2014 06 04 - laboratory loinc and relma workshop

©2014 Regenstrief Institute and James Case

Using RELMA Or…In Search of the Missing LOINC

James T. Case MS, DVM, PhD, FHL7, FACMIHealth Program Specialist, SNOMED CT

National Library of Medicine

Laboratory LOINC Meeting – June 2014


Acknowledgements

• LOINC Development Team• Clem McDonald, Dan Vreeman, Jami Deckard,

David Baorto, Kelly Malott• RELMA Development Team• John Hook, Anandhi Sowmyan, James Dennis,

Katy Holck• LOINC Committee • Supporters: NLM, Regenstrief Institute,

Regenstrief Foundation


What will we cover today?• Overview of LOINC• Reviewing new RELMA features!• Installing RELMA• Setting personal preferences• Loading a Local Observation File (LMOF)• Searching for a LOINC Term• Preparing LMOF for Mapping• Review of Map Screen Functions• Setting Search Limits• Mapping Local Terms to LOINC• Viewing LOINC Term Details• Proposing/Submitting New LOINC Terms• Exporting/Printing Mapped Terms• Mapping your own LMOF data


Why are we doing this?Goals of Health Information Standards

• Interoperability – the ability to exchange information between organizations

• Comparability – the ability to ascertain the equivalence of data from different sources

• Data Quality – the measurement of accessibility, completeness, accuracy and precision (and more)


Levels of Interoperability• Basic – allows data to be exchanged between

computer systems• Word processing documents, text messages

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

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


Comparability• Meaning of the data is consistent when shared

among different parties• Erysipelas – Human skin disease; Streptococcus Grp A• Erysipelas – Animal Septicemia/dermatitis; Erysipelothrix

rhusiopathiae• Common terminology required

• Should work in the background• Words are not enough

• Codes – uniquely identify terms• Vocabulary – specialized, precise terms that remove

ambiguity• Ontology – describes nature of entities and their relations• Classification – groups related terms by category


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

• Different for client/patient communications vs. clinical decision support vs. epidemiological analysis

• Often constrained by external forces• e.g. criteria for diagnosis often differs from the criteria

for reporting

• Unidirectional effect of data consolidation• Detailed → General• General → Detailed


The Problem“In attempting to arrive at the truth, I have applied

everywhere for information, but in scarcely an instance have I been able to obtain hospital records fit for any purpose of comparison. If they could be obtained, they would enable us to decide many other questions… They would show [subscribers] how their money was being spent [and] what amount of good was really being done with it…”

Florence Nightingale - Notes on a Hospital, 1873


Test comparisons

Lab ATest Name: Lyme Disease SerologyMeasures: B. burgdorferi Ab IgGMethod: ELISAScale: quantitativee.g.: Titer 1:40

Lab BTest Name: Lyme Disease AntibodyMeasures: B. burgdorferi Ab IgMMethod: Immune blotScale: qualitativee.g.: Positive

LOINC Code = 5062-5 LOINC Code = 6321-4

What you see in the order list


Why LOINC?“Within one laboratory, local jargon terms

may be used which are usually well understood between colleagues, but

would not be sufficiently widely known for communication with the outside world.”

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


LOINC® 101Emphasis on Laboratory

LOINC


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

5193-8 LOINC Code

Hepatitis B virus surface Ab

ACnc

Pt

Ser

Qn

EIA

Component

Property Measured

Timing

System

Scale

Method

There are six major LOINC axes

Anatomy of a LOINC Term


NOT part of a LOINC Name• Reason for the test (why it was ordered or the disease it

diagnoses)

• Testing instrument• Specific details about the specimen• Priority (e.g. STAT)• Where testing was done• Who did the test• Test interpretation• Pricing or cost• Anything not part of naming the test• Things from other fields in an HL7 artifact


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

Component/Analyte

- Sodium- Glucose- Brucella sp. organism- Influenza A Virus antigen- Cytomegalovirus Virus antibody- Lipids.Total



Component StructureAnalyte Name^Challenge^Adjustments

Formal analyte name

Specify “subanalytes”May have subclasses

ChallengeTwo parts separated by “post”

Adjustments

CalciumCoronavirus AgCalcium.ionized

1H post 100 g Glucose PO

<time delay>post<challenge type>

Adjusted to pH 7.4


• Mass: Observations reported with mass (milligrams, grams, etc.) in the numerator of their units of measure

• Substance: Observations reported with moles or milliequivalents in the numerator of their units of measure

• Catalytic activity: Observations that report enzymatic activity• Arbitrary: Results that report arbitrary units in the numerator of their units

of measure• Threshold: Results that represent the relation between a value and some

established limit or “cut-off”• Number: Counts

Property


The characteristic or attribute of the analyte that is measured, evaluated, or observed

the most difficult LOINC axis

Major Categories


• MCnc – mass concentration (mass/unit vol; e.g. mg/dL)• MCnt – mass content (mass/unit mass; e.g. mg/Kg)• NCnc – number concentration (number/unit vol; e.g. num/mL)• TmStp – time• CCnc – catalytic concentration (activity; e.g. kat/L)• Prid – presence or identity• Imp – impression/interpretation• Find – subjective or objective observation• Type – “Kind-of”

Property


the most difficult LOINC axis

Combine Major Categories with Subtypes for Full Property


Common Property Issues

Fraction = Part/WholeNFr: % Eosinophils / leukocytesSFr: % HGB which is A2

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

Relative Ratio = measures from different systemRelRto: Albumin.pericard fld/Albumin.SerPl

Fraction versus Ratio


Important property changes• ACNC – was always a “placeholder”

• For P/N results, changed to “Threshold”• Additional migrations occurring gradually• LOINC IDs being retained

• Flavors of Threshold Property• ThrSCnc – Threshold Substance Concentration• ThrMCnc – Threshold Mass Concentration• ThrACnc – Threshold Arbitrary Concentration

• PR vs PRID• Presence or absence of organisms now represented as

“PR” (presence)• For nominal results, property is still PRID


• Pt - at a point in time• 12H - a twelve hour collection• 24H - a twenty four hour collection

Timing*

*non-Pt timings are usually associated with Rate Property

The interval of time over which the observation or measurement was made



SystemThe system (context) or specimen type upon which the observation was made.

SerSer/PlasBldUrFluTissXXX

serumserum or plasmawhole blood urinebody fluidtissuespecified elsewhere

photo via AlishaV


http://www.flickr.com/photos/AlishaV/


System Structure

• Super System• Patient is the default• Used to indicate

• blood product unit• bone marrow donor• fetus

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

System^Super System

photo via Xurble

http://www.flickr.com/photos/xurble/


ScaleQn

Ord

Nom

Nar

Quantitativecontinuous numericcan have operators (<,>)

OrdinalRanked set (1+, 2+, 3+)

Nominalunranked collectionTaxonomy (e.g. bacteria)

Narrative

photo via puuikibeach


http://www.flickr.com/photos/puuikibeach/


Scale (Special)• OrdQn – Ordinal or Quantitative

• Primarily used for antimicrobial observations e.g. MIC reported as resistant, intermediate, susceptible or as the mm diameter of the inhibition zone

• Use is discouraged in other contexts• Multi – structured text “globs”

• e.g. chromatography output• Use is discouraged

• Doc – Clinical documents• Set – Clinical attachments (headers)


Method• Only needed if interpretation affected

• Different normal ranges• Test sensitivity/specificity

• Generally listed at the generic level• Agglutination• Enzyme Immunoassay• Probe with target amplification



Hierarchies• LOINC “Class”• One for each LOINC axis• Multi-axial

• Component | System• Separate download


Mapping Terms to LOINCThings to Remember

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

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

• The question (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl)• You are mapping the question, not the answer!

• Need to get the observation/result boundary correct.• Sample values help substantially


What is in LOINC?Content

• Term structures• Submitted units, Example UCUM units

• aiming toward preferred units sorting• Synonyms• Answer lists (increasing number)• Text descriptions – links to info sources

about individual tests • Panel structures• Foreign language translations

• And much more…


RELMA®Regenstrief LOINC Mapping Assistant


Download of latest version

• The latest version of the installation file may be downloaded from:

• https://iu.box.com/relma65

https://mail.nih.gov/owa/redir.aspx?C=o8GQqdYJF0ujslQb2WJqNOJ3QZnhUtEIqRsI1WQugFQgdWfLMQh9qJtXHSXaKyNNdbc1ZL4eLR8.&URL=https://iu.box.com/relma65


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

institution• Hang with some really cool folks


• LOINC files and indexes• Manual and automated mapping functions• RELMA tools transform local words in local file

• User creates file of local term/name and codes• Assigns LOINC term to local test/battery code• “Common tests” subset to speed mapping• Context sensitive hierarchies for local use.• Flexible “Google-like” search functions

RELMA Functions


New in This Version (Rel. 6.5) • Exciting news! The ability to send a new term request

directly to Regenstrief directly from RELMA. • Ability to attach files such as package inserts and other

documentation.• Original functionality retained

• New installer technology that should result in minimal screen changes during the install.

• Detail pages have been enhanced with hyperlinks. • All LOINC numbers, LOINC part numbers and LOINC Answer

list numbers are displayed as hyperlinks. • Answer string "LA" codes are now displayed in the list

of answers in the answer search screen.


LOINC Web Site


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

• HL7 message converter- Makes a database suitable for mapping

• LOINC database and spreadsheets • Accessory files (panels, forms, top 2000, etc.)• LOINC User guide; RELMA User Guide• Tools to assist language translations by part• Tools for building databases to map from HL7

messages• Guidance documents for mappers


RELMA Highlights• Browse-able hierarchies of LOINC parts• Display search results in tree view• Enhanced “details” view of terms/parts

• References• Descriptions• Sample units

• Empirically-derived common test list• Empirically-derived common order list• Special features for panels/forms• Enhanced export/copy-paste options


Installing RELMA®


Installation Steps• Requires Windows (or VM on a Mac)• Make sure you have enough free disk space!

• 2Gb is recommended

• From CD - Start – Run – <drive>:\RELMA\Setup

• Specify installation directory• Life will be easier if you accept the default

• Two database files installed• RELMA.MDB – LOINC Terms Database• LMOF3.MDB – Local Master Observation File

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


File Locations

• Database and Ancillary Files• Windows XP = C:\Documents and Settings\All Users\

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

• Sample files• Windows XP = C:\Documents and Settings\All Users\

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

Samples\


Running RELMA®Version 6.5


Copyright Screen


Join the LOINC Community


LOINC crowdsourcing


Main Menu/Welcome Screen


Set Preferred Language

Click File, Set Preferred Language


Select Linguistic Variant(s)

Selecting a translation may require indexes to be built


LOINC Terms with Spanish Linguistic Variant

All Spanish!


Setting User Preferences


Select User PreferencesFrom the File Menu

Set User Preferences

...or from Welcome Screen


Set User Preference Dialog

Startup Screen Preference

New File Locations:(See prior slide for location)

New Submissions tab


User Map Screen Preferences

Click Map Screen Tab

Include/Exclude Battery Terms

Add comments on Mappings

Auto create search terms


User Detail Pages Preferences

Download detail pages from LOINC.org


Request Submission Preference

Preferred method of request submission


Importing Local Terms into RELMA


5 Ways to Load LMOF Files• Direct entry into LMOF from within RELMA (painful)

• Handy for individual entries/edits

• Create an Access table that mimics the LMOF structure (less painful but tedious)• Appendix A: RELMA Manual

• Create a delimited ASCII file from your local test catalog (good choice)

• Import Excel file• Load directly from HL7 v2.x messages

• Pulls data from OBR and OBX segments• Stores NTE segment data


Constructing a Local DatasetCreate extract of your test catalog with:

• Battery/Panel Code• Battery/Panel Description or Name• *Local Code • *Test Description or Name

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


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 Description• Units (highly recommended)


Entering New Local Terms into RELMA


Manual Enter/Edit

View/Add/Edit Local Terms


Edit Term Dialog

Edit\Add\Delete TermsExport Terms

Print Preview ListText alignment option

User assigned tags


Export Local Term File

Delimiters supported:Tab, comma, bar (|)

Export to Microsoft Excel or Text File


Add Local Term

Click to Add to Current Working File

MICRO

BUBPLAG

BUBONIC PLAGUE – RRT PCR


Search Local Term File

Enter Keyword from any Field

Calcium

Return to Full List

Tags panel only appears if tags have been assigned


Using tags to filter local terms

Print preview local term file

Configure output prior to viewing and printing


Print Preview Local Term File

Only prints selected rows


Steps to Import Local Terms

1. Click Import Local Terms Button from Main Menu

a) File>Import Local Terms from Delimited File2. Locate your local terms text file3. Name your Working Set (Mandatory)

a) LMOF database can contain multiple work sets4. Define default section (Optional)5. Identify file delimiter 6. Assign fields to LMOF attributes

a) Ignore fields you don’t needb) Combine fields if needed

7. Check “Case-sensitive” if needed8. 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 OpenSample files stored in RELMA Directory


Open File in RELMA

Name your working set. RELMA allows multiple sets in

LMOF database

Select your delimiter

Import Button


Fields Segregated

Assign LMOF Attribute

Assign working set name


Working set importLOINC Workshop OBR


Ready to Import

Minimum assignments

Now you can click the Import button!


Post-Processing of Local File

• After import, RELMA Searches for terms (words) that it does not recognize

• Stored in a file for future reconciliation


Importing Excel file

Excel files now appear along with text files


Excel format for import


Local Term File Options


Change Local Term File

Select the Working Set

Current mapping status

Can delete local term set; not the active one


Alternative Pragmatic Way• Use large set of HL7 messages• Automatically make dataset of:

• OBR ID• OBR description• OBX ID• OBX description• Sample of results with

• Real values• Units• Abnormal flags• Normal ranges


Generate Local term file from HL7 messages

Select Import Terms from HL7 File


Select File to Import

Select HL7 File


Specify HL7 File Name and Sample Size

Name the Local Term File (working set)

Select which codes to store

Skip import of sample values

Select the number of sample values


HL7 Messages Data Statistics


New Terms added to LMOF

New Battery Code

Click on “Edit Term” to see Sample Data


Sample Results for ObservationNew 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 battery code and description

• Sample_HL7.HL7• Contains test code and

description and sample values• Create 2 working sets• Load your personal data set


Cleaning your data


Preparing your Data for Mapping

• Improve mapping success by:• Expanding abbreviations• Standardizing colloquial terms• Ignoring “administrative” terms• Standardizing time references

• Can be done prior to importing• Better to use tools built into RELMA


RELMA Cleaning ToolsUse this tool to edit

unknown terms

Only available if no language variant selected


Review Unknown Local Terms

May Re-Scan File for Unknown Terms


Replace Local Terms

Assign LMOF AttributeReplacement Options


RELMA Cleaning ToolsUse 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 sample file or your own data, take 15-20 minutes to clean up these unrecognized terms


Searching for LOINC Terms


Comprehensive Search Only Tool


Search Window

Enter Search Terms

Limit to Specific Units

Use different logic

Help File

Restrict Limits


Search Window

“Common Tests” selected“Common Tests” rank


RELMA Search Helpfile


Context Menu

Right click to bring up context menu


Changed search function – Max words

Large number of results

Keyword ComponentWordCount

restricts word countRestricting to “Common labs” refines further


Mapping Local Terms


Mapping Local Terms

• Select your Working Set to Map• File>Select Local Term File to Process

• Select “Map Local Terms to LOINC” from Welcome Screen

• Select the subset of terms to work with:• All• Mapped• Unmapped

• Set your Search Limits• Set Search Limits Button


Standard Mapping Window Features

• Customizable grid• View details of LOINC term• New! Add searchable tags to local term• Sort by column

• Click column • Custom Sort

• Print or export results grid• Spell check squiggly line to signify words

not known to RELMA


Mapping Screen

View or edit local term

Quick select button list

Custom Grid Configuration

Enter local term number

User assigned tags


Configure Grid

Reorder grid elements

Select elements to display

Reset Default ConfigurationVisually resize elements


Quick choice buttons

Viewing LOINC term detail


View Local Term Details

Select level of detail to display

Can scroll through returned subset of

terms

Change text size

Can scroll down a single formatted page


Details Text SizeSelect 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

keywordBattery terms

included in search


Revised Mapping Results

Number of matching

records found


Re-revised Mapping Results

Number of matching

records foundMatch units

selected



Clear all input fields

Enter keywords here

CANINE DISTEMPER VIRUS IF



Navigate through the local terms


Tabbed Access to Functions

Navigate to Functions from Mapping Page

Switch between Grid and Tree Views


Tree View


Tree View• Results displayed hierarchically

• Defined by the multi-axial hierarchy in search restrictions (covered later)

• Map to a term in tree by clicking Map button or double clicking term• Only to rows that have LOINC Codes


Tree View

Cannot map to terms

representing LOINC parts

Can map to terms with LOINC Codes

Tree Navigation Buttons


Assigning a LOINC Map

Highlight correct term

Click “Map” Button (or doubleclick)


Adding Mapping Comments

If comments option is selected, prompt appears

Check with Frank in Chemistry


Assigning a LOINC Map

LOINC Term Assigned


View Panel Children

Select View Panel Children from context menu


Panel Children


Configure Export Options

Output Options

Include column headersSave Configuration

and/or Export


Excel Export Format


More on Searching Search Screen


Basic Search SyntaxSpecial Character(s)

Example Definition

“ “ Influenza “virus A” Linked terms must appear together

AND Morphine AND Opiates

Both terms must appear in the search result term

OR Influenza OR Parainfluenza

Either or both terms must appear in the search result term

NOT Influenza NOT equine Excludes terms with the word following the NOT. Cannot be used alone.

? Gluc?se(glucose,glucase)

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

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

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


Search Qualifiers

Includes Glucuronidase, Glucosidase,

Glucosylceramidase, etc.

Detailed help available


Combining Search Terms

Reduced number of terms

Exclude Glucosidase


Advanced Search Syntax based on Google-like search syntax

Parameter Description

+ Term must be included in search

- Term must be excluded from the search

( ) Group terms for subquery (i.e. A OR B; A AND B)

Fieldname: Limit term search to the associated field (e.g. Component: glucose)

Fieldname:() Group multiple terms in a single field

~ Fuzzy search (e.g. Hemofhilus~)

“ “~ Proximity search for multiple terms (e.g. “function panel”~1)

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

\ Special character escape


Applying advanced search

91 terms



33 terms



19 terms



8 terms


Limiting Searches


Setting Search Limits

• Narrows search to specific subset of LOINC terms• Reduces number of candidate terms• Limits can be applied to all components• Component attribute can be further restricted by

number of words• Tree structure allows for hierarchical constraints


General Search Constraints• Controls features including:

• Limit to LOINC terms compatible with submitted units• Forced match with any specimen contained in name• Method-less terms only • Restrict by class type• Remove lateralized terms

• Use carefully or search may not be successful(Note parallel control switches at bottom of screen)



Click Hierarchy & Search Limits Tab


Setting search limitsCan also set most of them by toggling buttons

at the bottom of the screen

Toggle Buttons


Search Constraints

Expanded predefined, general search constraints

Attribute trees

Limit to LOINC terms consistent with local units


Terms Consistent with Units

Only terms consistent with mmol/L appear



Specimen constraints


Terms Consistent with Specimen

CSF

Enter default Specimen


Terms Consistent with Specimen

Only CSF Terms are returned



Exclude laterality


Exclude laterality

Laterality terms



Restrict to common orders


Restriction to common orders

Large number of candidates Common orders

rank



Methodless Terms Restriction

Override Methodless Terms Restriction


Limit to Methodless Terms

Both method and method-less terms


Limit to Methodless Terms

Only Methodless Terms Appear


More on Methodless Terms• Some LOINC categories do not have

methodless terms• Checking methodless only will remove these

from view on results grid• Checking additional box allows these to be

seen


Methodless Only Unchecked

All terms returned


Methodless Only Checked

Only Methodless terms returned

Differ in one or more components


Conditional Methodless

More terms returned

No method-less term; all shown



Include Trial, Deprecated or Discouraged LOINC Codes with

Returned Terms


Include Deprecated LOINC Terms

Deprecated LOINC Terms appear as Strikethrough Text with a “Do Not”

Symbol

• You cannot map to deprecated LOINC terms

• The map button is grayed out if one of these terms is selected

Discouraged LOINC Terms appear as an inverted triangle


Favor Property Restriction

Favor one type of property over others

All other components being equal MCnc

only will be displayed


Order/Observation Restriction

Order or Observation preference


LOINC Hierarchies – Class Tree

Three top-level branches

Tree Navigation Buttons


Before Class Restriction

Large number of candidate terms

Many terms have class of “CHAL”


Search Trees

Restrict eligible tests to non-challenge

chemistry tests only


Following Class Restriction

Only Non-Challenge Chemistry tests

returned


System Hierarchy


Component Hierarchy

Show the LOINC Codes associated with these

components

Click on details for more information about the

selection


Details Screen LOINC Part


Show Associated LOINCs


LOINC Term Details Screen


Tree Export Tools

Configure Export Format

Export according to Configuration


Tree Export Configuration


RELMA - Tree Features

• All trees operate the same way• Shows terms spelled out• Can expand and collapse parts or all of tree.• Tree is string searchable • Search can be based on one or more

branches of a tree with or without other criteria

• Use “Clear Most Limits” button on Mapping Screen to remove all tree selections


LOINC Part Search

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

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

• Demo• Campylobacter fetus, not Ab


LOINC Answer List Search

• Nominal LOINC terms are now “required” to be submitted with answer lists.

• Finding answer lists and the use of them can be done with “Answer List Search” tab


Answer List Search

Answer Lists associated with LOINC term


Navigating through the Mapping Process


• Limit effort to one lab section at a time and focus expertise

• Chemistry and hematology will be easiest• For manufactured assays, use package insert as

source information• Sample results give clue to property and scale• Consider prioritizing by frequency of use

LOINC Mapping Tactics


Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.


More LOINC Mapping Tactics• Try using method-less terms first

• Specific methods can be transmitted in:• OBX–17 (v2.x), Observation.methodCode (v3.0)

• Examine local units or real results to verify correct property and scale• Properties are rarely distinguishable in test names

• You don’t have to do it all at one sitting• Use the “Unmapped” function to return where you

left off• With every release - Update previous mappings

to identify deprecated terms


Common Mapping Issues

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

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

• Incongruent Value sets (Scale ambiguity)• Result vs. Interpretation• Available LOINC Terms too Specific/General• Panel vs. Discrete Test

• Common in Microbiology


Using your Mapped Terms

• Print results of LOINC Mapping• Export to File


Configure Export Format

Context Sensitive Export Configuration


LMOF Export Configuration

Select Fields to Export

Select Export Format

Save Configuration and Export


Print Mapped Terms from View/Add/Edit Menu

May highlight terms to be printed

Click Print button to Preview output


Formatted Report Output

Click Print button to output formatted report


Excel™ Export


Lab Auto Mapper

• Run in batch mode to find N- closest terms• Can then use this output to do final mapping• Again units are VERY important• Can pick all limits available to regular mapping


Picking the Lab Auto Mapper


Lab Auto Mapper Start Screen

Maximum number of terms to return

Can restrict search to common tests


Lab Auto Mapper Start Screen

Terms used for mapping

Local test code


Lab Auto Mapper - Mapping Screen


Exporting Mapped Terms

Export Terms to Delimited File


Export Terms Dialog

Check Fields you wish to export

Select Delimiter

Select Term Set

Direct export to Excel

Select file location


Other RELMA® Features


Panels, Forms and Survey Review

Review Panels, Forms and Surveys

Review Panels, Forms and Surveys


Laboratory Panels

Expand category to see panels

Double-click panel test to see

components


Expanded Panel Detail


Government Panels

Form Category

Panel Codes


Government Panel Children


Expanded Clinical Panel


Clinical Panels

Find where a term has been used

35089-2, 35090-0


LOINC Term Panel Usage


Other Survey Instruments


HIPAA Attachments

View Various HIPAA Attachments


HIPPA Attachment Tree


Expanded Attachment Data


Can’t find the term you

want?


Search Hints and Tips• Keywords with zero frequency are ignored

• May need to rephrase – use synonym• Some causes for no returned terms

• Too many keywords in search – uncheck some• Limits applied that 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 localizations• Is the distinction really important?

• Supply sufficient annotation to justify the new term• Package inserts, sample reports (email to Regenstrief)• The more the better!

• Construct new terms within RELMA• File>Propose a new LOINC• Linked to the “trees” to allow browsing

• Can review and submit them to LOINC from within RELMA


Propose new LOINC terms

Select Propose a new LOINC


Required fields in red Navigate through

proposed termsCreate 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

New! Direct submission via web


Submit Proposed Terms

Add additional information, if

necessaryAdd attachments


Submitting New Terms• Must supply name, organization, phone and

email of submitter• Must select at least one proposed term to

send• “Configure export” does not affect

submission output• Email resulting file to Regenstrief


Use Existing Terms as Template

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Use Existing Terms as Template

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Using LOINC and SNOMED Together


Where do LOINC and SNOMED Fit?

• LOINC represents the question:• Is there any Botulism toxin in my specimen?

(33708-9)• Organisms identified in specimen? (634-6)

• SNOMED represents the answer:• Negative (SCTID 260385009)• E. coli O157:H7 (SCTID 103429008)

Remember:


Where do LOINC and SNOMED Fit?

• In an HL7 message, LOINC may be used:• In OBR-4 (Universal Service Identifier)• In OBX-3 (Observation Identifier

• SNOMED may be used:• In OBX-5 (where nominal values are needed)• Almost anyplace else in an HL7 message where

coded values are needed


The code isfrom SNOMED

The code isfrom LOINC

OBX-5: DataA code for L.

monocytogenes

A code that identifies the data type in OBX-5 as a

coded element

OBX: With a Coded Value

OBX-3:A code that identifies the data in

OBX-5(Listeria culture)

OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT


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


ExerciseMap your own data