2011 01 27 - clinical loinc tutorial - intro and foundations

An Introduction to Clinical LOINC

Stanley M. Huff, M.D.Intermountain Healthcare

[email protected]

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Outline for All Tutorials

• LOINC Introduction and Foundation

• Documents

• Assessment Instruments and Survey Instruments

• Radiology and Imaging

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Outline

• LOINC background and goals

• LOINC structure and content– Clinical LOINC– Examples

• Attachments

• Context specific hierarchies

• Collections

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Important facts

• LOINC 2.27 (June 2009) contains 55,056 codes– 40,302 Lab LOINC codes– 10,773 Clinical LOINC codes– 1,354 Claims Attachment codes– 2,629 Survey codes

• LOINC is protected by copyright, but is licensed Free for Use

• Download files and tools from Regenstrief Web Site– http://loinc.org/ – Reference manual, submission database, RELMA

• RELMA – a tool for mapping local codes to LOINC

http://loinc.org/

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Coverage

• Laboratory LOINC– All laboratory categories including genetic

testing , veterinary medicine testing

• Clinical LOINC– Many routine measures, parts of H+P, EKG,

Cardiac echoes, OB ultrasound, Nursing survey instruments, Much more

• HIPAA attachments – (Content managed by HL7)

• Survey Questions– Skilled nursing facility Minimum Data Set (MDS)

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The Messaging Paradigm

SystemSystemAA

SystemSystemAA

SystemSystemBB

SystemSystemBB

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Segment

HL7 Result Message (ORU)

Data Field

Component

MSH|^~\&|||||19981105131523||ORU^R01|PID|||100928782^9^M11||Smith^John^J|OBR||||Z0063-0^BP^LN|OBX||CE|8361-4^POSITION^LN||SIT^Sitting|OBX||NM|8479-8^SBP^LN||138|mmHg|

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Status

A code that identifies the units of numerical data

in OBX-5

A code that identifies the

datatypeof OBX-5

A code

that identifies the data in

OBX-5(Temp

Reading)

OBX-5: Data

OBX: a name-value pair approach

OBX||NM|11289-6^^LN||38|C^^ISO+|||||F

Other data fields include: date of observation, identity of provider giving observation, normal ranges, abnormal flags

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The code isfrom SNOMED

The code isfrom LOINC

OBX-5: Data

A code for Group O

A code that identifies the datatype as a

coded element

OBX: with a coded value

A code that identifies the data in

OBX-5(ABO Blood Group)

OBX||CE|883-9^Blood Group^LN||58460004^Group O^SCT|

So we are all using HL7, what is the problem?

You and I may know that these are similar results, but our computers will not.

• Site 1:OBX|1|CE|SysBP^Systolic BP||132||mmHg|

• Site 2:OBX|1|CE|SBP^Systolic BP||132||mmHg|

• Site 3:OBX|1|CE|BP^Systolic BP||132/70||mmHg|

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• Site 1:OBX|1|CE|8479-8^SysBP^LN||132||mmHg|

• Site 2:OBX|1|CE|8479-8^SBP^LN||132||mmHg|

• Site 3:OBX|1|CE|8479-8^Systolic BP^LN||132/70||mmHg|

The Goal

Agree on a universal coding system for clinical observations.

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How terminologies fit into the model

• LOINC – attributes/observables

• SNOMED CT – findings/values (mostly) and observables (some)

• First Data Bank - values

• RxNORM - values

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Focus of LOINC

• Value for ‘Observation Identifier’ (Seq. #3) of OBX– Or the name of the observation in other standards, such

as ASTM or DICOM

• Individual result names first, then panels– Panels are built based on the tests they contain– Panels can contain other panels

• Name should facilitate automated or manual matching (fully specified)– Create local labels as needed– Standard LOINC short names

• One common identifier for tests that are ‘clinically’ the same

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Brief History of LOINC

• Logical Observation Identifier Names and Codes

• Organized by Clement McDonald, 1994

• Supported by Regenstrief Institute and NLM

• Create a universal language for observation identifiers

• Laboratory observations were created first

• Creation of clinical observations began in 1996

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Approach

• Collect result names and descriptions– IHC, VA, Regenstrief, Mayo Clinic, 3M, Vendors

• Formulate a model to represent the individual pieces of information in the name– Avoid strategies that lead to “combinatorial explosion”

• Create “fully specified names”

• Adjust model as needed– Do any distinct entities have the same name?– Do any entities that are the same have different names?

• Repeat the process until no more adjustments are needed

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LOINC makes names for things in use

• We do not make all possible permutations that the six axes would allow (no blind cross products)

• We try to only make names and codes for things that are real (exist in someone’s system)

• We do make names that allow both atomic (post coordinated) and molecular (pre coordinated) styles– Some people wish we would be more prescriptive– Name everything, let others dictate usage

• We do object to violations of the HL7 model– No names that include post coordinated fields from other

parts of the HL7 message (status, priority, user role)

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Two LOINC committees

• Laboratory LOINC– Clem McDonald, Chair– All aspects of tests/measurements done on specimens

• Chemistry, Hematology, Microbiology, Histology, Cytology, etc.

• Clinical LOINC– Stan Huff, Chair– All aspects of tests/measurements on a patient

• Vital signs, Hemodynamic measurements, Physical findings, Radiology, Ultrasound, etc.

• Both committees meet at least 2-3 times each year

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Current and Former Clinical LOINC Members

James Barthel , Dean Bidgood, Bruce Bray, Bill Francis, Alan Golichowski, Daniel Vreeman, Karl Hammermeister, Anders Thurin, Barry Gordon, Warren Williams, James Campbell, Jim Cimino, Sue Bakken, Pat Wilson, Stan Huff, Doug Martin, Clem McDonald, Dan Pollock, Angelo Rossi Mori, Susan Matney, Jeff Suico, Wayne Tracy, Pavla Frazier, Pat Wilson, Lee Min Lau, Shawn Shakib, Bill Karitis, Thomas White, Steven Steindel,

Elizabeth King, Loren Stevenson, Sundak Ganesan, Ted Klein, Vivian Auld

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Clinical LOINC Subject Areas

• Vital Signs

• Hemodynamics

• Fluid Intake/Output

• Body Measurements

• Operative Notes

• Emergency Department

• Respiratory Therapy

• Documents (collections)

• Standard survey instruments

• EKG (ECG)

• Cardiac Ultrasound

• Obstetrical Ultrasound

• Discharge Summary

• History & Physical

• Pathology Findings

• Colonoscopy/Endoscopy

• Radiology reports

• Clinical Documents

• Tumor Registry

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LOINC Mascot

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Outline



• Attachments


• Collections

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LOINC codes are created systematically using a six axis model

<component> : <property> :<component> : <property> :<timing> : <system> :<timing> : <system> :<scale> : <scale> : <method><method>

General Form of Clinical LOINC Names

The first 5 parts are mandatory, but method is optional. Subparts of the six axes are created as

needed in specific subject areas.

8331-1 Body Temperature :TEMP :PT :MOUTH :QN

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Summary of the six primary axes (clinical)• Component

– Ejection fraction, heart beats, cardiac output, circumference

• Kind of property– Angle, area, length, mass, pressure, temperature

• Timing– Point in time, study minimum, maximum in 8 hours

• System– Head of fetus, tricuspid valve, ventilator setting

• Scale– Quantitative, ordinal, nominal (coded), narrative

• Method– Stated, measured, estimated, ultrasound, spirometry

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Component

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

• RR INTERVAL• ORIFICE (OF A HEART VALVE)• EJECTION FRACTION• HEART BEATS• BREATHS• CARDIAC OUTPUT• SEGMENTAL WALL MOTION• PROSTHETIC VALVE TYPE• FLUID INTAKE

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Subtypes – period as a separator

• CAPACITY.VITAL.FORCED• GRADIENT.MAX (as across a valve)• INTERNAL DIAMETER.MINOR

AXIS.SYSTOLE• BIRTHS.TERM• GLASGOW SCORE.VERBAL• R' WAVE AMPLITUDE.LEAD II• ST SEGMENT AXIS.HORIZONTAL PLANE• PHYSICAL FINDINGS.SENSATION• CALORIE INTAKE.TOTAL• TIDAL VOLUME MAX.SETTING

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Challenge/Pre condition - ^ as a separator

• FLUID OUTPUT.URINE ^ POST VOID• FRACTIONAL COLLAPSE ^ INSPIRATION• BREATHS ^ AT MAX VOLUNTARY

VENTILATION• RR INTERVAL ^ AT TRICUSPID FLOW

MEASUREMENT• GAS FLOW.MIN ^ PRE THERAPY• FLOW ^ AT 25-75% OF FORCED EXPIRATION• INTRAVASCULAR DIASTOLIC ^ STANDING• NEONATAL APGAR ^ 5M POST BIRTH• MULTISECTION ^ WITH ANESTHESIA• BODY WEIGHT ^ WITH CLOTHES

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Adjustments - ^ ^ as a separator

• DIFFUSION CAPACITY.CARBON MONOXIDE ^ ^ ADJUSTED FOR HEMOGLOBIN

• DIFFUSION CAPACITY ^ ^ ADJUSTED TO BODY CONDITIONS

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Kind of Property

• TYPE – selection of subtype (nominal items)• PRID – presence or identified (nominal items)• TIME – duration of time• COLOR – color• ANGLE – degrees of arch• APER – appearance• AREA - area• ELPOT – voltage• LEN – length• MASS – mass• MRAT – mass rate (gm/hr)• PRES – pressure• TEMP – temperature• FCN – function (of a body part or system)

The characteristic or attribute of the component thatis measured, evaluated, or observed.

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Timing

• PT - at a point in time

• STDY^MIN – minimum over the period of a study

• 24H - a twenty four hour shift

• 10H^MEAN – mean value for a ten hour period

• 8H^MAX – maximum value in an eight hour period

The interval of time over which the observationor measurement was made.

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System

• YOLK SAC^FETUS• UPPER GI TRACT• TRICUSPID VALVE^PATIENT• TRICUSPID VALVE^FETUS• SYNOVIAL SPACE• HEART.VENTRICLE.RIGHT• VENTILATOR• ARTERIAL SYSTEM• BLADDER• EYE.LEFT

The system (context) or body part aboutwhich the observation was made.

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Patient, Control, or Donor (as part of system)

• CONTROL

• PATIENT

• DONOR

• BABY

• FETUS

Non-patient values for this axis should be used with care, or combinatorial explosion could result

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Scale

• QN - quantitative– 4, 7.4, 1:8

• ORD - ordinal, the answers can be ranked– +/-, 1+, 2+, 3+ ….– mild, moderate, severe– none, rare, few, moderate, many, loaded

• NOM - nominal, answers are coded but unranked– Stool appearance – liquid, formed– Skin color – pink, dusky, cyanotic– Chest tube type

• NAR - answer is a two or more words of natural language, or as much as a paragraph of text

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Method

• STATED – reported verbally

• MEASURED – actually observed

• CALCULATED – numeric calculation

• US – ultrasound

• EKG – electrocardiogram

• ESTIMATED – an educated guess at the real value

• HELIUM REBREATHING – helium rebreathing

• SPIROMETRY – spirometry

• MANUAL – done by hand

• AUTOMATED – used an instrument

Procedure used to make the measurement or observation. Only used when it makes an important distinction in sensitivity or specificity.

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Putting it all togetherCode Component Prop TIME System Scale Method

8302-2 BODY HGHT LEN PT ^PATIENT QN

3140-1 BODY SURF AREA PT ^PATIENT QN DERIVED

8331-1 BODY TEMP TEMP PT MOUTH QN

8319-6 BODY TEMP TEMP 12H^MIN XXX QN

8629-8 Q WAVE DPT ELPOT PT HEART QN EKG

8632-2 QRS AXIS ANGLE PT HEART QN EKG

8642-1 PUPIL DIA LEN PT EYE.RIGHT QN AUTO

21611-9 AGE TIME PT ^PATIENT QN EST

21612-7 AGE TIME PT ^PATIENT QN REPORT

19867-1 CAPACITY.VITAL VOL PT RESP SYS QN

9279-1 BREATHS NRAT PT RESP SYS QN

11882-8 GENDER FIND PT ^FETUS NOM US

Use of XXX and {} (curly braces)

• Old style– 8319-6 BODY TEMP TEMP 12H^MIN XXX QN

• New style– 8319-6 BODY TEMP TEMP 12H^MIN {Body Loc} QN

• LOINC codes of these styles imply that the code may be used in post-coordinated expressions

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# 36

70

Pre and post coordination with LOINC codes

Dry Weight:Site #1

kg

Weight:Site #2

DrykgWetIdeal

70

7070

# 37

Two ways to say the same thing

•A single name/code and value– Dry Weight is 70 kg

•Combination of two names/codes and values– Weight is 70 kg

• Weight type is dry

# 38

Model fragment in XML

Pre-coordinated representation<observation> <cd>Dry weight (LOINC 8340-2) </cd> <value>70 kg</value></observation>

Post-coordinated (compositional) representation<observation> <cd>Weight (LOINC 3141-9) </cd> <qualifier> <cd> Weight type (LOINC 8337-8) </cd> <value> Dry (SNOMED CT 13880007) </value> <qualifier> <value>70 kg</value></observation>

# 39

Relational database implications

How would you calculate the desired weight loss during the hospital stay?

Patient Identifier

Date and Time Observation Type Observation Value

Units

123456789 7/4/2005 Dry Weight 70 kg

123456789 7/19/2005 Current Weight 73 kg

Patient Identifier

Date and Time Observation Type

Weight type Observation Value

Units

123456789 7/4/2005 Weight Dry 70 kg

123456789 7/19/2005 Weight Current 73 kg

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More complex examples

9273-4 NEONATAL APGAR^2M POST BIRTH FCN PT^PATIENT ORD

9192-6 FLUID OUTPUT.URINE VRAT 24H URINARY TRACT QN

11892-7 GESTATIONAL AGETIME PT ^FETUS QNUS.ESTIMATED FROM AC.HADLOCK84

10105-5 ST SLOPE.LEAD V6 ELPOTRAT PT HEARTQN EKG

8431-9 INTRACHAMBER SYSTOLIC PRES PTHEART.VENTRICLE.LEFT.OUTFLOW TRACT QN

8283-4 CIRCUMFERENCE.MAX LEN PTCALF.RIGHT QN

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Outline



• Attachments


• Collections

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HL7 & the Claims Attachment Recommendation

• HIPAA Legislation was passed in Aug 1996

• Extended debate– Different motivations for payers and providers

• Initial proposal to use X12 messages, HL7 Version 2 messages, LOINC

• Notice of proposed rule making (NPRM) in Sept 2005– X12 messages– HL7 CDA Release 1 standard (probably will now be R2)

• XML based standard for transmitting documents– LOINC codes

• No final rule yet

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Unsolicited Attachment

Yes

No

X12N 837+

X12N 275Additional Information

Provider Payer

Deliver aservice

Sufficient toPay?

Submits a claimwith SupportingDocumentation

Pay the claimDeny the

claim

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Request for Additional Information

No

Yes

X12N 837

X12N 277Request for

Additional information

X12N 275Additional Information

Provider Payer

Deliver aservice

Need moreinfo to pay?

Providersubmits a

claim

Requestadditional

documentation

Assemblesupporting

documentation

Pay the claim

Sufficient toPay?

Yes

Deny theclaim

No

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Organizations & Documents

X12 277 Transaction

12748-1

9832-1

X12 275 Transaction

HL7 CDA R1

15748-3

7832-8

20118-5

4332-7

12748-1

9832-1

ASC X12 &ASC X12 & Subcommittee Subcommittee

X12NX12N

X12 X12 Trans.Trans.Sets Sets

277, 275277, 275

TG2 Impl.TG2 Impl.Guides Guides 277, 275277, 275

Health Level Seven

HL7 CDA R 1

HL7 Claims

AttachmentsImpl.

Guide

LOINC Consortium

LOINCCodes

LOINCAttachment

Booklets

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Attachment Types Selected for HIPAA

• Attachment types ultimately selected for development and HIPAA recommendation:

1. Ambulance

2. Emergency Department

3. Rehabilitative Services

4. Lab Results

5. Medications

6. Clinical Notes

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CDA: Semi- or fully-structured HIPAA Claims Attachments

Autoadjudicate

<section><caption>

<caption_cd V="8709-8"/>Skin</caption><paragraph>

<content>Erythematous rash, palmar surface,left index finger.

<observation_media><observation_media.valueMT="image/jpeg">

<REF V="rash.jpeg"/>

</observation_media.value></observation_media></content>

</paragraph></section>

Provider Payer

Transcription*

Scanned Paper or Document Imaging*

Level 3 CPR

<section><caption>







Image + XML

Semistructured

Structured and coded

Specific XML forms*

<section><caption>







04/10/23 48

Outline



• Attachments


• Collections

04/10/23 49

Use cases for Context Specific Hierarchies

• Roll-up in decision support– Body weight– Body height– Blood pressure

• Basis for queries– “All surgery notes”– “All head x-ray reports”– “All hematology lab results”

• Control of data access– Tabs for document types

• Radiology– (by body region) – Head, neck, chest, abdomen, …– (by modality) – X-ray, CT, Ultrasound, Scans, …

• Documents– (by subject) – cardiology, ob-gyn, heme-onc, surgery, internal medicine, …– (by setting) – inpatient, ambulatory, home care, SNF, …

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Consultation Note Example

• 11488-4 Consultation note Find Pt {Setting} Doc {Provider}

• 34100-8 Consultation note Find Pt Critical care unit Doc {Provider}

• 34101-6 Consultation note Find Pt Outpatient Doc {Provider}

• 34101-6 Consultation note Find Pt Outpatient Doc General medicine

• 34749-2 Consultation note Find Pt Outpatient Doc Anesthesia

• 34104-0 Consultation note Find Pt Hospital Doc {Provider}

• 34102-4 Consultation note Find Pt Hospital Doc Psychiatry

• NewCD Consultation note Find Pt {Setting} Doc Internal medicine

• 34764-1 Consultation note Find Pt {Setting} Doc General Medicine

• 34776-5 Consultation note Find Pt {Setting} Doc Gerontology

• 34781-5 Consultation note Find Pt {Setting} Doc Infect. Disease

• 34795-5 Consultation note Find Pt {Setting} Doc Nephrology

• 34797-1 Consultation note Find Pt {Setting} Doc Neurology

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Outline



• Attachments


• Collections

04/10/23 52

Issues related to “collections”

• Two “kinds” of items within LOINC– Individual measurements/observations/data elements– Collections of measurements/observations/data elements

• Different codes for orders versus results?

• Different codes for narrative vs nominal?– Medication history – paragraph versus coded list– Want to have a single code to get all medication history

• Two kinds of “collections” but different things– Panels (known explicit content)

• Vital Signs, ABGs, CBC, Chem 7 panel (known explicit content)– Documents (vague or abstract content)

• Operative note, discharge summary, consult

• Bone marrow exam – text table of discreet data

• Separate codes for: rtf, Word, pdf, scanned images?

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Proposed stragegy

• For individual measurements– Continue to create codes that distinguish between character

identifiers, strings, codes, dates, numbers– Create generic parents as needed, relate parent to children

using new hierarchies

• For collections– Continue to distinguish panels (explicit list of contained

elements) from documents (ill defined or vague contents)– For documents, do not make distinct names based on

narrative, nominal, pdf, Word, scanned image

• Use the same codes for orders as for results– Just a code for “hematocrit”, no code for “hematocrit order”

or “hematocrit result”– Use context to complete the meaning

04/10/23 54

Literature References

• McDonald CJ, Huff SM, etal. LOINC® a universal standard for identifying laboratory observations – a 5-year Update. Clinical Chemistry, 2003

• Huff SM, Rocha RA, McDonald CJ, De Moor GJE, etal. Development of the LOINC® (Logical Observation Identifier Names and Codes) Vocabulary. Journal of American Medical Informatics Association, 1998, 5:276-292.

• Dolin RH, Huff SM, Rocha RA, Spackman KA, Campbell, KE. Evaluation of a “Lexically Assign, Logically Refine”Strategy for Semi-Automated Integration of Overlapping Terminologies. Journal of American Medical Informatics Association, 1998, 5:203-213.

• Forrey AW, McDonald CJ, DeMoor G, Huff SM , Leavelle D, Leland Fiers DT, Charles L, Griffin B, Stalling F, Tullis A, Hutchins K, Baenziger J. Logical Observation Identifier Names and Codes (LOINC) Database: A public use set of codes and names for electronic reporting of clinical laboratory test results. Clinical Chemistry, 1995.