2011 06 06 - loinc workshop and tutorial

©2011 Regenstrief Institute and James Case

Using RELMA Or…In Search of the Missing LOINC

James T. Case MS, DVM, PhD Health Program Specialist, SNOMED CT

National Library of Medicine

Laboratory LOINC Meeting – June 2011


Acknowledgements •  RELMA Development Team

•  John Hook, Karen Ahmad, Mark Fisher, Craig Kelker

•  Dan Vreeman •  Clem McDonald •  Kathy Mercer •  The Lab LOINC CommiFee •  Funding Support

•  NLM, Regenstrief InsJtute, NCI, CDC


What will we cover today? •  Overview of LOINC •  Reviewing new RELMA features! •  Installing RELMA •  SeMng personal preferences •  Loading a Local ObservaJon File (LMOF) •  Searching for a LOINC Term •  Preparing LMOF for Mapping •  Review of Map Screen FuncJons •  SeMng Search Limits •  Mapping Local Terms to LOINC •  Viewing LOINC Term Details •  Proposing/SubmiMng 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 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

•  Func7onal – describes the standard syntax (format) of the data •  Document templates, forms, data structures •  Message standards

•  Seman7c – requires use of standardized content (vocabularies) within the data structure


Comparability •  Meaning of the data is consistent when shared among different 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 •  ClassificaJon – groups related terms


Potential Uses of Health Data are Constrained by Data Quality Factors •  Data quality issues

•  Different for client/paJent communicaJons vs. clinical decision support vs. epidemiological analysis

•  O\en constrained by external forces •  e.g. criteria for diagnosis o\en differs from the criteria for reporJng

•  UnidirecJonal effect of data consolidaJon •  Detailed → General •  General → Detailed


The Problem “In aFempJng to arrive at the truth, I have applied everywhere for informaJon, 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 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

Lab A Test Name: Lyme Disease Serology Measures: B. burgdorferi Ab IgG Method: ELISA Scale: quan7ta7ve e.g.: Titer 1:40

Lab B Test Name: Lyme Disease An7body Measures: B. burgdorferi Ab IgM Method: Immune blot Scale: qualita7ve e.g.: Posi7ve

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 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


5193-‐8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

5193-‐8 LOINC Code

Hepa77s 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


What is NOT part of a LOINC Name? •  The instrument used in tesJng •  Specific details about the specimen •  Priority (e.g. STAT) •  Where tesJng was done •  Who did the test •  Test interpretaJon •  Anything that is not an intrinsic part of the name of the result

•  Other things that are carried in; •  The OBR or OBX segment •  An HL7 Version 3 ObservaJon Object


The substance or enJty that is measured, evaluated, or observed

Component/Analyte

-‐ Sodium -‐ Glucose -‐ Brucella sp. organism -‐ Influenza A Virus anJgen -‐  Cytomegalovirus Virus anJbody -‐  Lipids.Total



Component/Analyte Structure

•  Formal name of Analyte (e.g. Calcium) •  Must specify any “subanalyte”

•  e.g. Coronavirus Ag •  May have a subclass – separated by “.”

•  e.g. Calcium.Free

•  Challenge -‐ e.g, 1H post 100 gm Glucose PO •  Two subparts separated by “post” •  <Jme delay> post <challenge type>

•  Adjustments/correcJons •  E.g. Adjusted to pH 7.4

Analyte Name^Challenge^Adjustments


•  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

•  Cataly7c ac7vity: ObservaJons that report enzymaJc acJvity •  Arbitrary: Results that report arbitrary units in the numerator of

their units of measure •  Number: Counts

Property


The characterisJc or aFribute of the analyte that is measured, evaluated, or observed

the most difficult LOINC axis

Major Categories


•  MCnc – mass concentraJon (mass/unit vol) •  MCnt – mass content (mass/unit mass) •  NCnc – number concentraJon (number/unit vol) •  TmStp – Jme •  CCnc – catalyJc concentraJon (acJvity) •  Prid – presence or idenJty •  Imp – impression/interpretaJon •  Find – subjecJve or objecJve observaJon •  Type – “Kind-‐of”

Property


the most difficult LOINC axis

Combine Major Categories with Subtypes for Full Property


Common Issues with LOINC Properties

•  FracJon = Part/whole •  Number fracJon (NFr): % Eosinophils •  Substance fracJon (SFr): % HGB which is A2

•  RaJo = Measures mulJple analytes from the same system (specimen) •  Mass concentraJon raJo -‐ MCrto

•  e.g., BUN/Creat in urine specimen •  Substance raJo-‐SCrto

•  Urea/CreaJnine expressed as mmol/L (SI units)

•  RelaJve RaJo = Measures from different systems •  RelRto – mulJple of the median •  RlTm – Jme from actual and normal control

FracJon (proporJon) vs. RaJo a/a+b vs. a/b


•  Pt -‐ at a point in Jme •  12H -‐ a twelve hour collecJon •  24H -‐ a twenty four hour collecJon

Timing*

*non-‐Pt Jmings are usually associated with RaJo Property

The interval of Jme over which the observaJon or measurement was made


•  Ser -‐ Serum •  Bld -‐ Whole blood (RBC) •  Ur-‐ Urine •  BldA -‐ Arterial blood •  Liver -‐ Liver •  Flu – Body Fluid, unspecified

•  Gast – Gastric fluid/contents •  Food – Food or feedstuff •  Tiss – Tissue •  XXX – To be specified in

another part of the message

System The system (context) or specimen type upon which

the observaJon was made.

Super System Second subpart (^). When not included, “paJent” is the default. Used to indicated blood product unit (BPU), a bone

marrow donor, or a fetus. (e.g. Serum^BPU)


•  Qn -‐ QuanJtaJve •  ConJnuous numeric (real, integer, raJo) •  OpJonal operator (>, ≥, ≤, <)

•  When assay detecJon limits are exceeded

•  Ord -‐ Ordinal •  a ranked set of possible values (1+, 2+, 3+)

•  Nom -‐ Nominal •  an unranked collecJon of possible values •  a taxonomy (e.g list of bacteria)

•  Nar -‐ NarraJve •  free text narraJve (e.g., visit note)

Scale


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 aFachments (headers)


Method •  Methods only needed if interpretaJon affected

•  Different normal ranges •  Test SensiJvity/Specificity

•  Generally listed only at the generic level •  AggluJnaJon (limited subtypes) •  Immunoassay •  Probe with target amplificaJon


Mapping Terms to LOINC Things to Remember

•  The thing ordered is not always the thing measured: •  Blood Culture – live organism(s) idenJfied •  VDRL – Treponema pallidum Ab •  Urinalysis – lots of different things

•  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!

•  You must know the specifics of the component being tested for (what is this test actually measuring?)


What is in LOINC? Content

•  Term structures •  SubmiFed 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


RELMA® Regenstrief LOINC Mapping Assistant


Purpose of Tutorial •  “Eliminate” need to read the User’s Manual •  Become familiar with RELMA features •  Provide some insight into mapping Jps/pi}alls •  Help begin the mapping process for your insJtuJon


•  LOINC files and indexes •  Manual and automated mapping funcJons •  Same free use as LOINC (see license) •  RELMA tools transform local words in local file

•  User creates file of local term/name and codes

•  Assigns LOINC term to local test/baFery code •  “Common tests” subset to speed mapping •  Context sensiJve hierarchies for local use. •  Flexible “Google-‐like” search funcJons

RELMA Functions


New in This Version (Rel. 5.2) •  Searches now have opJon to use “Auto Mapper” methods

•  Select "Use Auto Mapper Search" checkbox. •  Revised screen for reviewing Terms Mapped to Deprecated/

Discouraged LOINCs •  The "Replacement LOINC" secJon gives the user access to all the replacement LOINC codes.

•  The Comment field has been added. (RaJonal for replacement term)

•  Added navigaJon buFons. •  Lucene proximity and fuzzy searches are now supported on

the mapping and simple search screens. •  Lucene score is displayed on the mapping and the simple

search screens.


•  Column headers on screens are the same as Lucene field names. •  Example: [ ExUnits:mg ] -‐"ExUnits" = example units.

•  Double-‐clicking displays the details for selected row.

•  LOINC Part quoJents (e.g. "CreaJne kinase.MB/CreaJne kinase.total“) displayed in the Part secJon of details screen.

New in This Version (Rel. 5.2)


LOINC Web Site


What’s available to download? •  RELMA -‐ mapping and browsing tool

•  HL7 message converter-‐ Makes a database suitable for mapping

•  HL7 lint (finds bad messages) •  LOINC database and spreadsheets •  LOINC User guide; RELMA User Guide •  Tools to assist language translaJons by part •  Tools for building databases to map from HL7 messages

•  New guidance documents for mappers

32


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 •  Special features for panels/forms •  Enhanced export/copy-‐paste opJons


Installing RELMA®


Installation Steps •  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 files installed •  RELMA.MDB – LOINC Terms Database •  LMOF3.MDB – Local Master ObservaJon File

•  Two sample files included •  Run from Start – (All) Programs – Regenstrief – RELMA


File Locations •  Database and Ancillary Files

•  Windows XP = C:\Documents and SeMngs\All Users\Documents\RELMA\

•  Windows Vista = C:\Users\Public\Documents\RELMA\ •  Windows 7 = C:\Users\Public\Documents\RELMA\

•  Sample files •  Windows XP = C:\Documents and SeMngs\All Users\Documents\RELMA\Samples\

•  Windows Vista = C:\Users\Public\Documents\RELMA\Samples\

•  Windows 7 = C:\Users\Public\Documents\RELMA\Samples\


Running RELMA® Version 5.2


Copyright Screen


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)


User Map Screen Preferences

Click Map Screen Tab

Include/Exclude Battery Terms

Add comments on Mappings


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 file from your local test catalog (good choice)

•  Load directly from HL7 v2.x messages •  Pulls data from OBR and OBX segments •  Stores NTE segment data


Constructing a Local Dataset Create extract of your test catalog with:

•  BaFery/Panel Code •  BaFery/Panel DescripJon or Name •  *Local Code •  *Test DescripJon or Name

•  Include Method if Important •  Units •  Example Values •  Laboratory SecJon


Creating Delimited ASCII File •  RELMA can’t parse free text

•  Need to create separate fields •  Can use any of these delimiters

•  Tab, Semicolon, Comma, Space •  Can define your own

•  Fields can be in any order •  Minimum required fields

•  Local Code •  Local 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

Print Preview List Text alignment option


Export Local Term File

Delimiters supported: Tab, comma, bar (|)


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 Return to Full List

Calcium


Print Preview Local Term File


Steps to Import Local Terms 1.  Click Import Local Terms BuFon from Main Menu

a) File>Import Local Terms from Delimited File 2.  Locate your local terms text file

a)  E.g. WinXP Sample files loaded into C:\Documents and SeMngs\All Users\Shared Documents\RELMA

3.  Name your Working Set a)  LMOF database can contain mulJple work sets

4.  Define default secJon (OpJonal) 5.  IdenJfy file delimiter 6.  Assign fields to LMOF aFributes

a)  Ignore fields you don’t need b)  Combine fields 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…


Navigate to File Location Select File and Click Open Sample jiles 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

Choose jield name


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 file for future reconciliaJon


Local Term File Options


Change Local Term File

Select the Working Set

Current mapping status


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 flags •  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

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 L’OINC says: “Load the Sample Files Into RELMA now!”

•  Import the two sample files provided •  Import_Sample_OBR.txt

•  Contains baFery code and descripJon

•  Import_Sample_OBX.txt •  Contains test code and descripJon

•  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 •  BeFer 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 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 L’OINC says: “Begin to clean your

data now!”

•  Using the OBR or OBX sample files, take 15-‐20 minutes to clean up these unrecognized terms •  You may use your own data if you wish.


Searching for LOINC Terms


Simplijied Search Only Tool


Search Window

Enter Search Terms Limit to

Specijic Units Limit to Common

Tests

Use Automapper logic

Help File

“Common Tests” rank Restrict to “Common Tests”

New! Lucene score indicates relevance of search result


New RELMA Helpjile


Context Menu

Right click to bring up context menu


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 BuFon


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

Quick select button list

Custom Grid Conjiguration

Enter local term number


Conjigure Grid

Reorder grid elements

Select elements to display

Reset Default Conjiguration Visually resize elements


Quick choice buttons

Viewing LOINC term detail


View Local Term Details

Select level of detail to display


View Local Term Details Select text size


Select detail display level

Select level of detail to display


Standard Mapping Screen

Begin a search (or hit “enter”)

EEK! What’ll 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

Match units selected by default


Re-‐revised Mapping Results

Number of matching

records found Match units unselected



Clear all input jields

Enter keywords here

CANINE DISTEMPER VIRUS IF


Ad hoc term search



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 mulJ-‐axial hierarchy in search restricJons (covered later)

•  Map to a term in tree by clicking Map buFon or double clicking term •  Only 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 LOINC Term Details

View details for a specijic LOINC Term

Right clicking on a LOINC term brings up a Task Menu


LOINC Term Details

Can scroll through returned subset of

terms Change to expanded

details view

Change text size

Can scroll down a single formatted page


View Panel Children

Select View Panel Children from context menu


Panel Children


Conjigure Export Options

Output Options Include

column headers Save Conjiguration and/or Export


Excel Export Format


More on Searching Mapping Screen


Basic Search Syntax Special Character(s)

Example Defini7on

“ “ 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)

SubsJtutes a single character in the string. Cannot be used as the first character; cannot be used in “phrases”

* Gluc*se (glucose, glucuronidase, etc.)

SubsJtute mulJple characters in the string. Cannot be used as the first character; cannot be used in “phrases”


Search Qualijiers

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 Descrip7on

+ 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 mulJple terms in a single field

~ Fuzzy search (e.g. Hemo�ilus~)

“ “~ Proximity search for mulJple terms (e.g. “funcJon panel”~1)

{}, [] Upper and lower bounds; {} exclusive, [] inclusive

\ Special character escape


Applying advanced search


Limiting Searches


Setting Search Limits

•  Narrows search to specific subset of LOINC terms •  Reduces number of candidate terms •  Limits can be applied to all components •  Component aFribute 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 submiFed 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 Jming staJsJcs a\er each search •  Use carefully or search may not be successful

(Note parallel control switches at boFom of screen)



Click Hierarchy & Search Limits Tab


Setting search limits Can also set most of them by toggling buFons

at the boFom of the screen

Toggle Buttons


Search Constraints

Predejined, general search constraints

Attribute trees

Local Unit Constraint: Default is “ON”

New! Type toggle boxes


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



Methodless Terms Restriction

Override Methodless Terms Restriction


Limit to Methodless 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 methodless term; all shown



Limit to Lab Tests Only (No Clinical LOINC Terms)



Limit to common lab tests



Limit Number of Words in the Component Attribute


Limit Number of Component Words

Without Limit Applied: 792 terms returned


Limit Number of Component Words

With Limit Applied: 57 terms returned

Restriction appears on Toggle Bar

(cannot toggle off)

Component limited to 1 word



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 -‐  You are warned before mapping to discouraged LOINC terms

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

Most terms have class of “CHAL”


Search Trees

+Non +Chem

Restrict eligible tests to non-‐challenge

chemistry tests only


Following Class Restriction

Only Non-‐Challenge Chemistry tests

returned


Improvements to Trees

Continued reorganization to provide a Specimen

hierarchy


Improved Hierarchy for Component

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

Detailed Information on LOINC Parts


Tree Export Tools

Conjigure Export Format

Export according to Conjiguration


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” buFon on Mapping Screen to remove all tree selecJons


LOINC Part Search

•  Same look as term search •  Uses “Google-‐like” query language

•  Extremely fast •  Include and exclude criteria •  ParJal string matching (using wildcards)

•  Demo •  Campylobacter fetus, not Ab


Navigating through the Mapping Process


•  Limit effort 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

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 transmiFed in: •  OBX–17 (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 don’t have to do it all at one siMng •  Use the “Unmapped” funcJon to return where you le\ off

•  With every release -‐ Update previous mappings to idenJfy deprecated terms


Common Mapping Issues

•  Locally Defined Test Name Ambiguity •  Reuse of local test code

•  “Analyte-‐free” Local Test Names •  (Miscellaneous serology)

•  Incongruent Value sets (Scale ambiguity) •  Result vs. InterpretaJon •  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


Conjigure Export Format

Context Sensitive Export Conjiguration


LMOF Export Conjiguration

Select Fields to Export

Select Export Format

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


Custom Export Conjiguration

Select the Fields you wish to Export

Select the Format you wish to Export


Excel™ Export


New and Improved 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

Local 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


Other RELMA® Features


Panels, Forms and Survey Review

Review Panels, Forms and Surveys

Review Panels, Forms and Surveys


Government Forms

Form Name

Component LOINC terms


Laboratory Panels

Expand category to see panels

Double-‐click panel name to see

components


Expanded Panel Detail


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


Can’t jind 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 don’t make sense

•  E.g. Method-‐less tests plus Method tree set to EIA •  Did not find and revise words not in RELMA

•  Local units not in RELMA

•  Units are GREAT discriminators •  You may have tests that need to be added to LOINC


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 sufficient annotaJon to jusJfy the new term •  Package inserts, sample reports (email to Regenstrief) •  The more the beFer!

•  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 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

All proposed terms fully editable

Choose whether to send or postpone

X

X X

James T. Case DVM, PhD

NIH/NLM

[email protected]

301-555-1314

301-555-1315


Submitting New Terms •  Must supply name, organizaJon, phone and email of submiFer

•  Must select at least one proposed term to send

•  “Configure export” does not affect submission output

•  Email resulJng 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 jilled in


Using LOINC and SNOMED Together


Where do LOINC and SNOMED Fit?

•  LOINC represents the quesJon: •  Is there any Botulism toxin in my specimen? (33708-‐9)

•  Organisms idenJfied in specimen? (634-‐6)

•  SNOMED represents the answer: •  NegaJve (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 IdenJfier) •  In OBX-‐3 (ObservaJon IdenJfier

•  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 identijies the data type in OBX-‐5 as a

coded element

OBX: With a Coded Value

OBX-‐3:A code that identijies 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

2011 06 06 - loinc workshop and tutorial

Health & Medicine