Terminological Systems in Medicine Ronald Cornet, PhD Dept. of Medical Informatics Academic Medical...

Terminological Systems in Medicine

Ronald Cornet, PhD

Dept. of Medical Informatics

Academic Medical Center – University of Amsterdam

[email protected]

Overview

Part I – The role of Coding, Classification and Terminology in Registration of Patient Data

Part II – SNOMED CT

Registration of Patient Data –The role of Coding,

Classification and Terminology

Outline

ContextCoding & ClassificationCoding Systems OverviewCoding in PracticeCoding Systems, the next generationTypes of systems & Requirements

Starting point: E-record

Cost of careQuality of care

Motivation: cost of care

Digitizing medical records in the U.S. could save the health care industry as much as$81 billion a year and help medical practitioners avoid mistakes

The study found that electronic medical records systems save money by reducing redundant care, speeding patient treatment and improving safety.

“Can Electronic Medical Record Systems Transform Healthcare?An Assessment of Potential Health Benefits, Savings, and Costs” - Sep. 14, 2005

Hillestad R, Bigelow J, Bower A, Girosi F, Meili R, Scoville R, and Taylor R (Rand Corp.)Health Affairs, Vol. 24, No. 5.

Motivation for Clinical Terminology

Costs Terminology use benefits entire health system

» Save as much as 5% of total healthcare costs*

» up to $100 Billion per year in US

* Source - Walker J et al., Market Watch 2005:19th January;10-18

Documentation in the EPR/EHR Decision support Clinical audit Reporting Summaries Administrative & management information Epidemiology Billing Resource management

Direct

Indirect

[National Health Services – United Kingdom]

Use of Patient Data

Documentation of Patient Data

Free text Expressive, Maximal freedom, Precise Ambiguous Hardly computer-processable

Coded Limited expressiveness Potentially less ambiguous Computer-processable

Outline


Data reduction Standardization Avoiding problems with natural language

Acute heart attack Acute myocardial infarct Acute myocardial infarction Myocardial infarction acuta Acute coronary thrombosis Solution: 410 Acute myocardial infarction

Why using codes

A code is a sequence of symbols which refers to a concept and which can be used for identification and selection

Coding

Coding

Example: coding genderMale = m

Female = f

Principles for defining Codes

Explicit eligibility criteria (definitions) E.g. genotypic, phenotypic gender

Disjoint categories male, female

Exhaustive categories male, female, other, unknown

Reasonable… Klinefelter's syndrome (XXY) ?

Types of Codes

Significant Mnemonic Juxtaposition Hierarchical

Non-significant / context free Random Sequential

Mnemonic Codes

Formed from one or more of the characters of its related class M = Male, F = Female KL204 = KLM flight 204

Juxtaposition Codes

Composite codes consisting of segmentsRoom J-1B-115

building floor location

Hierarchical Codes

Example from ICD-9-cm: 003 Other Salmonella Infections

003.0 Salmonella Gastroenteritis 003.1 Salmonella Septicemia 003.2 Localized Salmonella Infections

» 003.20 Localized Salmonella Infection, unspecified

» 003.21 Salmonella Meningitis

» 003.22 Salmonella Pneumonia

Aggregation, retrieval on different levels

Reasons for using significant codes

Codes can be rememberedMeaning can be derived from code(Juxtaposition and hierarchical) codes can

be used for aggregation

Problems with significant codes

Mnemonics

07.45 KL 1124 Copenhagen Arrived 07.4107.45 KQ 1124 Copenhagen Arrived 07.4107.45 MH 9264 Copenhagen Arrived 07.4107.45 NW 8400 Copenhagen Arrived 07.41

KLMKenya AirwaysMalaysia AirlinesNorthwest Airlines

1 flight, 4 codes!

Problems with significant codes

Hierarchical codes: 003 Other Salmonella Infections

003.0 Salmonella Gastroenteritis 003.1 Salmonella Septicemia 003.2 Localized Salmonella Infections

» 003.20 Localized Salmonella Infection, unspecified» 003.21 Salmonella Meningitis» 003.22 Salmonella Pneumonia

No other aggregation than “Salmonella infections”, e.g. “Meningeal infections”

Non-significant codes

Random: pick any (unique) numberSequential: number consecutively, e.g.,

start by 1 and increase

Such meaningless codes should NOT be presented to users

Outline


Classification

Classifying:

1. Designing a classification

2. Assigning a class to an object

Classes of Objects

How many classes do you see below? Eagle Elephant Shark Telephone Television Videocamera

Classes of Objects

How many classes do you see below?

Classification Principles

Aristoteles (384BC - 322BC): “definitio per genus proximum et differentia specifica“(definition by the nearest higher class and differentiating properties).

Classes fulfill criteria of superclassesClasses are more specific than superclasses

Classification example: Biology

African Elephant TaxonomyKingdom: Animal

Phylum: Chordata / Craniata / Vertebrata» Class: Mammalia / Theria / Eutheria /

Afrotheria Order: Proboscidea

– Family: Elephantidae

* Genus: Loxodonta (African elephants)

+ Species: Loxodonta africana

Full lineage is over 20 levels!http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/

Example: ICD-10

Certain Infectious and parasitic diseases Viral infections of central nervous system

» A87 Viral meningitis A87.2 Lymphocytic choriomeningitis

Systems such as ICD-10 typically contain10.000s to 100.000s of terms (codes)

Classification “Chapters” ICD-10 (1) Certain Infectious and parasitic diseases Neoplasms Diseases of the blood and blood forming organs

and certain disorders involving the immune mechanism

Endocrine, nutritional and metabolic diseases Mental and behavioural disorders Diseases of the nervous system Diseases of the eye and adnexa

Classification “Chapters” ICD-10 (2)

Diseases of the ear and mastoid process Diseases of the circulatory system Diseases of the respiratory system Diseases of the digestive system Diseases of the skin and subcutaneous tissue Diseases of the musculoskeletal system and

connective system Diseases of the genitourinary system

Classification “Chapters” ICD-10 (3) Pregnancy, childbirth and the puerperium Certain conditions originating in the perinatal period Congenital malformations, deformations and chromosomal

abnormalities Symptoms, signs and abnormal clinical and laboratory

findings, n.e.c. Injury, poisoning and certain other consequences of external

causes External causes of mortality Factors influencing health status and contact with health

services

Single ordering (monohierarchy)Pros

Categories are mutually exclusive (disjoint) No double counts Straightforward, understandable

Cons Only 1 supported categorization Disjointness often “artificial”

Multiple Ordering (polyhierarchy)Pros

Multiple aspects (“axes”) for ordering, e.g.:Anatomic location, Etiology, Morphology

Multiple ‘paths’ to itemsCons

Double counts (e.g. “Viral Meningitis” is both “Infectious disease” and “Meningeal disease”)

More complex



Single or Multiple Classification?Coding

Cla

ssif

icat

ion

Coding: which information?

Shortly after dinner on the day before admission to the hospital, this 48-year-old obese woman developed a cramping, epigastric pain that radiated to the back, followed by nausea and vomiting. The pain was not relieved by position or antacids. The pain persisted, and 24 hours after onset, the patient sought medical consultation. The patient was admitted to the hospital with a diagnosis of acute pancreatitis. Radiological findings included widening of the duodenal “C” loop and blurring of the left psoas muscle margin. Serum amylase was 1120 units per liter. The day after admission, the patient seemed to improve. However, that evening she became disoriented, restless, and hypotensive. Despite intravenous fluids and norepinephrine, the patient remained hypotensive and died 8 hours later.

Lu TH, Shih TP, Lee MC, Chou MC, Lin CK.Diversity in death certification: a case vignette approach.J Clin Epidemiol. 2001 Nov;54(11):1086-93.

Classification: cause of death?

Shortly after dinner on the day before admission to the hospital, this 48-year-old obese woman developed a cramping, epigastric pain that radiated to the back, followed by nausea and vomiting. The pain was not relieved by position or antacids. The pain persisted, and 24 hours after onset, the patient sought medical consultation. The patient was admitted to the hospital with a diagnosis of acute pancreatitis. Radiological findings included widening of the duodenal “C” loop and blurring of the left psoas muscle margin. Serum amylase was 1120 units per liter. The day after admission, the patient seemed to improve. However, that evening she became disoriented, restless, and hypotensive. Despite intravenous fluids and norepinephrine, the patient remained hypotensive and died 8 hours later.

Lu TH, Shih TP, Lee MC, Chou MC, Lin CK.Diversity in death certification: a case vignette approach.J Clin Epidemiol. 2001 Nov;54(11):1086-93.

Outline


Overview of Coding Systems

Large number of systems Unified Medical Language System (UMLS)

Metathesaurus 1 includes over 100 systems, totaling more than 1.000.000 medical concepts

Systems are large Number of concepts has increased from ~ 100

to > 100.000

1 http://www.nlm.nih.gov/pubs/factsheets/umlsmeta.html


Diseases ICD

SpecialtiesAnatomyLiteratureGenomics

ICD

London Bills of Mortality(16th century) 60 disease categories Collected by parish clerks

International List of Causesof Death (19th century) – ICD

International Classificationof Diseases (20th century) –ICD-10, tenth revision of ICD


Diseases SNOMED – Systemized Nomenclature of

MedicineSpecialtiesAnatomyLiteratureGenomics

SNOMED CT

Aims at coding of detailed information“first episode of severe, acute E-coli pneumonia with sudden onset”

Formal definitions provide multiple classifications

1965 SNOP

1974 SNOMED

1998 SNOMED Version 3.5

2000 SNOMED RT (= 3.5 + READ)

2002 SNOMED CT


DiseasesSpecialties

DSM – Mental Health ICPC – Primary Care

AnatomyLiteratureGenomics


DiseasesSpecialtiesAnatomy

Terminologia Anatomica FMA – Foundational Model of Anatomy

LiteratureGenomics


DiseasesSpecialtiesAnatomyLiterature

MeSH – Medical Subject HeadingsGenomics


DiseasesSpecialtiesAnatomyLiteratureGenomics

GO – Gene Ontology


And many, many more…

http://www.nlm.nih.gov/research/umls/sources_by_categories.html

ICD-9-CM

DSM4ICD10

CDT5CPTNANDA

NIC

NOCOmaha

UltraSTAR

Loinc

COSTAR

MedDRA

WHOART

OMIM

Outline


Coding in Practice, scenario 1

Clinician records items as codes By entering (recollected) codes

» e.g. gender

By using a pick list

By searching for phrases» e.g. “meningo”

Coding in Practice, scenario 2

Clinician records free textClinical Coders derive codesDifferent codes are needed for different

purposes (billing, mortality, …)

“Patient trajectory”task terminological phrase

admission operation for lower third rectum cancer

scheduling abdominoperineal amputation of rectum

reporting low anterior resection of rectum with double stapling technique

discharge other anterior resection of rectum, ICD-9-CM 48.63

reimbursement operation for rectum cancer, DRG 147

cost analysis anterior resection of the rectum with double stapling technique

quality assurance low anterior resection of rectum without temporary colostomy and operation for lower third rectum cancer

[Rossi Mori]

ICD Code accuracy

Main error sources along the ‘‘patient trajectory’’ include amount and quality of information at admission, communication among patients and providers, the clinician’s knowledge and experience with the illness, and the clinician’s attention to detail.

Main error sources along the ‘‘paper trail’’ include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding.

O'malley KJ, et al.Measuring Diagnoses: ICD Code Accuracy.Health Serv Res. 2005 Oct;40(5 Pt 2):1620-39.

Coding consequences

Codes often lack detail that is clinically necessary

Coding can be time-consuming Searching the correct code Searching the correct description

Data in Patient Records

Patient data are attributes + valuesIn a record, these data are stored as record

items having a value.Male patient: gender = maleKidney patient: disease = renal failure

Coding practice

Patient record item

Blood pressure

Hemoglobin level

Disease

Patient data/code values

120/80

Normal

Serum Hepatitis

at rest?after exercise?

What is the “norm”?

The same as Hepatitis B?

Before or after dialysis?

Definitions are crucial!

Coding Quiz (1): Rh positive

Item Value

Blood type Rh positive

Rh D antigen status Positive

Rh blood type D positive

Blood bank test result Rh positive

… …

What is the record item, and what is the code value, for a statement that the patient is Rh positive?

Example from Kent Spackman

Coding Quiz (2): MRSA

Item Value

Blood Cult MRSA

Blood Cult

Methicillin

S.Aureus

Resistant

MRSA Cult Positive

… …

Example from Jim Cimino

What is the record item, and what is the code value, for a test on blood culture of Staph. Aureus for methicillin resistance?

Coding practice – Current status

ICD-9(CM) and ICD-10: used globally, both for mortality and morbidity

SNOMED CT: Licensed to 9 countries, Canada and UK as

frontrunners

Outline


3 generations of coding systems

First-generation systems, (e.g. ICD, MeSH) fixed organization (typically hierarchical) simple representation such as a systematic list that is

alphabetically indexed Second-generation (e.g. MedDRA, SNOMED Int)

dynamic organization (i.e. provide multiple hierarchies) compositional, combining the simple list representation of

concepts with a knowledge base to define and extend these concepts

Third-generation (e.g. SNOMED CT, Gene Ontology) based on formal models providing symbols denoting concepts and

a set of formal rules to manipulate them

First generation: Problems

One fixed hierarchy

Lung diseasesInflammation of lungs

Lung tumor

Liver diseasesInflammation of liver

Liver tumor

lung diseases

inflammatory diseases

First generation: Problems

More detail requires many combinations

Infective Pneumonia Severity: severe, mild, moderate, fatal Course: acute, subacute, chronic, cyclic Cause: virus, bacterium, fungus

at least 4*4*3=48 combinations

Second-generation systems(e.g. LOINC, SNOMED International)

Dynamic organization (i.e. provide multiple hierarchies)

Compositional, combining the simple list representation of concepts with a knowledge base to define and extend these concepts

Published electronically

Example: SNOMED International

T-28000 Lungs

T-62000 Liver

M-40000 Inflammation

M-8FFFF Neoplasm

D2-0007F Pneumonia = T-28000 | M-40000

D5-F150F Liver tumor = T-62000 | M-8FFFF

Topography

Morphology

Second generation: Problems

Different codes for one concept

D2-00004 Infective pneumoniaDE-00000|T-28000 Infectious Disease + LungsM-40000|L-00110|T-28000 Inflamm. + Infectious Agent + Lungs A problem for selection and grouping,

e.g. based on “T-28000”

Impossible combinationsM-12000|T-28000 Fracture + Lungs

Third-generation systems(e.g. SNOMED CT, GALEN)

Formal models providing symbols denoting concepts

and a set of formal rules to manipulate them

Published electronically, requiring dedicated software

Example: SNOMED CT

infective pneumonia

polyhierarchy

explicit relations

explicit qualifiers

Third generation: problems

Harder to comprehendHarder to implementHarder to maintain

Vision for the Future

Patient data are registered: Detailed, for everyday clinical care Structured, for automated processing Once, to reduce duplicate efforts

Patient data are used: For a wide range of purposes For automated support

Outline


Types of systems

Coding system, classification, vocabulary…

Many names for (often) the same thing!

We prefer “Terminological System” as an umbrella term

Terminology

a list of terms

Thesaurus

order list of terms, synonyms

enterovirus type 72HAV - Hepatitis A virushepatitis A virushuman enterovirus 72human enterovirus serotype 72human hepatitis A virusinfectious hepatitis virus

Vocabulary

Definitions!Infective pneumonia, free text definition:

Inflammation of the lung parenchyma characterized by consolidation of the affected part, the alveolar air spaces being filled with exudate, inflammatory cells, and fibrin.

Formal definition:

Classification

hierarchical order

Coding system

Codes!

Nomenclature

rules for combinationsor the result of applyingthese rules

Terminological Systems

TerminologyThesaurusClassificationVocabularyNomenclatureCoding System

list of terms

ordered terms/synonyms

member_of arrangement

definitions

composition rules

codes as designators

Examples

SNOMED-CT: Terminology, Thesaurus, Classification, Vocabulary, Nomenclature, Coding System

ICD-10: Terminology, (Thesaurus), Classification, Vocabulary, Nomenclature, Coding System

Requirements of TS (1)1. Terminology to adequately describe patients’

health problems and the care process

Requirements: Domain completeness

Post-coordination Context-free codes

Non-ambiguity Synonyms Multiple languages

Requirements of TS (2)

2. Structure that supports aggregation of homogeneous groups

Requirements: Domain completeness

Post-coordination Context free codes

Definitions Non-ambiguity Non-redundancy Multi-classification Explicit relations Crossmapping


Direct

Indirect


Summary

Summary

Terminological systemscan support a broad range of usecome in various types, each with their own

characteristicsstill need to be further developed and

researched

Steps towards use of coded data

1. Electronic Patient Record

2. Structure data items

3. Structure data values1. Determine/develop appropriate Term.Systems

2. Integrate Terminological Systems into EPR

4. Record detailed coded data as soon as possible

5. Use coded data and term. system for analyses

The 81.000.000.000$ question

“What is the best terminological system?”

The answer(s)

There is no such systemIt depends on your needsIt depends on your possibilities

(e.g. technical, financial)

The terminological system that satisfies your needs and is properly implemented …and used

Round-up of Part I

Part II – SNOMED CT

SNOMED CT

What it isWhat it isn’tWhy (a system like) SNOMED?How to use itChallenges

About SNOMED

In development more than 40 years 1965 SNOP (Systematized Nomenclature of

Pathology) 1974 SNOMED (Systematized Nomenclature of

Medicine) 2000 SNOMED RT (Reference Terminology) 2002 SNOMED CT (Clinical Terminology)

= RT + Clinical Terms V3 (a.k.a. Read codes)

Owner & Maintenance

Until 2006: SNOMED Organization Fully owned by CAP (College of American

Pathologists)Since 2007: IHTSDO

International Health Terminology Standards Development Organization

9 Member states: USA, Canada, Australia, New Zealand, UK, Sweden, Denmark, Lithuania, Netherlands

Figures (July 2007 release)

376,046 concepts


376,046 concepts62 types of relations; 1,359,435 instances

Is a Part of Causative agent Associated morphology Laterality …


376,046 concepts62 types of relations; 1,359,435 instances1,060,424 English descriptions

US and UK English Also Spanish translation Danish and Swedish translations underway No Dutch translation, only Latin alphabets

What is SNOMED?

Terminological system Codes identify concepts Relations between concepts Definitions based on relations Terms describe concepts and relations Rules to compose concepts

Wat is SNOMED?

Wat is SNOMED?

Codes

Terms

Composition rules

Definitions based onrelations

What is SNOMED…?

NO Software!NOT PerfectNO Silver bulletNO Total solution

Part of the solution… With numerous new challenges

Why SNOMED?

Information is recorded and searched forIn many different ways

Acute pneumococcal bronchitis = Pneumococcal bronchitis + course acute = Acute bronchitis + cause pneumococcus

At many different levels Lower respiratory tract infection Acute inflammatory disease

Acute pneumococcal

bronchitis

Acute streptococcal bronchitis

Acute bacterial bronchitis

Bacterial lower respiratory infection

Bacterial respiratory infection

Respiratory tract infection

Infection by site

Infectious disease

Disorder of respiratory system

Respiratory finding

Bacterial infection by site

Bacterial infectious disease

Lower respiratory tract infection

Disorder of thorax

Finding of region of thorax

Disorder of lower respiratory system

Lower respiratory tract finding

Acute infective bronchitis

Acute bronchitis

Acute inflammatory disease

Bronchitis

Inflammatory disorder of lower respiratory tract

Inflammatory disorder of the

respiratory tract

Inflammatory disorder of the

respiratory system

Inflammation of specific body

systems

Inflammation of specific body

organs

Disorder of bronchus

Bronchial finding

Infectious disorder of bronchus

Streptococcal infectious disease

Disease due to Gram-positive

coccus

Disease due to Gram-positive

bacteria

Pneumococcal bronchitis

Pneumococcal infectious disease

Coding versus classification

SNOMED CT enables recording data in detail, and abstracting based on these data

Classifications (e.g., ICD, DRG) aim at aggregation; i.e., putting exactly one “label” on patients

Applications

RegistrationExchange of patient dataDecision supportChecking protocols and guidelinesCreating homogeneous groups of patientsHealthcare evaluation

How to use SNOMED CT

Invisible Coding “data items” and “data values” using

SNOMED CT

Gender Male263495000 248153007


Invisible Coding “data items” and “data values” using

SNOMED CT (semi-)automatic conversion of free text to

SNOMED CT concepts


Visible Pick lists with SNOMED CT terms/concepts Support composition

Challenges

Quality: correctness and completeness Implementation

Registration using SNOMED CT Exchange of patient data Decision support Checking protocols and guidelines Creating homogeneous groups of patients Healthcare evaluation

(Semi-)automatic classification (e.g., cause of death)

Creating appropriate subsets

Suppose you want a terminology

1. Determine what you want it for E.g., what users, which domain

2. Perform a requirements analysis

3. Perform a content coverage study1. Take sample from collected data

More information

Online SNOMED CT browsers http://snomed.vetmed.vt.edu/sct/menu.cfm http://www.jdet.com/

International Health Terminology Standards Development Organisation www.ihtsdo.org

[email protected]

Terminological Systems in Medicine Ronald Cornet, PhD Dept. of Medical Informatics Academic Medical...

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