2013 06 06 - Laboratory LOINC and RELMA Workshop

Using
RELMA
OrIn Search of the Missing LOINC
Laboratory LOINC Meeting June 2013
James T. Case MS, DVM, PhD, FHL7, FACMI

Health Program Specialist, SNOMED CT National Library of Medicine
2013 Regenstrief Institute and James Case
Acknowledgements
LOINC Development Team
Clem McDonald, Dan Vreeman, Jami Deckard, David Baorto, Kelly Malo8
RELMA Development Team

John Hook, Anandhi Sowmyan, James Dennis
LOINC Commi7ee Supporters: NLM, Regenstrief InsEtute,

Regenstrief FoundaEon
What will we cover today?

Overview of LOINC Reviewing new RELMA features! Installing RELMA SeKng personal preferences Loading a Local ObservaEon File (LMOF) Searching for a LOINC Term Preparing LMOF for Mapping Review of Map Screen FuncEons SeKng Search Limits Mapping Local Terms to LOINC Viewing LOINC Term Details Proposing/SubmiKng New LOINC Terms ExporEng/PrinEng Mapped Terms Mapping your own LMOF data
Why are we doing this?Goals of Health Information

Standards
Interoperability the ability to exchange informaEon between organizaEons 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
FuncConal describes the standard syntax (format) of the data

Document templates, forms, data structures Message standards
SemanCc requires use of standardized content (vocabularies) within the data structure
Comparability
Meaning of the data is consistent when shared among dierent parEes

Erysipelas Human skin disease; Streptococcus Grp A Erysipelas Animal SepEcemia/dermaEEs; Erysipelothrix rhusiopathiae Should work in the background
Common terminology required
Words are not enough

Codes uniquely idenEfy terms Vocabulary specialized, precise terms that remove ambiguity Ontology describes nature of enEEes and their relaEons ClassicaEon groups related terms
Potential Uses of Health Data are Constrained by Data Quality Factors

Data quality issues
Dierent for client/paEent communicaEons 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 reporEng
UnidirecEonal eect of data consolidaEon

Detailed General General Detailed

The Problem
In a8empEng to arrive at the truth, I have applied everywhere for informaEon, 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 quesEons 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
Test Name: Lyme Disease Serology Measures: B. burgdorferi Ab IgG Method: ELISA Scale: quanCtaCve e.g.: Titer 1:40
Lab B
Test Name: Lyme Disease AnCbody Measures: B. burgdorferi Ab IgM Method: Immune blot Scale: qualitaCve e.g.: PosiCve
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 communicaEon with the outside world.
U. Forsum et al., Pure Appl. Chem 72:555-745, 2000 Proper3es and Units in the Clinical 2013 Regenstrief Institute and James Case
LOINC
101Emphasis on
Laboratory LOINC
Anatomy of a LOINC Term

5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA LOINC Code Component Property Measured Timing System Scale Method 5193-8 HepaCCs B virus surface Ab ACnc Pt Ser Qn EIA
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)
TesEng instrument Specic details about the specimen Priority (e.g. STAT) Where tesEng was done Who did the test Test interpretaEon Pricing or cost Anything not part of naming the test Things from other elds in an HL7 message
Component/Analyte
The substance or enEty that is measured, evaluated, or observed
- Sodium
- Glucose - Brucella sp. organism - Inuenza A Virus anEgen Cytomegalovirus Virus anEbody Lipids.Total
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
Component Structure
Analyte Name^Challenge^Adjustments Formal analyte name
Specify subanalytes May have subclasses
Calcium
Coronavirus Ag Calcium.ionized
Challenge
Two parts separated by post

1H post 100 g Glucose PO

<time delay>post<challenge type>
Adjustments
Adjusted to pH 7.4
Property
the most dicult LOINC axis
The characterisEc or a8ribute of the analyte that is measured, evaluated, or observed

Major Categories Mass: ObservaEons reported with mass (milligrams, grams, etc.) in the numerator of their units of measure Substance: ObservaEons reported with moles or milliequivalents in the numerator of their units of measure CatalyCc acCvity: ObservaEons that report enzymaEc acEvity Arbitrary: Results that report arbitrary units in the numerator of their units of measure Number: Counts
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA 2013 Regenstrief Institute and James Case
Property
the most dicult LOINC axis
Combine Major Categories with Subtypes for Full Property MCnc mass concentraEon (mass/unit vol; e.g. mg/dL) MCnt mass content (mass/unit mass; e.g. umol/L) NCnc number concentraEon (number/unit vol; e.g. mg/g) TmStp Eme CCnc catalyEc concentraEon (acEvity; e.g.) Prid presence or idenEty Imp impression/interpretaEon Find subjecEve or objecEve observaEon Type Kind-of
Common Property Issues

Fraction versus Ratio FracCon = Part/Whole
NFr: % Eosinophils / leukocytes SFr: % HGB which is A2
RaCo = mulEple analytes from same system MCrto: BUN/CreaEnine in urine RelaCve RaCo = measures from dierent system RelRto: Albumin.pericard d/Albumin.SerPl
Timing*
The interval of Eme over which the observaEon or measurement was made
Pt - at a point in Eme 12H - a twelve hour collecEon 24H - a twenty four hour collecEon
*non-Pt Emings are usually associated with Rate Property

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 uid tissue specied elsewhere
photo via AlishaV
System Structure
System^Super System
Super System

PaEent is the default Used to indicate

blood product unit bone marrow donor fetus
photo via Xurble
818-5:A Ag:ACnc:Pt:RBC^BPU:Ord: 54417-1:ABO+Rh group:Type:Pt:Bld^fetus:Nom:
Scale
Qn Ord Nom Nar Quantitative
continuous numeric can have operators (<,>)
Ordinal
Ranked set (1+, 2+, 3+)
Nominal
unranked collection Taxonomy (e.g. bacteria)
photo via puuikibeach
Narrative
Scale (Special)
OrdQn Ordinal or QuanEtaEve
Primarily used for anEmicrobial observaEons e.g. MIC reported as resistant, intermediate, suscepEble or as the mm diameter of the inhibiEon zone Use is discouraged in other contexts e.g. chromatography output Use is discouraged
MulE structured text globs

Doc Clinical documents Set Clinical a8achments (headers)

Method
Only needed if interpretaEon aected

Dierent normal ranges Test sensiEvity/specicity AggluEnaEon Enzyme Immunoassay Probe with target amplicaEon
Listed at the generic level

Hierarchies
LOINC Class One for each LOINC axis MulE-axial
Component | System Separate download
Panels, forms, surveys, and other paEent assessments
LOINC COLLECTIONS
photo via LuzA
Standardized Assessments and Collections
Vreeman DJ, McDonald CJ, Hu SM. Representing patient assessments in LOINC. AMIA Annu Symp Proc. 2010;832-836. PMID: 21347095 . Vreeman DJ, McDonald CJ, Hu SM. LOINC - A Universal Catalog of Individual Clinical Observations and Uniform Representation of Enumerated Collections. Int J Funct Inform Personal Med. 2010;3(4):273-291. 2013 Regenstrief Institute and James Case
IteraEvely expanded the base lab panel model to accommodate more complex a8ributes
Hierarchy of a Panel in LOINC
Purpose
Assessment instruments are widely used
and not unlike other clinical observations

LOINC could support a

master question le anduniform representation
Panels/Forms Available as Separate Download
LOINC.ORG/USAGE
A Few Tests Give Most Results
2013 Regenstrief Institute and James Case Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.
Cumulative Laboratory Observation Volume (%)
loinc.org/usage
Top 2000 Results
a.k.a. Top 300 Orders
http://loinc.org/ downloads/usage/ orders

a.k.a. Common Units of Measure
http://loinc.org/downloads/usage/units
Mapping Terms to LOINCThings to Remember

The thing ordered is not always the thing measured:

Blood Culture live organism(s) idenEed VDRL Treponema pallidum Ab Urinalysis lots of dierent things
The quesEon (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl)
You are mapping the quesEon, not the answer!
You must know the specics of the component being tested for (what is this test actually measuring?)
What is in LOINC?Content
Term structures Submi8ed units, Example UCUM units
aiming toward preferred units sorEng
Synonyms Answer lists (increasing number) Text descripEons links to info sources about individual tests

Panel structures Foreign language translaEons
Regenstrief LOINC Mapping Assistant
RELMA
Purpose of Tutorial
Eliminate need to read the Users Manual Become familiar with RELMA features Provide some insight into mapping Eps/pixalls Help begin the mapping process for your insEtuEon Hang with some really cool folks

RELMA Functions

LOINC les and indexes Manual and automated mapping funcEons Same free use as LOINC (see license) RELMA tools transform local words in local le
User creates le of local term/name and codes
Assigns LOINC term to local test/ba8ery code Common tests subset to speed mapping Context sensiEve hierarchies for local use. Flexible Google-like search funcEons
New in This Version (Rel. 6.1)

Bug xes

Fixed accessibility issues where large text did not display correctly. Fixed issue where the user was not returned to the Main Menu a]er closing the search screen. Fixed issue where mulEple forms were displaying when the user selected "Review HIPAA A8achments" from the top menu. Fixed issue where the "Common Tests" drop down list on the mapping form did not show all four opEons without the need for scrolling. Fixed issue where the search results language header did not properly show the RELMA dened preferred language.

Ability to delete a Local Term File from within the form Etled "Select Local Term File".
RELMA will not allow the user to delete the provided SAMPLE le.
Will not a8empt to connect to the internet if user has chosen to NOT show the log-in screen on RELMA start-up. RELMA now temporarily displays a warning text within the search text box when a search does not return search results.

Provides a more user-friendly message for LMOF3.mdb privilege error messages. Provide an expanded set of search exclusion criteria in the form of check boxes, which allows for mulEple-selecEon.
more detailed informaEon about these new restricEons in the user manual.
The Order/Obs constraints have been expanded with two new items:

Include subset Include unclassied


The Lucene "descripEon" eld has been expanded to include data from reference sources.
Results in a substanEal increase in the amount of disk space used by the applicaEon.
The "Export Local Term File" screen now supports direct export to a Microso] Excel spreadsheet.
LOINC Web Site
Whats available to download?

RELMA - mapping and browsing tool

HL7 message converter- Makes a database suitable for mapping HL7 lint (nds bad messages)
LOINC database and spreadsheets Accessory les (panels, forms, top 2000, etc.) LOINC User guide; RELMA User Guide Tools to assist language translaEons by part Tools for building databases to map from HL7 messages New 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 DescripEons Sample units
Empirically-derived common test list Empirically-derived common order list Special features for panels/forms Enhanced export/copy-paste opEons
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 installaEon directory
Life will be easier if you accept the default RELMA.MDB LOINC Terms Database LMOF3.MDB Local Master ObservaEon File
Two database les installed

Two sample les included Run from Start (All) Programs Regenstrief RELMA
File Locations
Database and Ancillary Files

Windows XP = C:\Documents and SeKngs\All Users\Documents \RELMA\ Windows Vista = C:\Users\Public\Documents\RELMA\ Windows 7 = C:\Users\Public\Public Documents\RELMA\ Windows XP = C:\Documents and SeKngs\All Users\Documents \RELMA\Samples\ Windows Vista = C:\Users\Public\Documents\RELMA\Samples\ Windows 7 = C:\Users\Public\Public Documents\RELMA \Samples\
Sample les

Running RELMA
Version 6.1
Copyright Screen
New Feature! 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
New 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
Importing Local Terms into RELMA
4 Ways to Load LMOF Files

Direct entry into LMOF from within RELMA (painful)
Handy for individual entries/edits
Create an Access table that mimics the LMOF structure (less painful but tedious)
Appendix A: RELMA Manual
Create a delimited ASCII le from your local test catalog (good choice) Load directly from HL7 v2.x messages

Pulls data from OBR and OBX segments Stores NTE segment data
Constructing a Local Dataset

Create extract of your test catalog with:

Ba8ery/Panel Code Ba8ery/Panel DescripEon or Name *Local Code *Test DescripEon or Name
Units Example Values Laboratory SecEon
Include Method if Important
Creating Delimited ASCII File

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

Fields can be in any order Minimum required elds

Local Code Local DescripEon 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
Text alignment option
Print Preview List
Export Local Term File
New! Direct export to Microsoft Excel
Delimiters supported: Tab, comma, bar (|)
Add Local Term

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

Calcium
Enter Keyword from any Return to Full List Field
Print Preview Local Term File

Only prints selected rows
Steps to Import Local Terms

1. Click Import Local Terms Bu8on from Main Menu 2. Locate your local terms text le 3. Name your Working Set (Mandatory) 4. Dene default secEon (OpEonal) 5. IdenEfy le delimiter 6. Assign elds to LMOF a8ributes
a. b.
a) File>Import Local Terms from Delimited File
a. LMOF database can contain mulEple work sets
7. Check Case-sensiEve if needed 8. Click Import.

Ignore elds you dont need Combine elds if needed
Example Tab-Delimited File
Importing Local Files

Select Import Local Terms from Delimited File
Navigate to File Location

Select File and Click i O pen Sample jiles stored n 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!
Post-Processing of Local File

A]er import, RELMA Searches for terms (words) that it does not recognize Stored in a le for future reconciliaEon
Local Term File Options
Change Local Term File

Select the Working Set Current mapping status
New! Can delete local term set; not the active one
Alternative Pragmatic Way

Use large set of HL7 messages AutomaEcally make dataset of:

OBR ID OBR descripEon OBX ID OBX descripEon Sample of results with

Real values Units Abnormal ags Normal ranges

Generate Local term jile 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 which codes to store Select the number of sample values
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
Import_Sample_OBX.txt
Contains ba8ery code and descripEon Contains test code and descripEon
Create 2 working sets Load your personal data set

Cleaning your data
Preparing your Data for Mapping Improve mapping success by:

Expanding abbreviaEons Standardizing colloquial terms Ignoring administraEve terms Standardizing Eme references
Can be done prior to imporEng Be8er to use tools built into RELMA
RELMA Cleaning Tools

Use this tool to edit unknown terms
Review Unknown Local Terms

May Re-Scan File for Unknown Terms
Replace Local Terms
Assign Replacement LMOF A Options 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 or OBX sample les, take 15-20 minutes to clean up these unrecognized terms
You may use your own data if you wish.
Searching for LOINC Terms
Comprehensive Search Only Tool
Search Window
Help File
Enter Search Terms
Limit to Specijic Units Restrict to Common Limits
Use different logic
Search Window
Common Tests selected
Common Tests rank
RELMA Search Helpjile
Context Menu
Right click to bring up context menu
Changed search function Max words
Large number of results
Keyword ComponentWordCount restricts word count
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 Bu8on

Standard Mapping Window Features

Customizable grid View details of LOINC term Sort by column

Click column Custom Sort
Print or export results grid Spell check squiggly line to signify words not known to RELMA
Mapping Screen
View or edit local term
Enter local term number
Quick select button list
Custom Grid Conjiguration
Conjigure Grid
Select elements to display Reorder grid elements
Visually resize elements Reset Default Conjiguration
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
Match units selected
Number of matching records found
CANINE DISTEMPER VIRUS IF
Enter keywords here Clear all input jields
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 mulE-axial hierarchy in search restricEons (covered later)
Map to a term in tree by clicking Map bu8on or double clicking term
Only to rows that have LOINC Codes
Tree View
Can map to terms with LOINC Codes Tree Navigation Buttons Cannot map to terms representing LOINC parts
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
Conjigure Export Options
Output Options Save Conjiguration and/or Export Include column headers
Excel Export Format
More on Searching Search Screen
Basic Search Syntax

Special Character(s) Example Definition AND Influenza virus A Morphine AND Opiates Linked terms must appear together Both terms must appear in the search result term
OR
Influenza OR Parainfluenza Influenza NOT equine
Either or both terms must appear in the search result term Excludes terms with the word following the NOT. Cannot be used alone. Substitutes a single character in the string. Cannot be used as the first character; cannot be used in phrases Substitute multiple characters in the string. Cannot be used as the first character; cannot be used in phrases
NOT
Gluc?se (glucose,glucase) Gluc*se (glucose, glucuronidase, etc.)
Search Qualijiers
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 + () Fieldname: Fieldname:() ~ ~ {}, [] \ 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) Limit term search to the associated field (e.g. Component: glucose) 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
Setting Search Limits

Narrows search to specic subset of LOINC terms Reduces number of candidate terms Limits can be applied to all components Component a8ribute can be further restricted by number of words Tree structure allows for hierarchical constraints

General Search Constraints

Controls features including:

Limit to LOINC terms compaEble with submi8ed units Forced match with any specimen contained in name Method-less terms only Limit to components/analytes with N or fewer words in their name Pop up search Eming staEsEcs a]er each search (Note parallel control switches at bo8om of screen)
Use carefully or search may not be successful
Click Hierarchy & Search Limits Tab

Setting search limits

Can also set most of them by toggling bu8ons at the bo8om of the screen
Toggle Buttons
Search Constraints
Attribute trees
Limit to LOINC terms consistent with local units
New! Expanded predejined, 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 addiEonal 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 2013 Regenstrief Institute and James Case
Favor Property Restriction
Favor one type of property over others
All other components being equal MCnc only will be displayed
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 Conjiguration
Conjigure Export Format
Tree Export Conjiguration
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 bu8on on Mapping Screen to remove all tree selecEons

LOINC Part Search

Same look as term search Uses Google-like query language

Extremely fast Include and exclude criteria ParEal string matching (using wildcards) Campylobacter fetus, not Ab
Demo
LOINC Answer List Search
Nominal LOINC terms are now required to be submi8ed 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
LOINC Mapping Tactics

Limit eort to one lab secEon at a Eme and focus experEse Chemistry and hematology will be easiest For manufactured assays, use package insert as source informaEon Sample results give clue to property and scale Consider prioriEzing 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 transmi8ed in:
OBX17 (v2.x), ObservaEon.methodCode (v3.0)
Examine local units or real results to verify correct property and scale
ProperEes are rarely disEnguishable in test names Use the Unmapped funcEon to return where you le] o
You dont have to do it all at one siKng
With every release - Update previous mappings to idenEfy deprecated terms

Common Mapping Issues

Locally Dened Test Name Ambiguity
Reuse of local test code (Miscellaneous serology, PCR)
Analyte-free Local Test Names
Incongruent Value sets (Scale ambiguity) Result vs. InterpretaEon 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
Conjigure Export Format
Context Sensitive Export Conjiguration
LMOF Export Conjiguration
Select Export Format
Select Fields to Export Save Conjiguration 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 New! Direct export to Excel
Select Delimiter
Check Fields you wish to export Select jile 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
Panel Codes
Form Category
Government Panel Children
Expanded Clinical Panel
Clinical Panels
35089-2, 35090-0
Find where a term has been used
LOINC Term Panel Usage
Other Survey Instruments
HIPAA Attachments
View Various HIPAA Attachments
HIPPA Attachment Tree
Expanded Attachment Data
Cant jind the term you want?
Search Hints and Tips

Keywords with zero frequency are ignored
May need to rephrase use synonym Too many keywords in search uncheck some Limits applied that dont make sense
Some causes for no returned terms

E.g. Method-less tests plus Method tree set to EIA Local units not in RELMA
Did not nd and revise words 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 localizaEons Is the disEncEon really important? Package inserts, sample reports (email to Regenstrief) The more the be8er!
File>Propose a new LOINC
Supply sucient annotaEon to jusEfy the new term

Construct new terms within RELMA
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
Advanced/Simple toggle Required jields 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 NIH/NLM 301-555-1314 301-555-1315 James.case@mail.nih.gov
X X X
Choose whether to send or postpone All proposed terms fully editable
Submitting New Terms

Must supply name, organizaEon, phone and email of submi8er Must select at least one proposed term to send Congure export does not aect submission output Email resulEng 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 jilled in
Using LOINC and SNOMED Together
Where do LOINC and SNOMED Fit? Remember:

LOINC represents the quesEon:

Is there any Botulism toxin in my specimen? (33708-9) Organisms idenEed in specimen? (634-6) NegaEve (SCTID 260385009) E. coli O157:H7 (SCTID 103429008)
SNOMED represents the answer:

Where do LOINC and SNOMED Fit?

In an HL7 message, LOINC may be used:

In OBR-4 (Universal Service IdenEer) In OBX-3 (ObservaEon IdenEer
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 identijies 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

identijies 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 First Order OBR PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^ (Culture a nd I D) Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090 First Result Value (SNOMED) OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult Second Order OBR ^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^ (Susceptibility) UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837 First Result Description Second First Result(s) esult OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility OBX (LOINC) (Culture OBXs and ID) 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
Q and A Session
Exercise Map your own data

2013 06 06 - Laboratory LOINC and RELMA Workshop

Diunggah oleh

Informasi Dokumen

Hak Cipta

Format Tersedia

Bagikan dokumen Ini

Bagikan atau Tanam Dokumen

Opsi Berbagi

Apakah menurut Anda dokumen ini bermanfaat?

Apakah konten ini tidak pantas?

Hak Cipta:

Format Tersedia

2013 06 06 - Laboratory LOINC and RELMA Workshop

Diunggah oleh

Hak Cipta:

Format Tersedia

Using

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

2013 Regenstrief Institute and James Case

RELMA Development Team

LOINC Commi7ee Supporters: NLM, Regenstrief InsEtute,

2013 Regenstrief Institute and James Case

What will we cover today?

2013 Regenstrief Institute and James Case

Why are we doing this?Goals of Health Information

2013 Regenstrief Institute and James Case

Word processing documents, text messages

FuncConal describes the standard syntax (format) of the data

Document templates, forms, data structures Message standards

Common terminology required

Words are not enough

Potential Uses of Health Data are Constrained by Data Quality Factors

UnidirecEonal eect of data consolidaEon

Detailed General General Detailed

2013 Regenstrief Institute and James Case

LOINC Code = 5062-5

LOINC Code = 6321-4

2013 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

2013 Regenstrief Institute and James Case

The characterisEc or a8ribute of the analyte that is measured, evaluated, or observed

Common Property Issues

*non-Pt Emings are usually associated with Rate Property

Ser Ser/Plas Bld Ur Flu Tiss XXX

photo via AlishaV

PaEent is the default Used to indicate

blood product unit bone marrow donor fetus

photo via Xurble

818-5:A Ag:ACnc:Pt:RBC^BPU:Ord: 54417-1:ABO+Rh group:Type:Pt:Bld^fetus:Nom:

2013 Regenstrief Institute and James Case

photo via puuikibeach

MulE structured text globs

Doc Clinical documents Set Clinical a8achments (headers)

Listed at the generic level

2013 Regenstrief Institute and James Case

Panels, forms, surveys, and other paEent assessments

Standardized Assessments and Collections

Hierarchy of a Panel in LOINC

2013 Regenstrief Institute and James Case

and not unlike other clinical observations

LOINC could support a

2013 Regenstrief Institute and James Case

2013 Regenstrief Institute and James Case

Panels/Forms Available as Separate Download

2013 Regenstrief Institute and James Case

2013 Regenstrief Institute and James Case

A Few Tests Give Most Results

Cumulative Laboratory Observation Volume (%)

Top 2000 Results

2013 Regenstrief Institute and James Case

a.k.a. Top 300 Orders

http://loinc.org/ downloads/usage/ orders

a.k.a. Common Units of Measure

2013 Regenstrief Institute and James Case

Mapping Terms to LOINCThings to Remember

You are mapping the quesEon, not the answer!

2013 Regenstrief Institute and James Case