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Clinical Vocabulary

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									   Clinical Terminology

Department of Medical Informatics
      Columbia University
               Definition

Terminology:

    A finite, enumerated set of terms intended
to convey information unambiguously
Some General Classes of Terms

      Diagnostic Procedures
      Therapeutic Procedures
      Medications
      Diagnoses
      Findings
      Organisms
      Anatomy
Uses of Terminology

    Storing in database

    Querying database

    Transfering data

    Billing

    Monitoring data
Term - Basic Features

   Unique Identifier (Code)
     12345

   Official Name
     aspirin

   Synonyms
     ASA

   Translations
     NDC:   5502; UMLS: C0004057
Term - Advanced Features

   Classes
     antipyretic,   anti-inflammatory, analgesic
   Semantic Links
     CAUSES: gastritis
     TREATS: arthritis

   Attributes
     UNITS:   mg
Desiderata for Terminology

   Content
   Concept Orientation
     Nonredundant
     Nonambiguous
     Permanent

   Nonsemantic Concept Identifiers
   Polyhierarchy
   Semantic relationships
               Strict Hierarchy

                     disease

         heart disease         lung disease

heart attack      arrhythmia         pneumonia
               Polyhierarchy

                     disease


  heart disease    lung disease   infectious disease



heart attack      arrhythmia         pneumonia
           Semantic Network

specimen               test                  substance

    is_a                 is_a                     is_a


 serum                                       potassium

  has_specimen                          measures_substance
                 serum potassium test
          ICD-9/10 and -CM

 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
            ICD9-CM Examples
------Diseases-----
003. @ OTHER SALMONELLA INFECTIONS
003.0   SALMONELLA GASTROENTERITIS
003.2 @ LOCALIZED SALMONELLA INFECTIONS
003.20 LOCALIZED SALMONELLA INFECTION, UNSPECIFIED
003.21 SALMONELLA MENINGITIS
003.29 OTHER LOCALIZED SALMONELLA INFECTIONS

------Procedures-----
01. @ INCISION AND EXCISION OF SKULL, BRAIN,...
01.0 @ CRANIAL PUNCTURE
01.01 CISTERNAL PUNCTURE
01.09 OTHER CRANIAL PUNCTURE
             SNOMED

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

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


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

   80+ sources
   1,358,891 strings
   626,893 concepts
   Strings have attributes
   Concepts have attributes,
    including Relations
       Metathesaurus
 Concept
   Lexical group    Lexical group
       String           String
       String           String


Concept
  Lexical group    Lexical group
      String           String
      String           String
     Metathesaurus - MRCON
C0153957|ENG|P|L0180790|PF|S1084242|benign
  neoplasm of heart
C0153957|ENG|P|L0180790|VC|S0245316|Benign
  neoplasm of heart
C0153957|ENG|P|L0180790|VO|S1446737|Benign
  neoplasm of heart, NOS
C0153957|ENG|S|L0524277|PF|S0599118|Benign
  tumor of heart
C0153957|ENG|S|L0524278|PF|S0599510|Benign
  tumour of heart
C0153957|ENG|s|L0018787|PF|S0900815|Heart <3>
C0153957|ENG|s|L0018787|VO|S0047194|Heart
C0153957|GER|P|L1258174|PF|S1500120|Gutartige
  Neubildung: Herz
      Metathesaurus - MRSO
C0153957|L0018787|S0047194|ICD10|PS|D15.1|3|
C0153957|L0018787|S0900815|MTH|MM|U003158|0|
C0153957|L0180790|S0245316|ICD10|PX|D15.1|3|
C0153957|L0180790|S0245316|ICD99|PT|212.7|0|
C0153957|L0180790|S0245316|RCD98|SY|B727.|3|
C0153957|L0180790|S1084242|MTH|PN|U001287|0|
C0153957|L0180790|S1446737|SNMI98|PT|D3-
  F0100|3|
C0153957|L0524277|S0599118|RCDAE|PT|B727.|3|
C0153957|L0524278|S0599510|RCD98|PT|B727.|3|
C0153957|L1258174|S1500120|DMDICD|PT|D15.1|1
  |
    Metathesaurus - MRSTY


C0153957|T191|Neoplastic Process|
    Metathesaurus - MRREL

C0002871|CHD|C0002891|isa|MSH99|MTH||
C0002871|CHD|C0002892||CSP98|||
C0002871|CHD|C0002893||RCD98|||
C0002871|RB|C0221016||MTH|MTH||
C0002871|RL|C0002886|mapped_to|SNMI98
  |SNMI98||
         MED

 Medical Entities Dictionary
 CPMC
 Multiple hierarchy
 Synonyms
 Translations
 Semantic links
 Attributes
 60,000 concepts
Central Controlled Vocabulary
                  MED Structure
                               Medical
                                Entity

          Substance               Laboratory        Event
                                  Specimen

     Chemical     Anatomic          Plasma         Diagnostic
                  Substance        Specimen        Procedure

                      Plasma                  Laboratory      Laboratory
                                                 Test         Procedure
Carbo-       Bioactive
hydrate     Substance
                                                Plasma               CHEM-7
                                                Glucose    Part of
      Glucose
What do we want to do with
       these data?

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



   Spit back the reports
Other Patient Care Reuse


     Summaries
       Comparability   of data
     Trending of data
       Time   representation
Retrieving Results Individually
            K#1 = 4.2
             K#1 = 3.3
           K#2 = 3.2
            K#1 = 3.0
           K#3 = 2.6




           K#1
             K#2 K#3
Retrieving Results by Class
          K#1 = 4.2
           K#1 = 3.3
         K#2 = 3.2
          K#1 = 3.0
         K#3 = 2.6



                 K
         K#1
           K#2 K#3
             Case Study:
          Summaries in the MED


              Lab Test                            Lab Display


     Intravascular Glucose Test                 Chem20 Display


Fingerstick Glucose Test   Serum Glucose Test


                Plasma Glucose Test
DOP Summary
WebCIS Summary
Financial


 Reporting
 Accounting
 Inventory
       Case Study:
      Orderable Tests

 HCFA   won’t pay for lab batteries
 Individual tests now treated as
  orderable procedures
 Need to appear in database as
  procedures and as tests
                    Case Study:
                   Orderable Tests

              Lab Test                          Lab Procedure


     Intravascular Glucose Test

Fingerstick Glucose Test   Serum Glucose Test      Chem 7


                Plasma Glucose Test
                    Case Study:
                   Orderable Tests

              Lab Test                             Lab Procedure


     Intravascular Glucose Test       Orderable Test

Fingerstick Glucose Test   Serum Glucose Test          Chem 7


                Plasma Glucose Test
    Management



 Quality assurance
 Case management
Information Transfer
    (messaging)



 Transfer to repository
 State reporting
         Clinical Research

 Epidemiology   - symptoms, incidence,
  history of disease
 Outcomes - effectiveness of therapy,
  ideal length of stay
       Expert systems


 Knowledge  base construction
 Case abstraction
 Automated decision support
          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
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?
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.
 How We Outsmarted the Lab
         (Before)


                        Medical Logic
                          Module



No Growth   No Growth
             to Date
 How We Outsmarted the Lab
         (After)

                    “No Growth”
                                           Medical Logic
                      Results
                                             Module



No Growth       No Growth           No Growth
                 to Date          after 24 Hours


     No Growth          No Growth           No Growth
   after 48 Hours     after 72 Hours         after ...
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
      Medical Entities Dictionary

     Laboratory                     Chemical                   Drug
        Test


      Serum                                Aminoglycoside
                       Antibiotic
     Gentamicin
       Test


Random Gentamicin Level         Gentamicin
Main-MeSH:                                        Injectable Gentamicin
                                               Trade-Name: Garamycin"
Supplementary-MeSH:                            Has-Ingredient: Gentamicin
"Gentamicin/bl"
Measures: Gentamicin
      Linking Text Reports to
    On-line Information Sources


   Natural Language Processing
   Data representation to support reuse
   Codification of information needs
             MED Tools

                                 MED
                                Browser
          MED
         Server   Translation     Data
                    Tables       Upload
MED       MED
Editor   Server                 Decision
                  Translation   Support
                    Tables
          MED
         Server   Translation     Data
                    Tables       Display
          MED Browsers

www.cpmc.columbia.edu/resources/
 med/browsers/wilcoxa/cgi-bin/mbrowser.cgi


www.cpmc.columbia.edu/homepages/elhanan

 Select “DynMEDviewer”
          Three Papers
Cimino JJ.    Coding systems in health
  care. Methods of Information in
  Medicine; 1996;35(4):273-284
Cimino JJ.    Formal descriptions and
  adaptive mechanisms for changes in
  controlled medical vocabularies.
  Methods of Information in Medicine;
  1996;35(3):202-210
Cimino JJ.   Desiderata for controlled
  medical vocabularies for the Twenty-
  First Century. Methods of Information
  in Medicine; 1998;37(4-5):394-403
        These Slides:

Informatics.cpmc.columbia.edu/
homepages/ciminoj/mbl1099.ppt
www.amia.org
Questions?

								
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