Principles of Controlled Terminology

1
Principles of Controlled Terminology

• James J. Cimino
• Department of Medical InformaticsColumbia
  University

2
Topics

• Motivations and issues
• Desiderata
• Available Terminologies
• Hands-on exercises
• Grand visions

3
Using and Reusing Clinical Data

• The case
• The patient is a 50 year old, Native American
  female who presents to the emergency room with
  the chief complaint of cough and chest pain.
• Using the Data
• Capturing the patient record
• Reusing the data
• Administration what room does the patient go in?

4
Mundane Symbolic Manipulation

• Patients get admitted to the hospital
• We dutifully record their gender
• Can the computer remind us about health
  maintenance?
• What about just assigning a bed?

5
Re-Using Gender

• Patient is an 50 year old, Native American
  female

6
Re-Using Gender

• But how does the computer know that the patient
  is female?
• The record could say
• female
• Female
• FEMALE
• F
• Woman
• Girl

7
Concept Definition

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

8
Concept Term - Basic Features

• Unique Identifier (Code)
• F
• Official Name
• Female
• Synonyms
• Woman, Girl

9
Concept General Classes of Terms

• Demographics
• Signs and symptoms
• Anatomy
• Diagnostic procedures
• Organisms
• Diagnoses
• Medications
• Therapeutic Procedures

10
Coding the Data Gender

• Data element - gender
• Controlled terminology Male, Female, Unknown
• Representation M,F,U 0,1,2
• What about other values?
• Genotypic
• Phenotypic
• Administrative

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Whats the Gender?
12
Isnt this Problem Already Solved?

• Easier to build than standardize (NIH)
• No agreed upon standards
• No interlingua between standards
• Maintaining a terminology costs money
• Proprietary interests
• Terminology modeling for symbolic manipulation is
  hard

13
Information Form and Reuse
14
Information Form and Reuse
15
Terminology Desiderata
Cimino JJ. Desiderata for controlled medical
vocabularies in the Twenty-First Century.
Methods of Information in Medicine
199837(4-5)394-403.

• Terminology content
• Concept orientation
• Concept permanence
• Nonsemantic identifiers
• Polyhierarchy
• Formal definitions
• Recognizing redundancy
• Reject NEC
• Graceful evolution

16
Coding the Case

• The patient is a 50 year old, Native American
  female who presents to the emergency room with
  the chief concern of cough and chest pain. The
  patient reports that she has had a productive
  cough for three days but that chest pain
  developed one hour ago. She gives a history of
  hypertension. She also reports that she was
  treated in the past for tuberculosis while she
  was pregnant.
• Assignment identify the terms in the above case
  that should be represented in a controlled
  terminology.
• 1) Go to courses.mbl.edu/mi/terminology/index_stud
  ent.html
• 2) Login to Exercise 1 (use your first initial
  and last name)
• 3) Type in some of the terms from the case
• 4) Submit
• 5) Repeat if necessary

17
Coding the Data

• Chief complaint Productive Cough, Chest Pain
• Past diagnoses Hypertension, Tuberculosis in
  Pregnancy
• Coding ICD9-CM

18
ICD9-CM and Beyond

• ICD9-CM US Dept of HHS - 1979
• added layer of hierarchy (14,473 terms)
• kept compatible with ICD9 (8,173 terms)
• Synonyms and index terms in printed book
• ICD10-CM pre-release version available

19
ICD

• Strict hierarchy
• No complete names
• Code determines place in hierarchy
• Not Otherwise Specified (NOS)
• Not Elsewhere Classified (NEC)

20
ICD9-CM Diagnoses
Translates to 005.0 STAPH FOOD
POISONING 005.1 BOTULISM 005.2 FOOD POIS D/T C.
PERFRIN 005.3 FOOD POIS CLOSTRID NEC 005.4 FOOD
POIS V. PARAHAEM 005.81 FOOD POISN D/T V.
VULNIF 005.89 BACT FOOD POISONING NEC 005.9 FOOD
POISONING NOS

• V21DIAG.TXT
• 005 OTHER FOOD POISONING
• 0050 STAPH FOOD POISONING
• 0051 BOTULISM
• 0052 FOOD POIS D/T C. PERFRIN
• 0053 FOOD POIS CLOSTRID NEC
• 0054 FOOD POIS V. PARAHAEM
• 0058 BACT FOOD POISONING NEC
• 00581 FOOD POISN D/T V. VULNIF
• 00589 BACT FOOD POISONING NEC
• 0059 FOOD POISONING NOS

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Coding the Case in ICD9-CM

• Assignment Code some of the terms in the case
  in ICD9-CM
• Go to courses.mbl.edu/mi/terminology/index_studen
  t.html
• 2) Login to Exercise 2 (use your first initial
  and last name)
• 3) Open a second Web browser window for
  http//icd9cm.chrisendres.com/index.php
• 3a) Backup site www.eicd.com/EICDMain.htm
• 4) Enter a Chief Complaint term from Exercise 2
  into the Criteria field
• 5) Find the best ICD9-CM Code and enter it in the
  Exercise 2 field
• 6) Repeat for all chief complaints
• 7) Repeat for Past Diagnosis terms
• 8) Hit Submit Information periodically
• 9) Clicking Return to Database Values will wipe
  out unsaved values!

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Strict Hierarchy
disease
26
Polyhierarchy
disease
Infectious disease
lung disease
27
ICD9-CM Examples420 Tuberculosis Codes (plus
69 hierarchical codes)
011. PULMONARY TUBERCULOSIS 012. OTHER
RESPIRATORY TB 013. CNS TUBERCULOSIS 014. INTEST
INAL TB 015. TB OF BONE AND JOINT 016. GENITOURI
NARY TB 017. TUBERCULOSIS NEC 018. MILIARY
TUBERCULOSIS

• 010. PRIMARY TB INFECTION
• 010.0 PRIMARY TB COMPLEX
• 010.00 PRIM TB COMPLEX-UNSPEC
• 010.01 PRIM TB COMPLEX-NO EXAM
• 010.02 PRIM TB COMPLEX-EXM UNKN
• 010.03 PRIM TB COMPLEX-MICRO DX
• 010.04 PRIM TB COMPLEX-CULT DX
• 010.05 PRIM TB COMPLEX-HISTO DX
• 010.06 PRIM TB COMPLEX-OTH TEST
• 010.1 PRIMARY TB PLEURISY
• 010.8 PRIM PROGRESSIVE TB NEC
• 010.9 PRIMARY TB INFECTION NOS

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ICD9-CM Examples More TB

• 137. LATE EFFECT TUBERCULOSIS
• 137.0 LATE EFFECT TB, RESP/NOS
• 137.1 LATE EFFECT CNS TB
• 137.2 LATE EFFECT GU TB
• 137.3 LATE EFF BONE JOINT TB
• 137.4 LATE EFFECT TB NEC
• 647. INFECTIVE DIS IN PREG
• 647.3 TUBERCULOSIS IN PREG
• 647.30 TB IN PREG-UNSPECIFIED
• 647.31 TUBERCULOSIS-DELIVERED
• 647.32 TUBERCULOSIS-DELIV W P/P
• 647.33 TUBERCULOSIS-ANTEPARTUM
• 647.34 TUBERCULOSIS-POSTPARTUM

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Polyhierarchy
disease
infectious disease
lung disease
30
NEC
31
Desideratum Reject"Not Elsewhere Classified"

• Can never have a formal definition
• Terminology changes induce semantic drift

32
Example Not Elsewhere Classified
1995
1996

• The Will Rodgers Phenomenon During the Great
  Dust Bowl Era, when Oakies moved to California,
  the IQ in both states increased.

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Available Terminology CPT

• Current Procedural Terminology
• Developed and owned by AMA
• Required for procedure reimbursement
• Required for physician visit reimbursement (EM
  Coding)
• Licensing fee per application, per seat

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CPT Examples

• 76090 Unilateral mammography
• 76091 Bilateral mammography
• 76092 Screening mammography, bilateral (two view
  film study of each breast)
• 76096 Mammographic guidance for needle
  placement, breast (e.g., for wire localization or
  for injection), each lesion, radiological
  supervision and interpretation
• 76085 Digitization of film radiographic images
  with computer analysis for lesion detection and
  further physician review for interpretation,
  screening mammography (List separately in
  addition to code for primary procedure)
• 76645 Ultrasound, breast(s) (unilateral or
  bilateral), B-scan and/or real time with image
  documentation

35
Available Terminology DRG

• Diagnosis Related Groups
• HCFA/CMS codes for prospective payment
• Adopted by many other payors
• Based on ICD9-CM disease and procedures
• Complex coding algorithms

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DRG Examples Pneumonia

• 75 Respiratory disease with major chest
  operating room procedure, no major complication
  or comorbidity
• 76 Respiratory disease with major chest
  operating room procedure, minor complication or
  comorbidity
• 77 Respiratory disease with other respiratory
  system operating procedure, no complication or
  comorbidity
• 79 Respiratory infection with minor
  complication, age greater than 17
• 80 Respiratory infection with no minor
  complication, age greater than 17
• 89 Simple Pneumonia with minor complication,
  age greater than 17
• 90 Simple Pneumonia with no minor
  complication, age greater than 17
• 475 Respiratory disease with ventilator support
• 538 Respiratory disease with major chest
  operating room procedure and major complication
  or comorbidity
• Respiratory disease, other respiratory system
  operating procedure and major complication or
  comorbidity
• 540 Respiratory infection with major
  complication or comorbidity
• Respiratory infection with secondary diagnosis of
  bronchopulmonary dysplasia
• 740 Respiratory infection with secondary
  diagnosis of cystic fibrosis
• 770 Respiratory infection with minor
  complication, age not greater than 17
• 771 Respiratory infection with no minor
  complication, age not greater than 17
• 772 Simple Pneumonia with minor complication,
  age not greater than 17
• 773 Simple Pneumonia with no minor
  complication, age not greater than 17
• 798 Respiratory infection with primary
  diagnosis of tuberculosis

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Available Terminology ICD10-PCS

• Procedure Coding System
• Replaces ICD9-CM Procedures
• For use in in-patient procedure coding
• www.cms.hhs.gov/providers/pufdownload/icd10.asp

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Using and Reusing Clinical Data

• The case
• The patient reports an allergy to Bufferin.
  Patient was given a 0.4mg nitroglycerin
  sublingual tablet with relief of her pain,
  started on ceftriaxone 500mg for her pneumonia,
  and admitted to the CCU for monitoring. In the
  CCU, she was started on 325mg of enteric-coated
  aspirin
• Using the Data
• Order entry
• Reusing the data
• Automated decision support (medical logic modules)

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Coding the Data

• Allergies Bufferin
• Medications Nitroglycerin Sublingual Tablet,
  Propranolol, Enteric-Coated Aspirin
• Coding NDC

40
National Drug Codes (NDC)

• US Food and Drug Administration
• Identifiers for labeled, regulated products
• Labelers get 4- or 5-digit code
• Product code set by labeler 3 or 4 digits
• Package code set by labeler 2 digits
• Codes can be reused

41
National Drug Codes Example

• 0000003412 007105690.3MGRTAB0039994NITROS
  TAT TABLETS
• 000000341224100BOT
• 0071-0569-24
• 0071056924
• (0071-0569-24 or 00710-569-24?)
• 71056924
• (0710-569-24, 0071-0569-24, 00710-569-24, or
  00071-0569-24?)

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Coding the Case in NDC

• Assignment Find NDC codes for the medication
  terms in the case.
• 1) Go to courses.mbl.edu/mi/terminology/index_stu
  dent.html
• 2) Login to Exercise 2 (use your first initial
  and last name)
• 3) Scroll down to Allergies
• 4) Open a second Web browser window for
  http//www.fda.gov/cder/ndc/database/default.htm
• 5) Search for allergy terms (e.g. Bufferin)
  using Proprietary Name or Ingredient Name
• 6) Find the best NDC Code and enter it in the
  Exercise 2 field
• 7) Scroll down to Medications in the Exercise 2
  page
• 8) Search for medication terms (e.g.
  Propranolol) using Proprietary Name or
  Ingredient Name
• 8) Hit Submit Information periodically
• 9) Clicking Return to Database Values will wipe
  out unsaved values!

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RxNorm

• Food and Drug Administration
• Veterans Health Administration
• National Library of Medicine
• Drug knowledge base vendors

47
RxNorm
C0350474 Diazepam 5 MG Oral Capsule Valium
Synonym Valium 5 MG Oral Capsule
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LOINC

• HL7 Message
• OBXObservationResult
• Observation CodeNameCoding System
• Logical Objects, Identifiers, Names and Codes
• Self-defining names for lab tests

49
LOINC - Structure

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

50
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

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Coding the Case in LOINC

• Assignment Find LOINC Codes for the laboratory
  tests in the case.
• 1) Go to courses.mbl.edu/mi/terminology/index_stu
  dent.html
• 2) Login to Exercise 2 (use your first initial
  and last name)
• 3) Scroll down to Laboratory Tests
• 3) Open a second Web browser window for
  http//nciterms.nci.nih.gov/NCIBrowser/Startup.do
  
• 4) Click on LOINC and hit Connect
• 5) Search for lab test terms using Quick Search
• 6) Find the best LOINC Code click on the text box
  icon

(Backup plan Install RELMA from
http//www.loinc.org, Open RELMA (desktop icon),
Click on Map Local Terms to LOINC (New), Enter
lab test terms in the Accept or enter OBR Name
field and Search)
7) Find the best LOINC Code and enter it in the
Exercise 2 field 8) Repeat for all laboratory
tests terms 9) Hit Submit Information
periodically 10) Clicking Return to Database
Values will wipe out unsaved values!
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Using and Reusing Clinical Data

• The case
• The patients nurse reported that the patient
  seemed depressed about her condition. On
  questioning, the nurse found that the patient was
  caring for her elderly father and was concerned
  that she would no longer be able to manage caring
  for herself and him. The nurse asked the
  patients physician to consider an antidepressant
  and a social work consult.
• Using the Data
• Patient management and discharge planning
• Reusing the data
• Utilization review

55
Available Nursing Terminologies

• NANDA Taxonomy
• 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

56
Coding Nursing Concepts

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

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Available Nursing Terminologies
58
Using and Reusing Clinical Data

• The case
• The patient was noted to be in moderate
  respiratory distress. Examination revealed rales
  and rhonchi in the left upper chest. Abdominal
  exam revealed a tender, palpable liver edge.
• Using the Data
• Clinical monitoring of patients physical exam
• Reusing the data
• Epidemiologic studies

59
Available Terminology SNOMED

• Systematized Nomenclature of Diseases and
  Organisms (SNDO) - 1928 - NY Academy of Medicine
• Systematized Nomenclature of Pathology (SNOP) -
  1965 - CAP (T, E, M, F)
• Systematized Nomenclature of Medicine (SNOMED) -
  1979 - CAP (seven axes)
• SNOMED-RT (Reference Terminology)
• SNOMED-CT (merger with Read)
• Semantic network with definitions
• US-wide site license

60
Semantic Representation inSNOMED-RT/CT
Pulmonary Tularemia
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Coding the Case in SNOMED-CT

• Assignment Code all terms in SNOMED-CT.
• 1) Go to courses.mbl.edu/mi/terminology/index_stu
  dent.html
• 2) Login to Exercise 2 (use your first initial
  and last name)
• 3) Scroll down to Physical Findings
• 4) Open a second Web browser window for
  http//nciterms.nci.nih.gov/NCIBrowser/Startup.do
  
• 5) Click on SNOMED_CT and hit Connect
• 5a) Use http//snomed.vetmed.vt.edu/sct/menu.cf
  m, Click on Concepts
• 6) Search for clinical terms using Quick Search
• 7) Find the best SNOMED term and click on the
  textbox icon

8) Find the Code in Source value and enter it
in the Exercise 2 field 9) Repeat for all
physical finding terms 10) As time permits,
repeat for other Exercise 2 terms (Chief
Complaint, etc.) 11) Hit Submit Information
periodically 12) Clicking Return to Database
Values will wipe out unsaved values!
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Using and Reusing Clinical Data

• The case
• A medical student reviewing the case is concerned
  about the risk of MRSA in patients with pneumonia
  and a recent myocardial infarction. She decides
  to do a literature search.
• Using the Data
• Recorded for patient care.
• Reusing the data
• Information retrieval

69
Available Terminology MeSH

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

70
MeSH Example

• 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

71
Available Terminology UMLS

• The purpose of the Unified Medical Language
  System is to improve the ability of computer
  programs to understand the biomedical meaning
  in user inquiries and to use this understanding
  to retrieve and integrate relevant
  machine-readable information for users.
• - Donald A.B. Lindberg, 1993

72
UMLS History

• 1986 UCSF, Utah-Pittsburgh-Carnegie Mellon,
  Yale, Harvard
• Large number of terminologies
• Large number of sources
• Do something

73
UMLS History

• Semantic modeling
• Tools
• Demonstration projects
• Ultimately chose current model
• Formation of Lexical Technologies Inc.
• Merger with Ontyx to form Apelon

74
Metathesaurus
2002 108 1,920,170 776,940
2003 109 2,146,907 875,256
2004 115 3,295,308 1,020,866
2005 132 4,673,237 1,179,179
2006 134 6,177,437 1,341,487

• Sources
• Strings
• Concepts

75
Metathesaurus
Concept
Lexical group
String
String
76
SUIs, LUIs and CUIs

• Heart
• String Unique Identifier S0047194
• Concept Unique Identifier C0018787
• Terminologies MeSHD006321 ReadXa8SM
  SNOMEDT-32000 SNOMEDU000438(hierarchy)
  AIRMFHRT LCHU002104 PSY22460 UWDA7088
  ICD10C38.0 ICD10D15.1
• HEART
• String Unique Identifier S0375948
• Concept Unique Identifier C0018787
• Terminologies SNOMED-IntT-32000 (Hierarchy)
  CCPSSU000039
• heart
• String Identifier S0419735
• Concept Unique Identifier C0018787
• Terminologies AOD0000002498 CSP1390-0233
• All of the above are in the same Lexical Unique
  Identifier L0018787

77
SUIs, LUIs and CUIs

• Heart
• String Unique Identifier S0047194
• Concept Unique Identifier C0018787
• Terminologies MeSHD006321 ReadXa8SM
  SNOMEDT-32000 SNOMEDU000438(hierarchy)
  AIRMFHRT LCHU002104 PSY22460 UWDA7088
  ICD10C38.0 ICD10D15.1
• HEART
• String Unique Identifier S0375948
• Concept Unique Identifier C0018787
• Terminologies SNOMED-IntT-32000 (Hierarchy)
  CCPSSU000039
• heart
• String Identifier S0419735
• Concept Unique Identifier C0018787
• Terminologies AOD0000002498 CSP1390-0233
• All of the above are in the same Lexical Unique
  Identifier L0018787

78
SUIs, LUIs and CUIs

• Heart
• String Unique Identifier S0047194
• Concept Unique Identifier C0018787
• Terminologies MeSHD006321 ReadXa8SM
  SNOMEDT-32000 SNOMEDU000438(hierarchy)
  AIRMFHRT LCHU002104 PSY22460 UWDA7088
  ICD10C38.0 ICD10D15.1
• HEART
• String Unique Identifier S0375948
• Concept Unique Identifier C0018787
• Terminologies SNOMED-IntT-32000 (Hierarchy)
  CCPSSU000039
• heart
• String Identifier S0419735
• Concept Unique Identifier C0018787
• Terminologies AOD0000002498 CSP1390-0233
• All of the above are in the same Lexical Unique
  Identifier L0018787

Heart String Unique Identifier S0047194 Concept
Unique Identifier C0153500 Terminologies
ICD10C38.0 Lexical Unique Idenifier L0018787
Heart String Unique Identifier S0047194 Concept
Unique Identifier C0153957 Terminologies
ICD10D15.1 Lexical Unique Idenifier L0018787
HEART String Unique Identifier
S0375948 Concept Unique Identifier
C0795691 Terminologies CCPSSU000039 Lexical
Unique Identifier L0018787
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Metathesaurus - MRCONSO

• C0153957ENGPL0180790PFS1084242YA1141630
  MTHPNU001287benign neoplasm of heart0N
• C0153957ENGPL0180790VCS0245316NA0270815
  ICD9CMPT 212.7Benign neoplasm of heart0N
• C0153957ENGPL0180790VCS0245316NA0270817
  RCDSYB727. Benign neoplasm of heart3N
• C0153957ENGPL0180790VOS1446737YA1406658
  SNMIPT D3-F0100Benign neoplasm of heart,
  NOS3N
• C0153957ENGSL0524277PFS0599118NA0654589
  RCDAEPTB727.Benign tumor of heart3N
• C0153957ENGSL0524277PFS0599118YA2996703121
  8640014 92132009SNOMEDCTSY92132009Benign
  tumor of heart4N
• C0153957ENGSL0524277VOS0599510NA0654975
  RCDPTB727. Benign tumour of heart3N
• C0153957ENGSL0018787PFS0047194YA0066366
  ICD10PSD15.1Heart3Y
• C0153957ENGSL0018787VOS0900815YA0957792
  MTHMMU003158Heart lt3gt0Y
• C0153957ENGSL1371329PFS1624801NA15830561
  0004245MDRLT10004245Benign cardiac
  neoplasm3N
• C0153957GERPL1258174PFS1500120YA1450314
  DMDICD10PT D15.1Gutartige Neubildung
  Herz1N
• C0153957SPAPL2354284PFS2790139NA2809706
  MDRSPALT 10004245Neoplasia cardiaca
  benigna3N

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Metathesaurus - MRCONSO

• Col. Description
• CUI Unique identifier for concept
• LAT Language of Term
• TS Term status
• LUI Unique identifier for term
• STT String type
• SUI Unique identifier for string
• ISPREF Atom status-preferred or not for this
  string within this concept
• AUI Unique identifier for atom
• SAUI Source asserted atom identifier optional
• SCUI Source asserted concept identifier
  optional
• SDUI Source asserted descriptor identifier
  optional
• SAB Source abbreviation
• TTY Term type in source
• CODE "Most useful" source asserted identifier
• STR String
• SRL Source Restriction Level
• SUPPRESS Suppressible flag - N or Y. Y indicates
  that the string may lack face validity or
  otherwise be problematic in many applications.
• CVT Content view flag not yet in use

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Metathesaurus - MRREL

• C0153957A0066366AUIPARC0348423A0876682AUIR
  06101405ICD10ICD10N
• C0153957A0066366AUIRQC0153957A0270815AUIdef
  ault_mapped_ fromR03575929NCISEERNCISEERN
  
• C0153957A0066366AUISYC0153957A0270815AUIuni
  quely_mapped_ toR03581228NCISEERNCISEERN
• C0153957A0270815AUIRQC0810249A1739601AUIcla
  ssifies R00860638CCSCCSN
• C0153957A0270815AUISIBC0347243A0654158AUIR
  06390094 ICD9CMICD9CMNN
• C0153957A0270815CODERNC0685118A3807697SCUIm
  apped_to R15864842SNOMEDCTSNOMEDCTYN
• C0153957A1406658AUIRLC0153957A0270815AUImap
  ped_from R04145423SNMISNMIN
• C0153957A1406658AUIROC0018787A0357988AUIloc
  ation_of R04309461SNMISNMIN
• C0153957A2891769SCUICHDC0151241A2890143SCUI
  isaR1984122047189027SNOMEDCTSNOMEDCT0YN
• C0153957A3807333SCUIROC0086692A3579828SCUIa
  ssociated_ morphology_ofR13712546907149029SNOME
  DCTSNOMEDCT1NN

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Semantic Network

• Each concept has one or more Semantic Types (135
  in all)
• Types are arranged in a strict hierarchy
• Types are related through potential Semantic
  Relations (54 in all)
• Relations are inherited
• Inheritance can be blocked

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UMLS Semantic Network - Event
Phenomenon or Process Injury or Poisoning
Human-caused Phenomenon or Process
Environmental Effect of Humans Natural
Phenomenon or Process Biologic Function
Physiologic Function
Organism Function Mental
Process Organ or Tissue Function
Cell Function Molecular
Function Genetic Function
Pathologic Function Disease or
Syndrome Mental or Behavioral
Dysfunction Neoplastic Process
Cell or Molecular Dysfunction
Experimental Model of Disease

• Activity
• Behavior
• Social Behavior
• Individual Behavior
• Daily or Recreational Activity
• Occupational Activity
• Health Care Activity
• Laboratory Procedure
• Diagnostic Procedure
• Therapeutic or Preventive Procedure
• Research Activity
• Molecular Biology Research
• Technique
• Governmental or Regulatory Activity
• Educational Activity
• Machine Activity

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UMLS Semantic Network - Entity
Conceptual Entity Organism Attribute
Clinical Attribute Finding Laboratory
or Test Result Sign or Symptom Idea
or Concept Occupation or Discipline
Biomedical Occupation or Discipline
Organization Health Care Related
Organization Professional Society
Self-help or Relief Organization Group
Professional or Occupational Group
Population Group Family Group Age
Group Patient or Disabled Group Group
Attribute Intellectual Product
Regulation or Law Classification
Language

• Physical Object
• Organism
• Anatomical Structure
• Embryonic Structure
• Fully Formed Anatomical Structure
• Body Part, Organ, or
• Organ Component
• Tissue
• Cell
• Cell Component
• Gene or Genome
• Anatomical Abnormality
• Congenital Abnormality
• Acquired Abnormality
• Manufactured Object
• Medical Device
• Drug Delivery Device
• Research Device
• Clinical Drug

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UMLS Semantic Network - Entity

• Organism
• Plant
• Alga
• Fungus
• Virus
• Rickettsia or Chlamydia
• Bacterium
• Animal
• Invertebrate
• Vertebrate
• Amphibian
• Bird
• Fish
• Reptile
• Mammal
• Human
• Archaeon

Idea or Concept Temporal Concept
Qualitative Concept Quantitative Concept
Spatial Concept Body Location
or Region Body Space or Junction
Geographic Area Molecular
Sequence Nucleotide Sequence
Amino Acid Sequence
Carbohydrate Sequence Functional Concept
Body System
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UMLS Semantic Network - Entity
Chemical Chemical Viewed Structurally
Organic Chemical Nucleic Acid,
Nucleoside, or Nucleotide
Organophosphorus Compound Amino
Acid, Peptide, or Protein
Carbohydrate Lipid
Steroid Eicosanoid
Element, Ion, or Isotope Inorganic
Chemical Chemical Viewed Functionally
Pharmacologic Substance Antibiotic
Biomedical or Dental Material
Biologically Active Substance
Neuroreactive Substance or Biogenic Amine
Hormone Enzyme
Vitamin Immunologic Factor
Receptor Indicator, Reagent, or
Diagnostic Aid Hazardous or Poisonous
Substance
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Semantic Network - SRDEF

• STYT191Neoplastic ProcessB2.2.1.2.1.2A new
  and abnormal growth of tissue in which the growth
  is uncontrolled and progressive. The growths may
  be malignant or benign.Abdominal Neoplasms
  stage IVB carcinoma of the vagina tonsillar
  lymphoepitheliomaAll neoplasms are assigned to
  this type. Do not also assign a type from the
  'Anatomical Abnormality' hierarchy.neop

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Metathesaurus - MRSTY

• C0153957T191B2.2.1.2.1.2Neoplastic
  ProcessAT08223379

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Specialist Lexicon

• A lexicon, not a terminology
• Provides syntactic, morphological, and graphemic
  information - but not semantic information

91
Specialist Lexicon

• basebeer
• entryE0012226
• catnoun
• variantsuncount
• variantsreg

92
Coding the Case in UMLS

• 1) Go to courses.mbl.edu/mi/terminology/index_stu
  dent.html
• 2) Login to Exercise 2 (use your first initial
  and last name)
• 3) Scroll down to Physician Assessments
• 4) Open a second Web browser window for
• http//umlsks.nlm.nih.gov/
• 5) Log on with User mbl, Password swope2
• 6) Use Metathesaurus Concept Search to find
  physician assessment terms
• 7) Find the best UMLS Concept and enter its CUI
  into Exercise 2
• 8) Repeat for all physician assessment terms
• 9) As time permits, repeat for other Exercise 2
  terms (Chief Complaint, etc.)
• 10) Hit Submit Information periodically
• 11) Clicking Return to Database Values will
  wipe out unsaved values!

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Appendix 14
96
Appendix 17
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Problems with UMLS

• No formal conceptual model (near-synonymy)
• No hierarchy
• Lots of redundancy
• Lots of ambiguity

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Unified Medical Language System

• The UMLS supports the development of
  user-friendly systems that can effectively
  retrieve and integrate relevant information from
  disparate machine-readable sources.
• - Betsy Humphreys, 1998

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Uses of UMLS

• Reconstructing source terminologies
• Finding additional synonyms for source terms
  (mapping)
• Automated translation

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Data Types
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Choice of Terminologies
HPI PMH Exam Labs Diag Dx Rx
Tx
ICD CPT DRG NDC RxNorm LOINC Nursing SNOMED MeS
H UMLS













HPI History of present illness PMH Past
medical history Exam-Physical exam
Labs-Clinical lab Diag Other tests
Dx Diagnoses Rx
Medications Tx Other therapy Coverage
minimal, partial, extensive
cost for use
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Reusing the Data

• Room assignment
• Billing
• Utilization review
• Summary reporting
• Automated decision support
• Information retrieval
• Infobuttons
• Expert systems
• Research subject recruiting
• Epidemiologic studies
• Syndromic surveillance

103
Reusing Data Summary Reports

• Lab summaries typically aggregate codes
• Hard-coded aggregations are hard to maintain
  (trying to put the terminology in the data model)

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Reusing Data Summary Reports

• Lab summaries typically aggregate codes
• Hardcoded aggregations are hard to maintain
  (trying to put the terminology in the data model)
• But, if you put the data model in the terminology

106
Reusing Data Summary Reports
107
Lab Result Summary 1990
108
Lab Result Summary 1995
109
Reusing Data Automated Decision Support

• Expert systems use patient information
• Why not integrate expert systems with clinical
  information systems?
• Clinical information systems often have low-level
  data
• Expert systems abound, but they use high-level
  concepts
• Some translation method is needed

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Reuse of Data DXplain Button
Serum Potassium Test
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Reusing the Data Infobuttons

• Need automated access to on-line information
  sources
• Solution use clinical data as seed for
  problem-specific retrievals
• Task translate from medical record terms to
  terminology used by information resource

115
Reusing the Data Infobuttons
116
Translations to Support Infobuttons
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Use and Reuse of Clinical Data

• a) What were all the patient's clinical
  laboratory tests and results, in chronological
  order?
• b) What were all the results of the patient's
  blood glucose tests (including serum, plasma and
  fingerstick)?
• c) What were all the results of the patient's
  serum glucose tests?
• d) Does the patient have any allergies to any
  ordered medications?

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Answering the Questions

• d) Does the patient have any allergies to any
  ordered medications?

Allergy Bufferin Ordered Medications
Enteric-Coated Aspirin If ingredient of allergic
drug equals ingredient of ordered drug, then send
alert
Bufferin
Enteric-Coated Aspirin
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Use and Reuse of Clinical Data

• a) What were all the patient's clinical
  laboratory tests and results, in chronological
  order?
• b) What were all the results of the patient's
  blood glucose tests (including serum, plasma and
  fingerstick)?
• c) What were all the results of the patient's
  serum glucose tests?
• d) Does the patient have any allergies to any
  ordered medications?

e) Does the patient meet the criteria for a
clinical trial of patients who are over the age
of 50 and have an elevated systolic blood
pressure (gt140)? f) If the patient has criteria
for the for the diagnosis of myocardial
infarction (any two of chest pain, elevated
cardiac enzymes (CKgt200 with more than 5 MB
fraction), and ischemic (elevation or depression
of the ST segment) changes on the cardiogram) has
he been started on aspirin?
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select patient_id , time primary_time from
visit2004_diagnosis where diagnosis_icd9_code
like '410' and b.primary_time between
'01/01/2000' and 12/31/2005' and b.comp_code
30366
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Now What?

• Data representation is everywhere in informatics
• Use discipline when
• choosing
• creating
• maintaining
• Look for ways to solve problems through
  terminology

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Take Home Messages

• What should be coded?
• What is the purpose?
• Is a standard appropriate? Useful?
• Selection of terminology
• Granularity and aggregation
• Fit to data model
• Desiderata!
• Multiple terminologies needed
• Patient Medical Record Information (PMRI)
• SNOMED-CT
• LOINC
• RxNorm, NDF-RT (VA), FDA
• www.ncvhs.hhs.gov

130
Additional Reading
Cimino JJ. Desiderata for controlled medical
vocabularies in the Twenty-First Century.
Methods of Information in Medicine
199837(4-5)394-403. Cimino JJ. Formal
descriptions and adaptive mechanisms for changes
in controlled medical vocabularies. Methods of
Information in Medicine 199635(3)202-210.
Cimino JJ. In defense of the Desiderata. J
Biomed Inform. 2006 Jun39(3)299-306. Humphreys
BL, Lindberg DA, Schoolman HM, Barnett GO. The
Unified Medical Language System an informatics
research collaboration. JAMIA. 19985(1)1-11.
Lindberg DAB, Humphreys BL, McCray AT. The
Unified Medical Language System. Meth Inform
Med. 199332281-291. Rosenbloom ST, Miller RA,
Johnson KB, Elkin PL, Brown SH. Interface
terminologies facilitating direct entry of
clinical data into electronic health record
systems.J Am Med Inform Assoc. 2006
May-Jun13(3)277-88. Wang AY, Sable JH,
Spackman KA. The SNOMED clinical terms
development process refinement and analysis of
content. Proc AMIA Symp. 2002845-9.