Window
Common Tests rank
Common Tests selected
RELMA Search Helpgile
Context Menu
Right click to bring

up context menu
Changed search function Max words
Large number of
Restricting to Common
results
labs regines further
Keyword
ComponentWordCount
restricts word count
Search function - Answerlist
Large number of
results
Restricting to terms that

have answer lists
Answerlist details
New advanced search syntax

Paneltype
Classies LOINC panel term in categories

LForms
This true/false eld indicates whether or
not the LOINC term is available for viewing
in the LForms data widget tool.
Restricting to terms that

have answer lists
Lforms widget demo

AssociatedObservations
AddiJonal terms that are related to a order
term.
Mapping Local Terms
Mapping Local Terms

Select your Working Set to Map
File>Select Local Term File to Process
Select Map Local Terms to LOINC from
Welcome Screen
Select the subset of terms to work with:
All
Mapped
Unmapped
Set your Search Limits
Set Search Limits
Bu_on
Standard Mapping Window Features
Customizable grid
View details of LOINC term
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
User assigned tags
Enter local term number
Quick select button list
Custom Grid Congiguration
Congigure Grid
Select elements to display
Reorder grid elements
Visually resize elements

Reset Default Congiguration
Quick choice buttons
Viewing LOINC term detail
View Local Term Details

Can scroll down a single
formatted page
Select level of detail to
display
Can scroll through

returned subset of
terms
Change text size
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
CANINE DISTEMPER VIRUS IF
Enter keywords here

Clear all
input gields
Navigate through
the local terms
Tabbed Access to Functions
Navigate to Functions
from Mapping Page
Switch between Grid and

Tree Views
Tree View
Tree View
Results displayed hierarchically
Dened by the mulJ-axial hierarchy in search

restricJons (covered later)
Map to a term in tree by clicking Map bu_on

or double clicking term
Only to rows that have LOINC Codes
Tree View
Cannot map to
terms
representing
LOINC parts
Can map to terms

with LOINC Codes
Tree Navigation
Buttons
Assigning a LOINC Map
Click Map Button

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

from context menu
Panel Children
Congigure Export Options
Output Options
Include
column headers
Save Congiguration
and/or Export
Excel Export Format
Linked answer lists

Adds answer list IDs to the answer tab of a
panel export
Allows linkage using the AnswerlistID with
the LOINC codes and the answer to see
which answers go with a specic LOINC
Search for a panel
Search for panel or

LOINC code
Find the panels

associated
Get panel details and export
Export the full panel

structure
Detailed answer data
LOINC code
AnswerListID
Answer String
Answer tab
More on Searching
Search Screen
Basic Search Syntax

Special
Character(s)
Example
Deni?on
Inuenza virus A
Linked terms must appear together
AND
Morphine AND
Opiates
Both terms must appear in the search result

term
OR
Inuenza OR
Parainuenza
Either or both terms must appear in the

search result term
NOT
Inuenza NOT equine
Excludes terms with the word following the

NOT. Cannot be used alone.
Gluc?se
(glucose,glucase)
SubsJtutes a single character in the string.

Cannot be used as the rst character; cannot
be used in phrases
Gluc*se
(glucose,
glucuronidase, etc.)
SubsJtute mulJple characters in the string.

Cannot be used as the rst character; cannot
be used in phrases
Search Qualigiers
Detailed help available

Includes Glucuronidase,
Glucosidase,
Glucosylceramidase, etc.
Combining Search Terms
Exclude Glucosidase
Reduced number of terms
Advanced Search Syntax

based on Google-like search syntax
Parameter
Descrip?on
Term must be included in search
Term must be excluded from the search
( )
Group terms for subquery (i.e. A OR B; A AND B)
Fieldname:
Limit term search to the associated eld (e.g. Component: glucose)
Fieldname:()
Group mulJple terms in a single eld
Fuzzy search (e.g. Hemoilus~)
Proximity search for mulJple terms (e.g. funcJon panel~1)
{}, []
Upper and lower bounds; {} exclusive, [] inclusive
Special character escape
Applying advanced search
91 terms
33 terms
19 terms
8 terms
Limiting Searches
Setting Search Limits

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

Controls features including:
Limit to LOINC terms compaJble with submi_ed units

Forced match with any specimen contained in name
Method-less terms only
Restrict by class type
Remove lateralized terms
Use carefully or search may not be successful

(Note parallel control switches at bo_om of screen)

Click Hierarchy & Search

Limits Tab
Setting search limits

Can also set most of them by toggling bu_ons
at the bo_om of the screen
Toggle Buttons
Search Constraints
Attribute trees
Limit to LOINC terms

consistent with local units
Expanded predegined,
general search constraints
Terms Consistent with Units
Only terms consistent

with mmol/L appear
Specimen
constraints
Terms Consistent with Specimen
CSF
Enter default
Specimen
Terms Consistent with Specimen
Only CSF Terms

are returned
Exclude laterality
Exclude laterality
Laterality terms
Restrict to
common orders
Restriction to common orders
Common orders
rank
Large number of
candidates
Methodless Terms
Restriction
Override Methodless Terms

Restriction
Limit to Methodless Terms
Both method and

method-less terms
Limit to Methodless Terms
Only Methodless
Terms Appear
More on Methodless Terms

Some LOINC categories do not have
methodless terms
Checking methodless only will remove these
from view on results grid
Checking addiJonal 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
You cannot map to

deprecated LOINC terms
The map button is grayed
out if one of these terms
is selected
Discouraged LOINC Terms appear as an

inverted triangle
Deprecated LOINC Terms appear as
Strikethrough Text with a Do Not
Symbol
Favor Property Restriction
Favor one type of

property over others
All other components

being equal MCnc
only will be displayed
Order/Observation Restriction
Order or Observation
preference
LOINC Hierarchies Class Tree
Three top-level
branches
Tree Navigation
Buttons
Before Class Restriction

Many terms have class
of CHAL
Large number of
candidate terms
Search Trees
Restrict eligible tests

to non-challenge
chemistry tests only
Following Class Restriction
Only Non-Challenge
Chemistry tests
returned
System Hierarchy
Component Hierarchy
Click on details for more
information about the
selection
Show the LOINC Codes

associated with these
components
Details Screen LOINC Part
Show Associated LOINCs
LOINC Term Details Screen
Tree Export Tools
Export according to
Congiguration
Congigure Export Format
Tree Export Congiguration
RELMA - Tree Features

All trees operate the same way
Shows terms spelled out
Can expand and collapse parts or all of tree.
Tree is string searchable
Search can be based on one or more
branches of a tree with or without other
criteria
Use Clear Most Limits bu_on on Mapping
Screen to remove all tree selecJons
LOINC Part Search

Same look as term search
Uses same Google-like query language
Extremely fast
Include and exclude criteria
ParJal string matching (using wildcards)
LOINC CLASS values may now be search

using "ClassList:<searchterm>" eld
Demo
Campylobacter fetus, not Ab

LOINC Answer List Search
Nominal LOINC terms are now required

to be submi_ed with answer lists.
Finding answer lists and the use of them
can be done with Answer List Search tab
Answer List Search
Answer Lists associated with

LOINC term
New! Revised and expanded

answer list export options
Navigating through the

Mapping Process
LOINC Mapping Tactics

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

Try using method-less terms rst
Specic methods can be transmi_ed in:
OBX17 (v2.x), ObservaJon.methodCode (v3.0)
Examine local units or real results to verify

correct property and scale
ProperJes are rarely disJnguishable in test names
You dont have to do it all at one siNng
Use the Unmapped funcJon to return where you

le\ o
With every release - Update previous mappings

to idenJfy deprecated terms
Common Mapping Issues

Locally Dened Test Name Ambiguity
Reuse of local test code
Analyte-free Local Test Names
(Miscellaneous serology, PCR)
Incongruent Value sets (Scale ambiguity)

Result vs. InterpretaJon
Available LOINC Terms too Specic/General
Panel vs. Discrete Test
Common in Microbiology
Using your Mapped Terms

Print results of LOINC Mapping
Export to File
Congigure Export Format
Context Sensitive Export

Congiguration
LMOF Export Congiguration
Select Export Format
Select Fields to Export

Save Congiguration and
Export
Print Mapped Terms from View/Add/Edit Menu
May highlight terms to be

printed
Click Print button to Preview

output
Formatted Report Output
Click Print button to output

formatted report
Excel Export
Lab Auto Mapper
Run in batch mode to nd N- closest terms

Can then use this output to do nal mapping
Again units are VERY important
Can pick all limits available to regular mapping
Picking the Lab Auto Mapper
Lab Auto Mapper Start Screen
Can restrict search to

common tests
Maximum number of terms

to return
Lab Auto Mapper Start Screen
Local test code
Terms used for

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

Select Term Set
Direct export to
Excel
Select Delimiter
Check Fields you

wish to export
Select gile location

Other RELMA
Features
Panels, Forms and Survey Review

Review Panels, Forms and
Surveys
Review Panels, Forms and

Surveys
Panels, forms and surveys

revised display
Expand category to
see panels
Double-click
panel test to see
components
Expanded Panel Detail
Expanded Clinical Panel
Clinical Panels
35089-2, 35090-0
Find where a term has

been used
LOINC Term Panel Usage
HIPAA Attachments
View Various HIPAA

Attachments
HIPPA Attachment Tree
Expanded Attachment Data
Cant gind 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 nd and revise words not in RELMA
Local units not in RELMA
Units are GREAT discriminators

You may have tests that need to be added to
LOINC
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 localizaJons
Is the disJncJon really important?
Supply sucient annotaJon to jusJfy the new term
Package inserts, sample reports (email to Regenstrief)

The more the be_er!
Construct new terms within RELMA
File>Propose a new LOINC
Linked to the trees to allow browsing
Can review and submit them to LOINC from within

RELMA
Propose new LOINC terms
Select Propose a
new LOINC
Required gields in
red

Navigate through
proposed terms
Create new term,

save current term
or Exit form
Preview Proposed Terms
Review your new

terms
Review Proposed Terms

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

fully editable
Direct submission
via web
Submit Proposed Terms

Add additional
information, if
necessary
Add attachments
Submitting New Terms

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

Click the Propose
Term button
Select your closest

match
Use Existing Terms as Template
All required
components gilled in
Using LOINC and SNOMED

Together
Where do LOINC and SNOMED Fit?

Remember:
LOINC represents the quesJon:
Is there any Botulism toxin in my specimen?

(33708-9)
Organisms idenJed in specimen? (634-6)
SNOMED represents the answer:
NegaJve (SCTID 260385009)

E. coli O157:H7 (SCTID 103429008)
Where do LOINC and SNOMED Fit?

In an HL7 message, LOINC may be used:
In OBR-4 (Universal Service IdenJer)

In OBX-3 (ObservaJon IdenJer
SNOMED may be used:
In OBX-5 (where nominal values are needed)

Almost anyplace else in an HL7 message where
coded values are needed
OBX: With a Coded Value

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

identigies the data in
OBX-5
(Listeria culture)
OBX-5: Data
A
c ode
for L.
monocytogenes
HL7 2.5 Example (ER-7 format)

MSH|^~\&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01|
LABGL1199510221838581| P| 2.3||| NE| NE
PID||| 6910828^First
Y^ C8||
Newman^
Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^
Order
OBR
Whatmeworry^(Culture
UT^ 85201^^
773789090
and ID)P||(
555) 777- 6666|( 444) 677- 7777|| M||
First
Result Value
(SNOMED)
OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult
^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^
Second Order OBR
UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN
(Susceptibility)
OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium
^SCT|||||| F||| 199812292128|| CA20837
OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility
First Result Description
Second
First Result(s)
esult

Panel^
LN||| 199812300934||||||||Bacterial
isolate| IN2973^ Schadow^
OBX
(
LOINC)

(Culture
OBXs
and
ID) MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^
Gunther^^^^
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
Q and A Session
Exercise
Map your own data

2015 06 03 - LOINC Workshop

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Using

James T. Case MS, DVM, PhD, FHL7, FACMI

2014 Regenstrief Institute and James Case

2014 Regenstrief Institute and James Case

Clem McDonald, Dan Vreeman, Jami Deckard, David

RELMA Development Team

John Hook, Anandhi Sowmyan, James Dennis

NLM, Regenstrief InsJtute, Regenstrief FoundaJon,

2014 Regenstrief Institute and James Case

What will we cover today?

2014 Regenstrief Institute and James Case

Why are we doing this?

Interoperability the ability to exchange

2014 Regenstrief Institute and James Case

Word processing documents, text messages

Func?onal describes the standard syntax

Document templates, forms, data structures

Seman?c requires use of standardized

Erysipelas Human skin disease; Streptococcus Grp A

Common terminology required

Should work in the background

Words are not enough

Codes uniquely idenJfy terms

Potential Uses of Health Data are

Dierent for client/paJent communicaJons vs.

e.g. criteria for diagnosis o\en diers from the criteria

UnidirecJonal eect of data consolidaJon

This is a problem even

2014 Regenstrief Institute and James Case

Test Name: Lyme Disease Serology

Test Name: Lyme Disease An?body

LOINC Code = 5062-5

LOINC Code = 6321-4

2014 Regenstrief Institute and James Case

2014 Regenstrief Institute and James Case

Anatomy of a LOINC Term

There are six major LOINC axes

NOT part of a LOINC Name

1H post 100 g Glucose PO

<time delay>post<challenge type>

The characterisJc or a_ribute of the analyte that is

Mass: ObservaJons reported with mass (milligrams, grams, etc.) in the

Combine Major Categories with Subtypes for Full Property

MCnc mass concentraJon (mass/unit vol; e.g. mg/dL)

Common Property Issues

Important property changes

For P/N results, changed to Threshold

Flavors of Threshold Property

ThrSCnc Threshold Substance ConcentraJon

Presence or absence of an analyte now represented as

*non-Pt Jmings are usually associated with Rate Property

photo via AlishaV

PaJent is the default

blood product unit

2014 Regenstrief Institute and James Case

photo via Xurble

photo via puuikibeach

Primarily used for anJmicrobial observaJons e.g.

MulJ structured text globs

e.g. chromatography output

Doc Clinical documents

Dierent normal ranges

Generally listed at the generic

One for each LOINC axis