2011 08 21 - LOINC Tutorial and Mapping Bootcamp - PHI 2011 Conference

LOINC Introduction and Mapping Boot Camp

Daniel J. Vreeman, PT, DPT, MSc Assistant Research Professor, Indiana University School of Medicine

Research Scientist, Regenstrief Institute, Inc

Public Health Informatics 2011 Conference, Atlanta, GA Interoperability Vocabulary Messaging Standards & Tools

08.21.2011 © 2011 [email protected]

Kathy Mercer Senior LOINC Developer, Regenstrief Institute, Inc

http://loinc.org/slideshows

Acknowledgements LOINC Development Team Kathy Mercer, Jaci Phillips, Ian Pyle, David Baorto, Fran Brahmi

RELMA Development Team John Hook, Mark Fisher, Karen Ahmed, Anandhi Sowmyan, James Dennis

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

Overview

1.  Origins of LOINC 2.  LOINC 101 3.  LOINC Collections 4.  Domain-specific Approaches 5.  Mapping Tools and Resources

photo via Vernio77

Origins of LOINC The lingua franca of clinical observation exchange

Similar name, different meaning…

meerkat meerkat mere cat meerkat photo via Caption Time

Soda or Pop?

Lab A Test Name: Lyme Disease Serology

Measures: B. burgdorferi Ab IgG

Method: ELISA Scale: quantitative

e.g.: Titer 1:40

Lab B Test Name: Lyme Disease Antibody

Measures: B. burgdorferi Ab IgM

Method: Immune blot Scale: qualitative

e.g.: Positive

what you see in the order list

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

Logical

Observation

Identifiers

Names and

Codes A universal code system that facilitates exchange,

pooling, and processing of results

If an observation is a question and the observation value is an answer…

LOINC provides codes for questions

Other vocabularies provide codes for the answers

What is my patient’s hemoglobin level? 718-7:Hemoglobin:MCnc:Pt:Bld:Qn

How fast does my patient usually walk? 41959-8:Walking speed:Vel:1W^mean:^Patient:Qn:Calculated

photo via Ed Yourdon

Institutional Repository

A

A Message Processor

MSH|^~\&|HOSPITAL_A|SAMPLE_HOSPITAL_A|||$YearMonthDay||||||||||||||| PID|||$patientId$||$patientName$|||||||||||||||||||| PV1|||||||$attendingDoctor$||$consultingDoctor$|||||||| OBR|1|||012^CBC/Auto Diff^HSPA^57021-8^CBC W Auto Diff^LN||$reqDate||||||||| OBX|2|NM|123^WBC^HSP_A^26464-8^Leukocytes [#/volume] in Blood^LN||10.8|K/MM3|||||F| OBX|3|NM|234^RBC^HSP_A^26453-1^Erythrocytes [#/volume] in Blood^LN||4.82|MIL/MM3|||||F| OBX|4|NM|345^HGB^HSP_A^718-7^Hemoglobin [Mass/volume] in Blood^LN||15.7|GM/DL|||||F| OBX|5|NM|456^HCT^HSP_A^20570-8^Hematocrit [Volume Fraction] of Blood^LN||45|%|||||||F|

HL7 v.2.X Message

LocalCode^LocalName^CodeSystem^LOINCcode^LOINCname^CodeSystem

Indiana Network for Patient Care

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

Result with a Coded Value

Data type of result (OBX-5) is a

coded element

This code is from LOINC

Code identifying this observation

(what are these results? Listeria culture)

This code is from SNOMED

Code identifying the result (L. monocytogenes)

A brief aside about terminology…

LOINC Terminology LOINC (noun) To LOINC, LOINCing, LOINCed (verb) [Chief, Head, etc] LOINCer (noun) LOINCification (noun) SNOMED Terminology SNOMED (noun) SNOMEDicated???

From “Standardizing the MDS with LOINC® and Vocabulary Matches”

http://aspe.hhs.gov/daltcp/reports/2007/MDS-LOINC.htm

Laboratory LOINC

Clinical LOINC

The LOINC Community Open. Nimble. Pragmatic.

Open Development Worldwide distribution at no cost

End-user content additions Welcome all comers

Volunteers

Regenstrief Institute Steward Developer of content

Developer of tools Developer of community Distributor

Voice

LOINC Codes Over Time By Release

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000 LOINC Codes

Lab Codes

laboratory terms only

Slope = 600

Slope = 2200

0

2,000

4,000

6,000

8,000

10,000

12,000 loinc.org members

14 new members per day 410 new members per month

12,200+ users in 143 countries

Downloads: ~1400/month

The LOINC Distribution

http://search.loinc.org

7,900 views

120 views 280 views

http://forum.loinc.org

http://loinc.org/usage

a.k.a. “Top 300 Orders”

International Adoption participation, translation, implementation

LOINC Submitters

Since 2009, 84 organizations from 14 countries

LOINC Translators

18 organizations

New and Updated

Estonian

French German

Greek Italian

Spanish

In-progress Catalan

Dutch French

Russian

Large Implementations

SIGA Saúde project Canada Health Infoway ePSOS Assistance publique - Hôpitaux de Paris Hong Kong Hospital Authority Red Agrolab BiTAC

Lots more…success is often silent

US Adoption A few key highlights

US Federal Agencies NLM VA

DoD IHS NCI

CDC

Other Key US Adoptions

HITSP eLINCS

NAACCR CDISC

NCQA/HEDIS, NQF

HL7

HIPAA

HIE’s

EHR Incentive Program

a.k.a. “Meaningful Use”

LOINC 101 LOINC for newbs (not nOObs)

LOINC Names fully-specified, with 6 parts

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 Testing instrument Specific details about the specimen Priority (e.g. STAT) Where testing was done Who did the test Test interpretation Anything not part of naming the test Stuff carried in other parts of HL7 message

Component

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

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


Component Structure

Analyte Name^Challenge^Adjustments

Formal analyte name Specify “subanalytes” May have subclasses

Challenge Two parts separated by “post”

Adjustments

Calcium Coronavirus Ag Calcium.ionized

1H post 100 g Glucose PO

<time delay>post<challenge type>

Adjusted to pH 7.4

Property

Major Categories: mass substance catalytic activity arbitrary number

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

* the most difficult LOINC axis



Fully Named Properties MCnc mass concentration

SCnc substance concentration

MCnt mass content

CCnc catalytic concentration

Prid presence or identity

Imp impression

Type “kind of”

Property is related to units of measure

mg/dL umol/L

mg/g U/L

Property * the most difficult LOINC axis

photo via jurvetson

MAPPING DANGER ZONE

Common Property Issues

Fraction = Part/Whole NFr: % Eosinophils / leukocytes

SFr: % HGB which is A2

Ratio = multiple analytes from same system MCrto: BUN/Creatinine in urine

Relative Ratio = measures from different system RelRto: actual to normal control

Fraction versus Ratio

Non-Pt timings are often found with Rate Property

Timing The interval of time over which the observation

or measurement was made

Pt 12H 24H

point in time 12 hour collection 24 hour collection


System The system (context) or specimen type upon which the

observation was made.


Ser Ser/Plas Bld Ur Flu Tiss XXX

serum serum or plasma whole blood urine body fluid tissue specified elsewhere

photo via AlishaV

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:

11670-7:Blood flow.mean:Vel:Pt:Aortic arch^fetus:Qn:US.doppler

System^Super System

photo via Xurble

Scale


Qn Ord Nom Nar

Quantitative continuous numeric can have operators

Ordinal Ranked set (1+, 2+, 3+)

Nominal unranked collection Taxonomy (e.g. bacteria)

Narrative

photo via puuikibeach

Method Only needed if interpretation affected

Different normal ranges Test sensitivity

Listed at the generic level Agglutination

Immunoassay Probe with target amplification


LOINC “Parts”

Uses translation, synonymy, building hierarchies, creating display names, linking descriptions

Hierarchies LOINC ‘class’ Each LOINC axis

Multi-axial Component | System

Separate download

LOINC Collections Panels, forms, surveys, and other patient assessments

photo via LuzA

Standardized Assessments

Vreeman DJ, McDonald CJ, Huff SM. Representing patient assessments in LOINC®. AMIA Annu Symp Proc. 2010;832-836. PMID: 21347095 .

Vreeman DJ, McDonald CJ, Huff SM. LOINC® - A Universal Catalog of Individual Clinical Observations and Uniform Representation of Enumerated Collections. Int J Funct Inform Personal Med. 2010;3(4):273-291.

Assessments are widely used…

…and not unlike other clinical observations

Purpose

LOINC could be a

master question file and

uniform representation

Hierarchy of a Panel in LOINC

Assessment Items

Question Text Question Source

External Copyright Terms of Use

Description/Definition

Units of Measure (UCUM)

HL7 Data Types (v2, v3)

Structured Answer Lists Answer List Attributes

OID External Link (URL)

Answer Item Attributes ID (contains “LA” prefix)

String Sequence

Local code Score

Attributes of Items in a Panel Instance

Display name override Coding instructions Cardinality

Local code on that form Skip logic Data type in form

Answer sequence override Consistency/validation checks Relevance equation

Panels/Forms Available as Separate Download

Assessments Currently in LOINC US Government Forms

CARE, MDSv2, MDSv3, OASIS B1, OASIS C, RFC US Surgeon General’s Family Health Portrait

Brief Interview for Mental Status (BIMS)

Confusion Assessment Method (CAM)

Geriatric Depression Scale (GDS)

HIV Signs and Symptoms Checklist

Home Health Care Classification howRU

Living with HIV (LIV-HIV)

Morse Fall Scale

OMAHA

PHQ (9 and 2) Quality Audit Marker (QAM)

Translational Research Variables

11,000+ variables

Oh snap!

photo via kimubert

CDC Immunization Panel

NAACCR

More Cooking…

photo via liber

Lots more already there!

Government Forms Lab Panels

Clinical Panels Other Surveys

HIPAA Attachments

HEDIS

photo via Rainbirder

Consolidated Health Informatics

Mapping Guidance and Approaches to Special Domains Microbiology, Reportable Conditions, Newborn Screening

Not just an IT problem photo via wakefielddavid

Get real. units, results, experts

Don’t be a one hit wonder.

photo via gsz

Introduction to LOINC Microbiology Kathy Mercer Senior LOINC Developer, Regenstrief Institute, Inc

Property/Scale Prid/Nom & Type/Nom

Prid (Presence or identity)/Nom (Nominal) Expected result comes from a list Coded or free text

SNOMED recommended “No growth”

Type/Nom As above, but no negative

Property/Scale ACnc/Ord

ACnc (Arbitrary concentration)/Ord (Ordinal) Expected results

Positive

Negative Detected Not detected

Yes No

System XXX = “to be specified in another part of the message” Specified

Ser

Urine

Wound

Cvx

Stool Isolate

Etc.

Routine Cultures

Routine Cultures Component = “Bacteria identified” Property = “Prid” Time = “Pt” System = Scale = Nom Method = “Culture”

Routine Cultures Component

Bacteria identified Fungus identified Virus identified

Routine Cultures “Bacteria identified”

Anything that will grow on routine culture media

Bacteria

Yeasts

Does not mean only positive results No growth Normal flora

No significant growth

Routine Cultures Method

Culture Anaerobic culture Aerobic culture

Organism Specific Cultures

Organism Specific Cultures Model 1

Component = * Property = “ACnc” Time = “Pt” System = Scale = “Ord” Method = “Organism specific culture”

Organism specific culture Model 1 Component

Genus & species of the organism (s) you are looking for

Bacillus anthracis

Campylobacter jejuni Staphylococcus aureus.methicillin resistant isolate

Organism Specific Cultures Model 2

Component = * Property = “Prid” Time = “Pt” System = Scale = “Nom” Method = “Organism specific culture”

Organism specific culture Model 2 Component

Salmonella sp &or Shigella sp identified Yeast identified Influenza virus identified

Mycobacterium sp identified Etc.

Smears

Smears Component = “Microscopic observation” Property = “Prid” Time = “Pt” System = Scale = Nom Method = *

Smears Method

Acid fast stain Acid fast stain.Kinyoun

Acid fast stain.Kinyoun modified Acid fast stain.Ziehl-Neelsen

Acridine orange stain Gram stain India ink preparation KOH preparation Wet preparation Microscopy.electron Microscopy.light Rhodamine-auramine fluorochrome stain XXX stain Etc.

Molecular testing

Molecular testing Component

Adenovirus DNA HIV1 RNA Chlamydia trachomatis DNA Chlamydia trachomatis rRNA Bacterial beta-glucuronidase (uidA) gene

Molecular testing Property/Scale

Property/Scale Units

Prid/Nom -‐

ACnc/Ord -‐

ACnc/Qn IU/mL

LaCnc/Qn Log IU/ml

NCNC/Qn Copies/mL

LnCnc/Qn Log copies/mL

MCnc/Qn pg/mL

Molecular testing Method

Probe Probe.amp.tar

Probe.amp.tar detection limit = 50 copies/mL

Probe.amp.tar detection limit = 0.5 log copies/mL Probe.amp.tar detection limit = 500 IU/mL

Probe.amp.sig Amplification/Sequencing

Antigen detection

Antigen detection Component

Organism name + Ag Adenovirus Ag Campylobacter jejuni+Campylobacter coli Ag

HIV 1 p24 Ag Haemophilus influenzae A Ag Hepatitis B virus little e Ag

Hepatitis B virus surface Ag

Antigen detection Method

Null = methodless Aggl = agglutination LA = latex agglutination Comp Fix = complement fixation EIA = any immunoassay HAI = hemagglutination inhibition IF Immune diffusion Immune stain RIA - no longer performed (replaced by EIA)

Toxins

Toxins Component

Organism + toxin Clostridium botulinum toxin

Organism + toxin + gene Clostridium botulinum toxin A gene

Staphylococcus aureus enterotoxin A (sea) gene

Bacterial + toxin + gene Bacterial cytolethal distending toxin (Cdt) gene

Bacterial shiga-like toxin 1 (STX1) gene

Toxins Method

Null = methodless Animal inoculation Cytotoxin tissue culture assay EIA IF Mouse bioassay Mouse bioassay.neutralization Probe.amp.tar

Antibody detection

Antibody detection Component

Organism name + Ab – e.g. Filaria Ab Ab.IgG – e.g. Filaria Ab.IgG

AB.IgG4 - e.g. Filaria Ab.IgG4 Ab.IgM - e.g. Filaria Ab.IgM Streptococcus pneumoniae 12 Ab (Streptococcus pneumoniae 12f Ab)

Antibody detection Property/Scale

ACnc/Ord ACnc/Qn Titr/Qn MCnc/Qn Ratio

Antibody detection Method

Null = methodless Aggl = agglutination LA = latex agglutination Comp Fix = complement fixation EIA = any immunoassay HAI = hemagglutination inhibition IB = immune blot IF Immune diffusion Immune stain RIA - no longer performed, replaced by EIA RPR VDRL

Susceptibilities

Susceptibility Testing Component

Generic antibiotic name Ampicillin Vancomycin

Gene Bacterial aminoglycoside resistance (aacA) gene

Mycobacterium tuberculosis pyrazinamide resistance (pncA) gene

Susceptibility Testing Property/Scale

Susc/OrdQn Acnc/Ord Prid/Nom Titr/Qn

Susceptibility Testing System

Isolate Isolate+Ser XXX

Susceptibility Testing Culture Method

Null = Methodless Agar diffusion Gradient strip MIC MLC SBT Method for Slow-growing mycobacteria

Susceptibility Testing Molecular Method

Genotyping Phenotyping Probe.amp.tar

Reportable Condition Mapping Table Reportable Condition | Lab Test Name | Lab Result

phinvads.cdc.gov

Future Goal

Interaction with PHIN VADS to associate LOINCs and conditions within RELMA

Great Scott!

Newborn Screening

photo via maile&justin

Newborn Screening (loinc.org/newborn-screening)

The LOINCer’s Toolbox

photo via Robert S Donovan

search.loinc.org If you want to poke around…start here!

RELMA® REgenstrief LOINC Mapping Assistant

Browse LOINC Map your local terms to LOINC

import/export

translate local words to LOINC-speak

manual/automated mapping

What’s it Good For?

RELMA Highlights Search Enhanced details view

Common test list Hierarchies Panels and forms

Export, copy, paste

Search Syntax Google-like

AND, OR, -<word>, +<word> Limit by category (e.g. micro)

Wildcards (? and *)

Assumes EXACT MATCH unless you use wildcards

More RELMA Features User Specified Search Limits

Selectable trees for: Class

Multi-axial (component/system)

System (specimen)

Component Method

Main Menu/Welcome Screen

Simple Search

Search Window

enter search terms

limit to specific units

limit to common tests

Detailed help

Search Window

“common tests” rank

photo via x-ray delta one

A brief aside… Developing convenience sets

A Few Tests Give Most Results

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

0 500 1000 1500 2000 2500 3000 3500 4000 Number of Laboratory Observation Codes (N)

Cum

ulat

ive

Labo

rato

ry O

bser

vati

on V

olum

e (%

)

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

http://loinc.org/usage

Mapper’s Guide to Top 2000

loinc.org/usage

We now return to our regularly scheduled program…

Importing Local Terms into RELMA

4 Ways to Build LMOF 1.  Hand enter 2.  Make your own table

3.  Import your test catalog from text file

4.  Import from real HL7 v2.x messages

bad bad

good

best

Searching and Mapping to LOINC

Photo via Jeffrey Beall

what RELMA was born to do

Main Menu/Welcome Screen

Hit it!

Core Mapping Screen Features

Customizable grid Sort by columns View term details

Export results grid Stores mappings

Context Menu

right click to bring up context menu

Mapping Screen

View or edit local term

Quick select button list

Navigate through the local terms

Standard Mapping Screen

Begin a search

(or hit “enter”)

Initial Mapping Results

Click to show words

used in search

Fiddlesticks !#*$%!! What now???

Initial Mapping Results

Use term checkbox

Number of LOINC terms containing

keyword

Battery terms included in

search

Revised Mapping Results

Units restriction selected by default

Re-revised Mapping Results

Number of matching

records found Match units unselected

Click any column header to re-sort

Ad hoc term search

Clear all input fields

Enter keywords here

CANINE DISTEMPER VIRUS IF

Tabbed Access to Functions

Navigate to Functions from Mapping Page

Switch between Grid and Tree Views

Tree View

Assigning a LOINC Map

Highlight correct term

Click “Map” Button (or doubleclick)

Assigning a LOINC Map LOINC Term

Assigned

View LOINC Term Details

View details for a specific LOINC Term

Right clicking on a LOINC term brings up a Task Menu

LOINC Term Details

Change to expanded details view

Change text size

LOINC Term Details: Panels

Exporting Rows from Grid

export

Configure Export Options

Output options

Include

column headers Save configuration and/or export

More on Search Syntax

Photo via Jeffrey Beall

Tips and Tricks

Search in a Field Field Example

Component component:chemotherapy

Property glucose property:CCnc

Timing glucose timing:24H

System glucose system:CSF

Scale glucose scale:Nar

Method mycobacterium method:EIA

Class glucose class:UA

Other Cool Tricks Use parentheses Fuzzy search (~)

glucose (phosphate OR phosphatase) rbc -ord

Bergdorferi~

component:(norepinephrine creatinine)

Limiting Your Searches Sometimes 65,000+ terms is too many

Photo via Joe Shlabotnik

Setting Search Limits

Reduces number of candidate terms

Many, many options for limits Hierarchy allows domain restrictions

with great power comes great responsibility

Photo via [cipher]

Setting Search Limits

click Hierarchy & Search Limits tab

Search Constraints

Predefined, general search constraints

Attribute trees

Local Unit Constraint:

Default is “ON”

Search Constraints

include Trial, Deprecated or Discouraged LOINC codes with

returned terms

Hierarchies

Restrict eligible tests to non-challenge

chemistry tests only

A Reminder About Search Limits

Indicates that you’ve got something set over here

Hierarchy Wrap-up All trees operate the same way All grids operate the same way Combine tree limits with others

“Mulligan” button

Search Hints and Tips Zero hit keywords are ignored

(may need to rephrase) Common causes of Zero results

Too many keywords Limits and keyword contradictions Local term weirdness

Units are GREAT discriminators

RELMA’s Auto Mapper Starting with our best guesses may save you time

Not exactly…

What Does It Do?

Batch processes local term file to get N- closest candidate LOINCs Uses words and units from local terms

Produces a ranked list for your review

Recent Improvements Faster. Way faster. Better clean-up routine New specimen guesser Better local to LOINC word finder Break ties with frequency data

(Lab) Auto Mapper

launch it here

a couple of options

print report or work through the ranked list when done

Intelligent Mapper - Mapping Screen

Auto Mapper On-Demand

photo via milos milosevic

The Race is On!

Get LOINCing! photo via ryarwood

2011 08 21 - LOINC Tutorial and Mapping Bootcamp - PHI 2011 Conference

Health & Medicine

Transcript of 2011 08 21 - LOINC Tutorial and Mapping Bootcamp - PHI 2011 Conference