2011 12 08 - loinc and relma workshop and tutorial

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©2011 Regenstrief Institute and James Case

Using RELMA Or…In Search of the Missing LOINC

James T. Case MS, DVM, PhDHealth Program Specialist, SNOMED CT

National Library of Medicine

Laboratory LOINC Meeting – December 2011

©2011 Regenstrief Institute and James Case

Acknowledgements• LOINC Development TeamClem Mcdonald, Dan Vreemen, Kathy Mercer, Jaci Phillips, Ian Pyle, David Baorto, Fran Brahmi

• RELMA Development TeamJohn Hook, Mark Fisher, Karen Ahmed, Anandhi Sowmyan, James Dennis

• LOINC Committee • Supporters: NLM, Regenstrief (including the Indiana Center of Excellence in Public Health Informatics), Regenstrief Foundation

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

©2011 Regenstrief Institute and James Case

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)

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

LOINC® 101Emphasis on Laboratory

LOINC

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

What is NOT part of a LOINC Name?

• The instrument used in testing• Specific details about the specimen• Priority (e.g. STAT)• Where testing was done• Who did the test• Test interpretation• 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 Observation Object

©2011 Regenstrief Institute and James Case

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

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

©2011 Regenstrief Institute and James Case

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”• <time delay> post <challenge type>

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

Analyte Name^Challenge^Adjustments

©2011 Regenstrief Institute and James Case

• 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• Number: Counts

Property

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

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

the most difficult LOINC axis

Major Categories

©2011 Regenstrief Institute and James Case

• MCnc – mass concentration (mass/unit vol)• MCnt – mass content (mass/unit mass)• NCnc – number concentration (number/unit vol)• TmStp – time• CCnc – catalytic concentration (activity)• Prid – presence or identity• Imp – impression/interpretation• Find – subjective or objective observation• Type – “Kind-of”

Property

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

the most difficult LOINC axis

Combine Major Categories with Subtypes for Full Property

©2011 Regenstrief Institute and James Case

Common Issues with LOINC Properties

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

• Ratio = Measures multiple analytes from the same system (specimen)• Mass concentration ratio - MCrto

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

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

• Relative Ratio = Measures from different systems• RelRto• RlTm – time from actual and normal control

Fraction (proportion) vs. Ratioa/a+b vs. a/b

©2011 Regenstrief Institute and James Case

• 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

©2011 Regenstrief Institute and James Case

• 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

SystemThe system (context) or specimen type upon which

the observation was made.

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

• Qn - Quantitative • Continuous numeric (real, integer, ratio)• Optional operator (>, , , <)

• When assay detection limits are exceeded

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

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

• Nar - Narrative • free text narrative (e.g., visit note)

Scale

©2011 Regenstrief Institute and James Case

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)

©2011 Regenstrief Institute and James Case

Method• Methods only needed if interpretation affected

• Different normal ranges• Test Sensitivity/Specificity

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

©2011 Regenstrief Institute and James Case

Hierarchies• LOINC ‘class’• Each LOINC axis• Multi-axial

• Component | System• Separate download

©2011 Regenstrief Institute and James Case

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

• 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!

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

RELMA®Regenstrief LOINC Mapping Assistant

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

• LOINC files and indexes• Manual and automated mapping functions• 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/battery code• “Common tests” subset to speed mapping• Context sensitive hierarchies for local use.• Flexible “Google-like” search functions

RELMA Functions

©2011 Regenstrief Institute and James Case

New in This Version (Rel. 5.4) • Default - latest copy of LOINC details retrieved from the

loinc.org website. • Configurable from File -> User Preferences -> Details Pages ->

Get from Internet. • Build locally File -> User Preferences -> Details Pages -> Build

Locally.

• Common order rank displayed as "Common Order Rank" in the LOINC Details displays.

• New search restriction - "Exclude LOINCs containing 'left' or 'right'“. Bilateral LOINCs and LOINCs without laterality remain in the search results.

©2011 Regenstrief Institute and James Case

• "Terms consistent with local units" search restriction status is saved between editing sessions.

• Answer string descriptions displayed with answer string (configurable).

• Images are now displayed on Part details pages, if available.

• Obsolete LOINC fields deleted from the Details displays -- ANSWERLIST and DEFINITION_DESCRIPTION_HELP.

New in This Version (Rel. 5.4)

©2011 Regenstrief Institute and James Case

LOINC Web Site

©2011 Regenstrief Institute and James Case

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 translations by part• Tools for building databases to map from

HL7 messages• New guidance documents for mappers

35

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Installing RELMA®

©2011 Regenstrief Institute and James Case

Installation Steps• 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

©2011 Regenstrief Institute and James Case

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\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\Documents\RELMA\

Samples\

©2011 Regenstrief Institute and James Case

Running RELMA®Version 5.4

©2011 Regenstrief Institute and James Case

Copyright Screen

©2011 Regenstrief Institute and James Case

Main Menu/Welcome Screen

©2011 Regenstrief Institute and James Case

Set Preferred Language

Click File, Set Preferred Language

©2011 Regenstrief Institute and James Case

Select Linguistic Variant(s)

Selecting a translation may require indexes to be built

©2011 Regenstrief Institute and James Case

LOINC Terms with Spanish Linguistic Variant

All Spanish!

©2011 Regenstrief Institute and James Case

Setting User Preferences

©2011 Regenstrief Institute and James Case

Select User PreferencesFrom the File Menu

Set User Preferences

...or from Welcome Screen

©2011 Regenstrief Institute and James Case

Set User Preference Dialog

Startup Screen Preference

New File Locations:(See prior slide for location)

©2011 Regenstrief Institute and James Case

User Map Screen Preferences

Click Map Screen Tab

Include/Exclude Battery Terms

Add comments on Mappings

Auto create search terms

©2011 Regenstrief Institute and James Case

Importing Local Terms into RELMA

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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)

©2011 Regenstrief Institute and James Case

Entering New Local Terms into RELMA

©2011 Regenstrief Institute and James Case

Manual Enter/Edit

View/Add/Edit Local Terms

©2011 Regenstrief Institute and James Case

Edit Term Dialog

Edit\Add\Delete TermsExport Terms

Print Preview ListText alignment option

©2011 Regenstrief Institute and James Case

Export Local Term File

Delimiters supported:Tab, comma, bar (|)

©2011 Regenstrief Institute and James Case

Add Local Term

Click to Add to Current Working File

MICRO

BUBPLAG

BUBONIC PLAGUE – RRT PCR

©2011 Regenstrief Institute and James Case

Search Local Term File

Enter Keyword from any Field

Calcium

Return to Full List

©2011 Regenstrief Institute and James Case

Print Preview Local Term File

©2011 Regenstrief Institute and James Case

Steps to Import Local Terms

1. Click Import Local Terms Button from Main Menu a) File>Import Local Terms from Delimited File

2. Locate your local terms text filea) E.g. WinXP Sample files loaded into C:\Documents and

Settings\All Users\Shared Documents\RELMA3. Name your Working Set

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.

©2011 Regenstrief Institute and James Case

Example Tab-Delimited File

©2011 Regenstrief Institute and James Case

Importing Local Files

Select Import Local Terms from Delimited File…

©2011 Regenstrief Institute and James Case

Navigate to File Location

Select File and Click OpenSample files stored in RELMA Directory

©2011 Regenstrief Institute and James Case

Open File in RELMA

Name your working set. RELMA allows multiple sets in

LMOF database

Select your delimiter

Import Button

©2011 Regenstrief Institute and James Case

Fields Segregated

Assign LMOF Attribute

Choose field name

©2011 Regenstrief Institute and James Case

Ready to Import

Minimum assignments

Now you can click the Import button!

©2011 Regenstrief Institute and James Case

Post-Processing of Local File

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

• Stored in a file for future reconciliation

©2011 Regenstrief Institute and James Case

Local Term File Options

©2011 Regenstrief Institute and James Case

Change Local Term File

Select the Working Set

Current mapping status

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Generate Local term file from HL7 messages

Select Import Terms from HL7 File

©2011 Regenstrief Institute and James Case

Select File to Import

Select HL7 File

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

HL7 Messages Data Statistics

©2011 Regenstrief Institute and James Case

New Terms added to LMOF

New Battery Code

Click on “Edit Term” to see Sample Data

©2011 Regenstrief Institute and James Case

Sample Results for ObservationNew Test Code

Sample Values from Messages

©2011 Regenstrief Institute and James Case

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

• Import_Sample_OBX.txt• Contains test code and

description• Create 2 working sets• Load your personal data set

©2011 Regenstrief Institute and James Case

Cleaning your data

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

RELMA Cleaning ToolsUse this tool to edit

unknown terms

©2011 Regenstrief Institute and James Case

Review Unknown Local Terms

May Re-Scan File for Unknown Terms

©2011 Regenstrief Institute and James Case

Replace Local Terms

Assign LMOF AttributeReplacement Options

©2011 Regenstrief Institute and James Case

RELMA Cleaning ToolsUse this tool to make global substitutions

©2011 Regenstrief Institute and James Case

Term Substitution

Save this global substitution for only this working set

©2011 Regenstrief Institute and James Case

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.

©2011 Regenstrief Institute and James Case

Searching for LOINC Terms

©2011 Regenstrief Institute and James Case

Simplified Search Only Tool

©2011 Regenstrief Institute and James Case

Search Window

Enter Search Terms

Limit to Specific Units

Use Automapper logic

Help File

Restrict to “Common Orders”

Restrict to “Common Results”

©2011 Regenstrief Institute and James Case

Search Window

Hematocrit bld qn

“Common Tests” rank

©2011 Regenstrief Institute and James Case

New RELMA Helpfile

©2011 Regenstrief Institute and James Case

Context Menu

Right click to bring up context menu

©2011 Regenstrief Institute and James Case

Mapping Local Terms

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Mapping Screen

View or edit local term

Quick select button list

Custom Grid Configuration

Enter local term number

©2011 Regenstrief Institute and James Case

Configure Grid

Reorder grid elements

Select elements to display

Reset Default ConfigurationVisually resize elements

©2011 Regenstrief Institute and James Case

Quick choice buttons

Viewing LOINC term detail

©2011 Regenstrief Institute and James Case

View Local Term Details

Select level of detail to display

©2011 Regenstrief Institute and James Case

View Local Term DetailsSelect text size

©2011 Regenstrief Institute and James Case

Select detail display level

Select level of detail to display

©2011 Regenstrief Institute and James Case

Standard Mapping Screen

Begin a search(or hit “enter”)

EEK! What’ll I do?!

©2011 Regenstrief Institute and James Case

Standard Mapping Screen

Click to show words

used in search

©2011 Regenstrief Institute and James Case

Initial Mapping Results

Use term checkbox

Number of LOINC terms containing

keywordBattery terms

included in search

©2011 Regenstrief Institute and James Case

Revised Mapping Results

Number of matching

records found

Match units selected by

default

©2011 Regenstrief Institute and James Case

Re-revised Mapping Results

Number of matching

records foundMatch units unselected

©2011 Regenstrief Institute and James Case

Standard Mapping Screen

Clear all input fields

Enter keywords here

CANINE DISTEMPER VIRUS IF

©2011 Regenstrief Institute and James Case

Ad hoc term search

©2011 Regenstrief Institute and James Case

Standard Mapping Screen

Navigate through the local terms

©2011 Regenstrief Institute and James Case

Tabbed Access to Functions

Navigate to Functions from Mapping Page

Switch between Grid and Tree Views

©2011 Regenstrief Institute and James Case

Tree View

©2011 Regenstrief Institute and James Case

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 rows that have LOINC Codes

©2011 Regenstrief Institute and James Case

Tree View

Cannot map to terms

representing LOINC parts

Can map to terms with LOINC Codes

Tree Navigation Buttons

©2011 Regenstrief Institute and James Case

Assigning a LOINC Map

Highlight correct term

Click “Map” Button (or doubleclick)

©2011 Regenstrief Institute and James Case

Adding Mapping Comments

If comments option is selected, prompt appears

Check with Frank in Chemistry

©2011 Regenstrief Institute and James Case

Assigning a LOINC Map

LOINC Term Assigned

©2011 Regenstrief Institute and James Case

View LOINC Term Details

View details for a specific LOINC Term

Right clicking on a LOINC term brings up a Task Menu

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

View Panel Children

Select View Panel Children from context menu

©2011 Regenstrief Institute and James Case

Panel Children

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Configure Export Options

Output Options

Include column headersSave Configuration

and/or Export

©2011 Regenstrief Institute and James Case

Excel Export Format

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More on Searching Mapping Screen

©2011 Regenstrief Institute and James Case

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”

©2011 Regenstrief Institute and James Case

Search Qualifiers

Includes Glucuronidase, Glucosidase,

Glucosylceramidase, etc.

Detailed help available

©2011 Regenstrief Institute and James Case

Combining Search Terms

Reduced number of terms

Exclude Glucosidase

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Applying advanced search

©2011 Regenstrief Institute and James Case

Limiting Searches

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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 • Limit to components/analytes with N or fewer words in their

name• Pop up search timing statistics after each search

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

©2011 Regenstrief Institute and James Case

Setting Search Limits

Click Hierarchy & Search Limits Tab

©2011 Regenstrief Institute and James Case

Setting search limitsCan also set most of them by toggling buttons

at the bottom of the screen

Toggle Buttons

©2011 Regenstrief Institute and James Case

Search Constraints

Predefined, general search constraints

Attribute trees

Local Unit Constraint:Default is “ON”

Type toggle boxes

©2011 Regenstrief Institute and James Case

Terms Consistent with Units

Only terms consistent with mmol/L appear

New! - Status saved between

editing sessions

©2011 Regenstrief Institute and James Case

Setting Search Limits

Specimen constraints

©2011 Regenstrief Institute and James Case

Terms Consistent with Specimen

CSF

Enter default Specimen

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Terms Consistent with Specimen

Only CSF Terms are returned

©2011 Regenstrief Institute and James Case

Setting Search Limits

New! - Exclude laterality

©2011 Regenstrief Institute and James Case

Exclude laterality

Laterality terms

©2011 Regenstrief Institute and James Case

Setting Search Limits

New! - Restrict to common orders

©2011 Regenstrief Institute and James Case

Restriction to common orders

Large number of candidates New! Common

orders rank

©2011 Regenstrief Institute and James Case

Setting Search Limits

Methodless Terms Restriction

Override Methodless Terms Restriction

©2011 Regenstrief Institute and James Case

Limit to Methodless Terms

Both method and method-less terms

©2011 Regenstrief Institute and James Case

Limit to Methodless Terms

Only Methodless Terms Appear

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Methodless Only Unchecked

All terms returned

©2011 Regenstrief Institute and James Case

Methodless Only Checked

Only Methodless terms returned

Differ in one or more components

©2011 Regenstrief Institute and James Case

Conditional Methodless

More terms returned

No method-less term; all shown

©2011 Regenstrief Institute and James Case

Setting Search Limits

Limit to Lab Tests Only (No Clinical LOINC Terms)

©2011 Regenstrief Institute and James Case

Setting Search Limits

Limit to common lab tests

©2011 Regenstrief Institute and James Case

Setting Search Limits

Limit Number of Words in the Component Attribute

©2011 Regenstrief Institute and James Case

Limit Number of Component Words

Without Limit Applied: 850 terms returned

©2011 Regenstrief Institute and James Case

Limit Number of Component Words

With Limit Applied: 68 terms returned

Restriction appears on Toggle Bar

(cannot toggle off)

Component limited to 1 word

©2011 Regenstrief Institute and James Case

Setting Search Limits

Include Trial, Deprecated or Discouraged LOINC Codes with

Returned Terms

©2011 Regenstrief Institute and James Case

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

©2011 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

©2011 Regenstrief Institute and James Case

Order/Observation Restriction

Order or Observation preference

©2011 Regenstrief Institute and James Case

LOINC Hierarchies – Class Tree

Three top-level branches

Tree Navigation Buttons

©2011 Regenstrief Institute and James Case

Before Class Restriction

Large number of candidate terms

Many terms have class of “CHAL”

©2011 Regenstrief Institute and James Case

Search Trees

Restrict eligible tests to non-challenge

chemistry tests only

+Chem* +non

©2011 Regenstrief Institute and James Case

Following Class Restriction

Only Non-Challenge Chemistry tests

returned

©2011 Regenstrief Institute and James Case

System Hierarchy

©2011 Regenstrief Institute and James Case

Component Hierarchy

Show the LOINC Codes associated with these

components

Click on details for more information about the

selection

©2011 Regenstrief Institute and James Case

Details Screen LOINC Part

©2011 Regenstrief Institute and James Case

Show Associated LOINCs

©2011 Regenstrief Institute and James Case

LOINC Term Details Screen

Detailed Information on LOINC Parts

©2011 Regenstrief Institute and James Case

Tree Export Tools

Configure Export Format

Export according to Configuration

©2011 Regenstrief Institute and James Case

Tree Export Configuration

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

LOINC Part Search

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

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

• Demo• Campylobacter fetus, not Ab

©2011 Regenstrief Institute and James Case

Navigating through the Mapping Process

©2011 Regenstrief Institute and James Case

• 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

©2011 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.

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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. Interpretation• Available LOINC Terms too Specific/General• Panel vs. Discrete Test

• Common in Microbiology

©2011 Regenstrief Institute and James Case

Using your Mapped Terms

• Print results of LOINC Mapping• Export to File

©2011 Regenstrief Institute and James Case

Configure Export Format

Context Sensitive Export Configuration

©2011 Regenstrief Institute and James Case

LMOF Export Configuration

Select Fields to Export

Select Export Format

Save Configuration and Export

©2011 Regenstrief Institute and James Case

Print Mapped Terms from View/Add/Edit Menu

May highlight terms to be printed

Click Print button to Preview output

©2011 Regenstrief Institute and James Case

Formatted Report Output

Click Print button to output formatted report

©2011 Regenstrief Institute and James Case

Custom Export Configuration

Select the Fields you wish to Export

Select the Format you wish to Export

©2011 Regenstrief Institute and James Case

Excel™ Export

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Picking the Lab Auto Mapper

©2011 Regenstrief Institute and James Case

Lab Auto Mapper Start Screen

Maximum number of terms to return

Can restrict search to common tests

©2011 Regenstrief Institute and James Case

Lab Auto Mapper Start Screen

Local terms used for mapping

Local test code

©2011 Regenstrief Institute and James Case

Lab Auto Mapper - Mapping Screen

©2011 Regenstrief Institute and James Case

Exporting Mapped Terms

Export Terms to Delimited File

©2011 Regenstrief Institute and James Case

Export Terms Dialog

Check Fields you wish to export

Select Delimiter

Select Term Set

©2011 Regenstrief Institute and James Case

Other RELMA® Features

©2011 Regenstrief Institute and James Case

Panels, Forms and Survey Review

Review Panels, Forms and Surveys

Review Panels, Forms and Surveys

©2011 Regenstrief Institute and James Case

Government Forms

Form Name

Component LOINC terms

©2011 Regenstrief Institute and James Case

Laboratory Panels

Expand category to see panels

Double-click panel name to see

components

©2011 Regenstrief Institute and James Case

Expanded Panel Detail

©2011 Regenstrief Institute and James Case

Expanded Clinical Panel

©2011 Regenstrief Institute and James Case

Clinical Panels

Find where a term has been used

35089-2, 35090-0

©2011 Regenstrief Institute and James Case

LOINC Term Panel Usage

©2011 Regenstrief Institute and James Case

Other Survey Instruments

©2011 Regenstrief Institute and James Case

HIPAA Attachments

View Various HIPAA Attachments

©2011 Regenstrief Institute and James Case

HIPPA Attachment Tree

©2011 Regenstrief Institute and James Case

Expanded Attachment Data

©2011 Regenstrief Institute and James Case

Can’t find the term you

want?

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Proposing New LOINC Terms

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Propose new LOINC terms

Select Propose a new LOINC

©2011 Regenstrief Institute and James Case

Required fields in red

Navigate through proposed terms

Create new term, save current term

or Exit form

Advanced/Simple toggle

©2011 Regenstrief Institute and James Case

Preview Proposed Terms

Review your new terms

©2011 Regenstrief Institute and James Case

Review Proposed Terms

All proposed terms fully editable

Choose whether to send or postpone

X

X

X

James T. Case DVM, PhD

NIH/NLM

James.case@mail.nih.gov

301-555-1314

301-555-1315

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

Use Existing Terms as Template

Select your closest match

Click the Propose Term button

©2011 Regenstrief Institute and James Case

Use Existing Terms as Template

All required components filled in

©2011 Regenstrief Institute and James Case

Using LOINC and SNOMED Together

©2011 Regenstrief Institute and James Case

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:

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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

©2011 Regenstrief Institute and James Case

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)

©2011 Regenstrief Institute and James Case

Q and A Session

©2011 Regenstrief Institute and James Case

ExerciseMap your own data

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