Principles of Controlled Terminology

1
Principles of Controlled Terminology

• James J. Cimino
• Department of Medical InformaticsColumbia
  University

2
Lecture Outline

• Definitions and desiderata
• Survey of whats out there
• The Medical Entities Dictionary
• Advanced uses of coded data
• Case studies
• Learning more

3
Definition

• Terminology
• A finite, enumerated set of terms intended to
  convey information unambiguously

4
Some General Classes of Terms

• Diagnostic Procedures
• Therapeutic Procedures
• Medications
• Diagnoses
• Findings
• Organisms
• Anatomy

5
Uses of Terminology

• Storing in database
• Querying database
• Transfering data
• Billing
• Monitoring data

6
Term - Basic Features

• Unique Identifier (Code)
• 12345
• Official Name
• aspirin
• Synonyms
• ASA
• Translations
• NDC 5502 UMLS C0004057

7
Term - Advanced Features

• Classes
• antipyretic, anti-inflammatory, analgesic
• Semantic Links
• CAUSES gastritis
• TREATS arthritis
• Attributes
• UNITS mg

8
Desiderata for Terminology

• Content
• Concept Orientation
• Nonredundant
• Nonambiguous
• Permanent
• Nonsemantic Concept Identifiers
• Polyhierarchy
• Semantic relationships

9
Strict Hierarchy
disease
10
Polyhierarchy
disease
11
Semantic Network
has_specimen
measures_substance
serum potassium test
12
NEC
13
Survey of Whats Out There

• ICD9-CM and ICD-10
• SNOMED
• Read
• Nursing terminologies
• MEDCIN
• LOINC
• MeSH
• UMLS

14
ICD-9-CM and ICD-10

• 9th International Classification of Diseases
• WHO for collecting health statistics
• Clinical Modifications added
• 10th edition
• Clinical modifications under construction
• Strict hierarchy
• Synonyms and index terms
• Code determines place in hierarchy

15
ICD9-CM Examples

• ------Diseases-----
• 003. _at_ OTHER SALMONELLA INFECTIONS
• 003.0 SALMONELLA GASTROENTERITIS
• 003.2 _at_ LOCALIZED SALMONELLA INFECTIONS
• 003.20 LOCALIZED SALMONELLA INFECTION,
  UNSPECIFIED
• 003.21 SALMONELLA MENINGITIS
• 003.29 OTHER LOCALIZED SALMONELLA INFECTIONS
• ------Procedures-----
• 01. _at_ INCISION AND EXCISION OF SKULL, BRAIN,...
• 01.0 _at_ CRANIAL PUNCTURE
• 01.01 CISTERNAL PUNCTURE
• 01.09 OTHER CRANIAL PUNCTURE

16
SNOMED

• Systematized Nomenclature of Medicine
• College of American Pathologists
• Organized into axes
• Synonyms
• Assemble complex terms from axes
• SNOMED-RT (Reference Terminology) under
  development

17
SNOMED - Axes

• D - Diseases
• C - Drugs
• F - Function
• L - Living Organisms
• X - Manufacturers
• G - Modifiers
• M - Morphology
• J - Occupations
• A - Physical Agents
• P - Procedures
• S - Social Context
• T - Topography

18
SNOMED - Examples

• "D3-15000" "01" "Myocardial infarction,
  NOS" "(T-32020) (M-54700)"
• "D3-15000" "02" "Infarction of heart,
  NOS" "(T-32020) (M-54700)"
• "D3-15000" "02" "Cardiac infarction, NOS"
  "(T-32020) (M-54700)
• "D3-15000" "02" "Heart attack, NOS
  "(T-32020) (M-54700)"
• "D3-15010" "01" "Microinfarct of heart
  "(T-32000) (M-54701)
• "C-C137A" "01" "Bufferin Analgesic
  Tablets"
• "C-C137B" "01" "Bufferin Analgesic
  Caplets"
• "M-54700" "01" "Infarct, NOS"
• M-54700" "02" "Infarction, NOS"
• "M-54700" "05" "Infarcted"
• "M-54701" "01" "Focal infarct"
• "M-54701" "02" "Microscopic infarct"
• "S-10120" "01" "Mother, NOS"

19
Read Codes

• James Read's personal code set (1980's)
• Adopted by NHS 1990
• Summarization and patient care applications
• Directed acyclic graph
• Care-giver level of expression
• Natural clinical terms

20
Read Codes - Examples

• 182..A Y7CmDC P Chest pain
  
• Xa0wWK Y7CmFC P Pleurodynia
  
• 182Z.A Y7CmGC P Chest pain NOS
  
• Xa0wWK Y7CmIC S Painful breathing -pleurodynia
  
• 1826.A Y7CmJC P Parasternal pain
  
• 1823.A Y7CmLC P Precordial pain
  
• 1821.A Y7CmNC P Chest pain not present
  
• X75rWC Y7CmYC P Pain in heart
  
• 1829.A Y7CmZC P Retrosternal pain

21
Read Codes - Examples
22
Read and SNOMED

• SNOMED CT (Clinical Terms)
• Unified data model
• Merged content

23
Nursing Terminologies

• NANDA Taxonomy I
• Georgetown Home Health Care Classification
• Patient Care Data Set
• Omaha System
• AORN Perioperative Data Set
• International Classification of Nursing Practice
• Nursing Interventions Classification
• International Classification of Nursing Practice
• Nursing Outcomes Classification

24
Nursing Terminology Domains

• Diagnoses/judgments
• Ineffective individual coping (NANDA)
• Interventions
• Caregiving/Parenting - Teach (Omaha)
• Outcomes
• Family Functioning (NOC)
• Goals
• Patient moods will stabilize (PCDS)

25
Nursing Terminologies

26
MEDCIN

• Medicomp Systems, Inc.
• 100,000 clinical propositions
• Concept-oriented/concept-permanence
• Strict hierarchy
• Rich synonymy
• Cross-mapping to ICD-9, CPT-4, ICD-10, HCPCS,
  DSM-IV and others

27
MEDCIN - Examples

• 39448 Diagnoses, Syndromes and Conditions
• 32874 Pulmonary Medicine
• 31257 Bacterial Pneumonia
• 31259 Pneumococcal
• 90250 Drug Resistant
• 31260 Streptococcal Group A
• 35224 Salmonella
• 31264 Staphylococcal
• 31267 Geriatric Presentation
• 31265 Gram Negative
• 31261 Klebsiella
• 31262 Pseudomonas
• 31263 Hemophilus Influenzae
• 34821 Acinetobacter
• 31266 Neisseria Meningitidis
• 31268 Legionnaires Disease
• 31258 Pittsburgh Pneumonia Agent

28
LOINC

• HL7 Message
• MSHOBROBXObserveration, Result
• CodeNameCoding System
• Laboratory Objects, Identifiers, Names and Codes
• Self-defining names for lab tests
• Laboratory ? Logical
• Cooperative agreement with SNOMED

29
LOINC - Structure

• Component.subspecieschallenge
• Property
• Timing
• System
• Scale (Precision)
• Method
• Related names
• Other codes

30
LOINC - Examples

• 4764-5 GLUCOSE3H POST 100 G GLUCOSE PO SCNC
  PT SER/PLAS QN
• 1530-5 GLUCOSE3H POST 100 G GLUCOSE PO MCNC
  PT SER/PLAS QN
• 5955-0 COAGULATION THROMBIN INDUCED TIME PT
  PPPCONTROL QN
  TILT TUBE
• 12189-7 CREATINE KINASE.MB/CREATINE
  KINASE.TOTAL CFR PT SER/PLAS QN
  CALCULATION
• 13969-1 CREATINE KINASE.MB MCNC PT
  SER/PLAS QN

31
MeSH

• Medical Subject Headings
• National Library of Medicine
• Indexing the medical literature
• Multiple hierarchy
• Synonyms

32
MeSH Examples

• D011014 Pneumonia
• D018410 Pneumonia, Bacterial
• D007877 Legionnaires' Disease
• D011018 Pneumonia, Pneumococcal
• D011019 Pneumonia, Mycoplasma
• D009175 Mycoplasma Infections
• D011002 Pleuropneumonia,
  Contagious
• D011022 Pneumonia, Rickettsial
• D011023 Pneumonia, Staphylococcal
• D001996 Bronchopneumonia
• D009956 Ornithosis
• D011001 Pleuropneumonia
• D011015 Pneumonia, Aspiration
• D011017 Pneumonia, Lipid
• D011020 Pneumonia, Pneumocystis carinii
• D011024 Pneumonia, Viral

33
UMLS

• Unified Medical Language System
• National Library of Medicine
• Metathesaurus groups terms under single concept
  id
• No new hierarchy
• Translation of terms

34
Metathesaurus

• 92 sources
• 1,598,176 strings
• 730,155 concepts
• Strings have attributes
• Concepts have attributes, including Relations

35
Metathesaurus
Lexical group
String
String
36
Metathesaurus - MRCON

• C0153957ENGPL0180790PFS1084242benign
  neoplasm of heart
• C0153957ENGPL0180790VCS0245316Benign
  neoplasm of heart
• C0153957ENGPL0180790VOS1446737Benign
  neoplasm of heart, NOS
• C0153957ENGSL0524277PFS0599118Benign tumor
  of heart
• C0153957ENGSL0524278PFS0599510Benign tumour
  of heart
• C0153957ENGsL0018787PFS0900815Heart
• C0153957ENGsL0018787VOS0047194Heart
• C0153957GERPL1258174PFS1500120Gutartige
  Neubildung Herz

37
Metathesaurus - MRSO

• C0153957L0180790S0245316ICD10PXD15.13
• C0153957L0180790S0245316ICD99PT212.70
• C0153957L0180790S0245316RCD98SYB727.3
• C0153957L0180790S1084242MTHPNU0012870
• C0153957L0180790S1446737SNMI98PTD3-F01003
• C0153957L0018787S0047194ICD10PSD15.13
• C0153957L0018787S0900815MTHMMU0031580
• C0153957L0524277S0599118RCDAEPTB727.3
• C0153957L0524278S0599510RCD98PTB727.3
• C0153957L1258174S1500120DMDICDPTD15.11

38
Metathesaurus - MRSTY

• C0153957T191Neoplastic Process

39
(No Transcript)
40
Metathesaurus - MRREL

• C0002871CHDC0002891isaMSH99MTH
• C0002871CHDC0002892CSP98
• C0002871CHDC0002893RCD98
• C0002871RBC0221016MTHMTH
• C0002871RLC0002886mapped_toSNMI98SNMI98

41
MED

• Medical Entities Dictionary
• CPMC
• Multiple hierarchy
• Synonyms
• Translations
• Semantic links
• Attributes
• 60,000 concepts

42
Central Controlled Vocabulary
43
MED Structure
Medical Entity
CHEM-7
Plasma Glucose
44
Retrieving Results Individually
K1 4.2
K1 3.3
K2 3.2
K1 3.0
K3 2.6
K1
K2
K3
45
Retrieving Results by Class
K1
K2
K3
46
Advanced Uses of Coded Data

• Primary use
• Other patient care reuse
• Financial
• Management
• Information transfer (messaging)
• Clinical research
• Expert systems
• Information retrieval
• Vocabulary discovery

47
Case Studies

• Summary reporting

48
Case StudySummary Reporting
Chem20 Display
Serum Glucose Test
Fingerstick Glucose Test
Plasma Glucose Test
49
DOP Summary
50
WebCIS Summary
51
Case Studies

• Summary reporting

• HCFA requirements

52
Case StudyHCFA Requirements

• HCFA wont pay for lab batteries
• Individual tests now treated as orderable
  procedures
• Need to appear in database as procedures and as
  tests

53
Case StudyHCFA Requirements
Lab Procedure
Lab Test
Intravascular Glucose Test
Chem 7
Serum Glucose Test
Fingerstick Glucose Test
Plasma Glucose Test
54
Case StudyHCFA Requirements
Lab Procedure
Lab Test
Orderable Test
Intravascular Glucose Test
Chem 7
Serum Glucose Test
Fingerstick Glucose Test
Plasma Glucose Test
55
Case Studies

• Summary reporting
• HCFA requirements

• Clinical research

56
Clinical Research

• Epidemiology - symptoms, incidence, history of
  disease
• Outcomes - effectiveness of therapy, ideal length
  of stay
• Recruitment - identifying eligible participants

57
Case Studies

• Summary reporting
• HCFA requirements
• Clinical research

• Expert systems

58
From Test Result to Finding
59
(No Transcript)
60
(No Transcript)
61
(No Transcript)
62
(No Transcript)
63
Case Studies

• Summary reporting
• HCFA requirements
• Clinical research
• Expert systems

• Automated decision support

64
Terminology and Automated Decision Support

• Data monitor checks for triggering conditions
• Medical Logic Modules decide if warning
  conditions are present
• Message sent to appropriate channel
• Example Tuberculosis culture result

65
Decision Support Example TB

• Monitors for delayed culture results
• Sends message if result not equal to the code No
  growth
• One day, dozens of alerts about positive results
  but no organism was reported
• What happened?

66
How the Lab Fooled the Alert

• Alert looked for results No Growth
• Lab started reporting No Growth to Date
• No Growth to Date ? No Growth
• Solution Use the controlled terminology to map
  all No-Growth-like lab terms into a single class,
  and have the alert logic refer to the class.

67
How We Outsmarted the Lab(Before)
Medical Logic Module
No Growth to Date
No Growth
68
How We Outsmarted the Lab(After)
Medical Logic Module
No Growth to Date
No Growth
69
Case Studies

• Summary reporting
• HCFA requirements
• Clinical research
• Expert systems
• Automated decision support

• Linking to on-line information sources

70
Linking to On-line Resources with Terminology

• Clinician reviewing reports will have information
  needs
• On-line information sources can satisfy that need
• Data from report can be used to automate the query

71
Translations with the MED
Injectable Gentamicin
Serum Gentamicin Level
Gentamicin
Gentamicn Sensitivity Test
Gentamicin Toxicity
72
(No Transcript)
73
(No Transcript)
74
(No Transcript)
75
(No Transcript)
76
(No Transcript)
77
(No Transcript)
78
(No Transcript)
79
(No Transcript)
80
Linking Text Reports to On-line Information
Sources

• Natural Language Processing
• Data representation to support reuse
• Codification of information needs

81
(No Transcript)
82
(No Transcript)
83
(No Transcript)
84
(No Transcript)
85
(No Transcript)
86
(No Transcript)
87
(No Transcript)
88
(No Transcript)
89
(No Transcript)
90
(No Transcript)
91
(No Transcript)
92
(No Transcript)
93
Case Studies

• Summary reporting
• HCFA requirements
• Clinical research
• Expert systems
• Automated decision support
• Linking to on-line information sources

94
Learning More
SNOMED http//www.snomed.org/ UMLS
http//www.nlm.nih.gov/research/umls LOINC
http//www.regenstrief.org /loinc/loinc.htm ME
D http//www.cpmc.columbia.edu /homepages
/ciminoj/med.html Standards http//www.hl7.org
/standards/developer.htm
95
(No Transcript)