Post on 13-Apr-2017
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 dvreeman@regenstrief.org
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
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
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
Component Structure
Analyte Name^Challenge^Adjustments
Formal analyte name Specify “subanalytes” May have subclasses
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
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
System The system (context) or specimen type upon which the
observation was made.
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
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
DEEDS
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