Principles of Controlled Terminology

1
Principles of Controlled Terminology

• James J. Cimino
• NIH Clinical Center

2
Topics

• Motivations and issues
• Desiderata
• Available Terminologies
• Hands-on exercises
• Reusing coded clinical data
• Take-home messages

3
Case Presentation

• The patient is a 50 year old, Native American
  female who present to the emergency room (ER)
  with the chief complaint of lip numbness, nausea
  and chest pain.
• The patient was generally well until about one
  half hour prior to arrival in the ER, while
  eating dinner at as seafood restaurant in Rock
  Harbor, MA. She was finishing a dinner of New
  England clam chowder, lobster, steamed clams, and
  corn on the cob when she noted onset of symptoms.
  Others in her party ate fish and chips, although
  two other people ate the clam chowder none at
  the steamers.
• She gives a history of hypertension and states
  that she was getting a "capsule, half green, half
  blue-green" from her private doctor. She also
  reports that she was treated in the past for
  tuberculosis while she was pregnant, but doesn't
  remember what she was treated with or for how
  long. She reports that she was at another
  hospital on the other side of town, where she had
  a liver biopsy. She reports that he thinks the
  diagnosis was "hemachromatosis". The patient
  reports an allergy to Bufferin.
• Physical examination revealed a well-developed,
  well-nourished diaphoretic female in moderate
  respiratory distress. Vital signs showed a pulse
  of 110, a respiratory rate of 8, an oral
  temperature of 100.3, and a blood pressure of
  150/100. Examination revealed rales over both
  lower lung fields. Abdominal exam revealed a
  tender, palpable liver edge. Neurologic exam
  reveals dysarthria, diffuse muscle weakness, and
  hyperreflexia.
• Chem7 (serum) Glucose 100 (70-105) Chem7
  (plasma) Glucose 150 (75-110)
• CBC Hgb 15 (12.0-15.8), Hct 45 (42.4-48.0), WBC
  11,000 (3,540-9,060), Platelets 145K (165-415K)
• A fingerstick blood sugar was 80
• Urinalysis showed protein of 1 and glucose of 0
• A blood culture was positive for
  methicillin-resistant Staphylococcus aureus
  (MRSA)
• ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST
  segment 2mm elevated and
• T-waves down in leads I, L, V5 and V6
• Chest X-ray Left upper lobe infiltrate, left
  ventricular hypertrophy
• The patient's nurse reported that the patient
  seemed more worried about who would care for her
  elderly father if anything happened to her.
• A medical student reviewing the case wonders
  whether paralytic shellfish poisoning could cause
  a myocardial infarction she decides to do a
  literature search.
• The patient was treated with activated charcoal
  and stomach lavage, followed by enteric-coated
  aspirin. Due to worsening respiratory
  insufficiency, she was intubated and placed on
  mechanical ventilation.

4
Using and Reusing Clinical Data

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

5
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?

6
Re-Using Gender

• Patient is an 50 year old, Native American
  female

7
Re-Using Gender

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

8
Concept Definition

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

9
Concept Term - Basic Features

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

10
Concept General Classes of Terms

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

11
Coding the Data Gender

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

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.
16
Coding the Case

• The patient is a 50 year old, Native American
  female who present to the emergency room (ER)
  with the chief complaint of lip numbness, nausea
  and chest pain. The patient was generally well
  until about one half hour prior to arrival in the
  ER, while eating dinner at as seafood restaurant
  in Rock Harbor, MA. She was finishing a dinner
  of New England clam chowder, lobster, steamed
  clams, and corn on the cob when she noted onset
  of symptoms. Others in her party ate fish and
  chips, although two other people ate the clam
  chowder none at the steamers.
• Assignment identify the terms in the above case
  that should be represented in a controlled
  terminology.
• Go to
• http//miproject.mbl.edu/terminology/terminologyl
  ab/student.html
• 2) Login to Exercise 1 (use your last name, all
  lower case, no spaces or punctuation)
• 3) Type in some of the terms from the case
• 4) Submit
• 5) Repeat if necessary

17
Coding the Data

• Chief complaint
• lip numbness, nausea 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
• No date set for adoption in US
• ICD-11 in development

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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22
http//www.eicd.com/EICDMain.htm  
23
http//icd9cm.chrisendres.com/index.php  
24
Strict Hierarchy
disease
25
Polyhierarchy
disease
Infectious disease
lung disease
26
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

27
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

28
Polyhierarchy
disease
infectious disease
lung disease
29
NEC
30
Desideratum Reject"Not Elsewhere Classified"

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

31
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.

32
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

33
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

34
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
• 2007 Medicare Severity DRGs (MS-DRGs)

35
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

36
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

37
Using and Reusing Clinical Data

• The case
• The patient reports an allergy to Bufferin.
• The patient was given activated charcoal and
  enteric-coated aspirin.
• Using the Data
• Order entry
• Reusing the data
• Automated decision support (medical logic modules)

38
Coding the Data

• Allergies Bufferin
• Medications Activated Charcoal,
  Enteric-Coated Aspirin
• Coding NDC

39
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

40
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?)

41
http//www.fda.gov/cder/ndc/database/default.htm
42
RxNorm

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

43
RxNorm
C0350474 Diazepam 5 MG Oral Capsule Valium
Synonym Valium 5 MG Oral Capsule
44
LOINC

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

45
LOINC - Structure

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

46
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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49
Using and Reusing Clinical Data

• The case
• The patient's nurse reported that the patient
  seemed more worried about who would care for her
  elderly father if anything happened to her.
• Using the Data
• Patient management and discharge planning
• Reusing the data
• Utilization review

50
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

51
Coding Nursing Concepts

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

52
Available Nursing Terminologies
53
Using and Reusing Clinical Data

• The case
• Physical examination revealed a well-developed,
  well-nourished diaphoretic female in moderate
  respiratory distress. Vital signs showed a pulse
  of 110, a respiratory rate of 8, an oral
  temperature of 100.3, and a blood pressure of
  150/100. Examination revealed rales over both
  lower lung fields. Abdominal exam revealed a
  tender, palpable liver edge. Neurologic exam
  reveals dysarthria, diffuse muscle weakness, and
  hyperreflexia.
• Using the Data
• Clinical monitoring of patients physical exam
• Reusing the data
• Epidemiologic studies

54
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
• IHTSDO

55
Semantic Representation inSNOMED-RT/CT
Pulmonary Tularemia
56
http//nciterms.nci.nih.gov/NCIBrowser/Startup.do
57
http//snomed.vetmed.vt.edu/sct/menu.cfm
58
Using and Reusing Clinical Data

• The case
• A medical student reviewing the case wonders
  whether paralytic shellfish poisoning could cause
  a myocardial infarction she decides to do a
  literature search.
• Using the Data
• Recorded for patient care.
• Reusing the data
• Information retrieval

59
Available Terminology MeSH

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

60
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

61
http//www.nlm.nih.gov/mesh/MBrowser.html
62
Foundational Model of Anatomy

• The Foundational Model of Anatomy ontology (FMA)
  is an evolving computer-based knowledge source
  for bioinformatics
• Classes and relationships necessary for the
  symbolic modeling of the structure of the human
  body
• Designed to provide anatomical information needed
  by any user group and is intended to accommodate
  any viewpoint.
• Strictly constrained to pure anatomy
• Inheritance hierarchy or taxonomy in a strictly
  structural context

63
FMA Structure

• Incorporates all of Terminologia Anatomica
• Four interrelated components
• Anatomy taxonomy
• Anatomical Structural Abstraction (part-whole and
  spatial relationships)
• Anatomical Transformation Abstraction
  (morphological transformation)
• Metaknowledge (principles, rules and definitions
  for which classes and relationships in the other
  three components of FMA are represented)
• 75,000 classes
• 120,000 terms
• 2.1 million relationship instances from 168 types

64
FMA Examples Aort

• 38037 Anterior cusp of aortic valve
• 40575 Wall of descending aorta
• 52599 T5 part of thoracic aorta
• 56459 Right lateral aortic lymphatic chain
• 56460 Left lateral aortic lymphatic chain
• 89693 Set of mediastinal branches of thoracic
  aorta
• 118442 Blood in summit of arch of aorta
• 140668 Endothelium of left posterior cusp of
  aortic valve
• 154263 Tunica intima of aorta
• 179104 Thoracic aortic wall
• 184783 Lateral aortic lymph nodes set
• 189421 Lunule of aortic valvular cusp
• 192638 Lumen of thoracic aorta
• 195775 Lateral aortic lymph node
• 195782 Left lateral aortic node
• 197415 Lumen of segment of arch of aorta
• 197416 Lumen of ascending trunk of arch of aorta
• 247057 Thoracic aortic nerve plexus

65
http//fme.biostr.washington.edu8089/FME/index.ht
ml
66
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67
Gene Ontology (GO)

• Gene Ontology Consortium (1998)
• Started with Flybase, Saccharomyces Genome
  Database and Mouse Genome Database
• Three ontologies molecular function,
  biological process and cellular component
• DAG, with cross-linkages between ontologies

68
GO Example

• id GO0043234 name protein complex
• namespace cellular_component
• def "Any protein group composed of two or more
  subunits, which may or may not be identical.
  Protein complexes may have other associated
  non-protein prosthetic groups, such as nucleic
  acids, metal ions or carbohydrate groups."
• GOcurators comment Note that although at some
  level almost all cellular components can be
  thought of as protein complexes\, this term is
  intended to exclude structures composed of the
  same repeating subunit or subunits, for example
  microtubules. Protein complexes encompassed by
  this term are generally not structural, and
  usually have a defined set of subunits.
• subset gosubset_prok
• is_a GO0005575 ! cellular_component
• id GO0000214 name tRNA-intron endonuclease
  complex
• namespace cellular_component
• def "Catalysis of the endonucleolytic cleavage
  of pre-tRNA, producing 5'-hydroxyl and
  2',3'-cyclic phosphate termini, and specifically
  removing the intron." EC3.1.27.9
• is_a GO0043234 ! protein complex
• relationship part_of GO0005634 ! nucleus

69
Unified Medical Language System

• 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

70
UMLS History

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

71
UMLS History

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

72
Metathesaurus
2006 134 6,177,437 1,341,487
2009 152 8,006,171 2,125,395
2004 115 3,295,308 1,020,866
2005 132 4,673,237 1,179,179
2008 145 7,781,500 1,553,638

• Sources
• Strings
• Concepts

73
Metathesaurus
Concept
String
String
74
SUIs 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

75
SUIs 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

76
SUIs 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

Heart String Unique Identifier S0047194 Concept
Unique Identifier C0153500 Terminologies
ICD10C38.0
Heart String Unique Identifier S0047194 Concept
Unique Identifier C0153957 Terminologies
ICD10D15.1
HEART String Unique Identifier
S0375948 Concept Unique Identifier
C0795691 Terminologies CCPSSU000039
77
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

79
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

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Specialist Lexicon

• basebeer
• entryE0012226
• catnoun
• variantsuncount
• variantsreg

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http//www.nlm.nih.gov/research/umls/
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The UMLS is not a Terminology!

• 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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Coding the Case

• Go to http//miproject.mbl.edu/terminology/termi
  nologylab/student.html
• 2) Login to Exercise 2 (use your last name, all
  lower case)
• 3) Open a separate window (or tab) for the MBL
  Terminology Server http//miproject.mbl.edu/Terms
  Browser/
• 4) For each term taken from the case, attempt to
  identify the appropriate term in the controlled
  terminology (only where it makes sense e.g.,
  dont try to find lab test terms in NDC or drug
  terms in LOINC)
• 5) Enter the Unique Identifier for the best term
  or terms into the exercise web page (as
  demonstrated in class)
• 6) Hit Submit Information periodically
  (warning clicking Return to Database Values
  will wipe out unsaved values!)

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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

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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
• Use a high-quality controlled terminology

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Reusing Data Summary Reports
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Lab Result Summary 1990
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Lab Result Summary 1995
104
Eclipsys Summary
What are the blood glucose test results?
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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

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Reusing the Data Infobuttons
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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
120
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
• National Center for Biomedical Ontologies
  (bioontology.org)

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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
• National Center for Biomedical Ontologies
  (bioontology.org)

• Open Biomedical Ontologies (www.obofoundry.org)

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126
Now What?

• Data representation is everywhere in informatics
• Use discipline when
• choosing
• creating
• maintaining
• Look for ways to solve problems through
  terminology
• National Center for Biomedical Ontologies
  (bioontology.org)
• Open Biomedical Ontologies (www.obofoundry.org)

127
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

128
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.