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Tutorial T13 Practical Considerations for Choosing Terminologies

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Tutorial T13 Practical Considerations for Choosing Terminologies Powered By Docstoc
					Principles of Controlled Terminology


            James J. Cimino
           NIH Clinical Center
           Topics

•   Motivations and issues
•   Desiderata
•   Available Terminologies
•   Hands-on exercises
•   Reusing coded clinical data
•   Take-home messages
                            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.
 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?
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?
          Re-Using Gender
“Patient is an 50 year old,
  Native American female…”


              Electronic
               Medical
               Record


              Admission
              Discharge    “Put the patient in
               Transfer      Room 5, Bed B…”
               System
          Re-Using Gender
But: how does the computer know that the
 patient is female?
The record could say:
          “female”
          “Female”
          “FEMALE”
          “F”
          “Woman”
          “Girl”
        Concept: Definition


Terminology:

A finite, enumerated set of terms intended to
convey information unambiguously
Concept: Term - Basic Features

    • Unique Identifier (Code)
      – “F”
    • Official Name
      – Female
    • Synonyms
      – Woman, Girl
Concept: General Classes of Terms

       •   Demographics
       •   Signs and symptoms
       •   Anatomy
       •   Diagnostic procedures
       •   Organisms
       •   Diagnoses
       •   Medications
       •   Therapeutic Procedures
Coding the Data: Gender
• Data element - gender
• Controlled terminology:
  – Male
  – Female
  – Unknown (don’t know)
  – Unknown (can’t tell)
• Representation: M,F,U; 0,1,2
• What about other values?
  – Genotypic
  – Phenotypic
  – Administrative
Isn’t 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
Information Form and Reuse
Information Form and Reuse


  7
  6
  5
  4
  3
  2
  1
      21 22 23 24 25 26 27 28 29
         Terminology Desiderata



Cimino JJ. Desiderata for controlled medical vocabularies in
  the Twenty-First Century. Methods of Information in
  Medicine; 1998;37(4-5):394-403.
                 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.
1) Go to:
   http://miproject.mbl.edu/terminology/terminologylab/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
            Coding the Data

Chief complaint:
 “lip numbness”, “nausea” “chest pain”

Past diagnoses:
 “hypertension”, “tuberculosis in pregnancy”

Coding: ICD9-CM
       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
                ICD


•   Strict hierarchy
•   No complete names
•   Code determines place in hierarchy
•   Not Otherwise Specified (NOS)
•   Not Elsewhere Classified (NEC)
              ICD9-CM Diagnoses

V21DIAG.TXT:                     Translates to:
005 OTHER FOOD POISONING*        005.0    STAPH FOOD POISONING
0050 STAPH FOOD POISONING        005.1    BOTULISM
0051 BOTULISM                    005.2    FOOD POIS D/T C. PERFRIN
0052 FOOD POIS D/T C. PERFRIN    005.3    FOOD POIS: CLOSTRID NEC
0053 FOOD POIS: CLOSTRID NEC     005.4    FOOD POIS: V. PARAHAEM
0054 FOOD POIS: V. PARAHAEM      005.81 FOOD POISN D/T V. VULNIF
0058 BACT FOOD POISONING NEC*    005.89 BACT FOOD POISONING NEC
00581 FOOD POISN D/T V. VULNIF   005.9    FOOD POISONING NOS
00589 BACT FOOD POISONING NEC
0059 FOOD POISONING NOS
http://www.eicd.com/EICDMain.htm
http://icd9cm.chrisendres.com/index.php
            Strict Hierarchy


                       disease


  Infectious disease        lung disease



cholera           meningitis               tuberculosis
              Polyhierarchy


                       disease


  Infectious disease        lung disease



cholera           meningitis               tuberculosis
             ICD9-CM Examples:
           420 Tuberculosis Codes
         (plus 69 hierarchical codes)
010.     PRIMARY TB INFECTION*       011.   PULMONARY TUBERCULOSIS*
010.0    PRIMARY TB COMPLEX*         012.   OTHER RESPIRATORY TB*
                                     013.   CNS TUBERCULOSIS*
010.00   PRIM TB COMPLEX-UNSPEC
                                     014.   INTESTINAL TB*
010.01   PRIM TB COMPLEX-NO EXAM     015.   TB OF BONE AND JOINT*
010.02   PRIM TB COMPLEX-EXM UNKN    016.   GENITOURINARY TB*
010.03   PRIM TB COMPLEX-MICRO DX    017.   TUBERCULOSIS NEC*
010.04   PRIM TB COMPLEX-CULT DX     018.   MILIARY TUBERCULOSIS*
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*
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
              Polyhierarchy


                       disease


  infectious disease        lung disease



cholera           meningitis               tuberculosis
    infectious disease
       in pregnancy
                         tuberculosis in pregnancy
NEC
      Desideratum: Reject
   "Not Elsewhere Classified"


• Can never have a formal definition

• Terminology changes induce semantic drift
    Example: Not Elsewhere Classified
                1995                                        1996

  Diagnosis ICD9-CM      ICD9-CM            Diagnosis ICD9-CM           ICD9-CM
              Code         Name                         Code              Name
 Hepatitis A   070.1     Hepatitis A        Hepatitis A    070.1       Hepatitis A
 Hepatitis B   070.3     Hepatitis B        Hepatitis B    070.3       Hepatitis B

 Hepatitis C   070.5   Hepatitis NEC        Hepatitis C    070.4       Hepatitis C
 Hepatitis E   070.5   Hepatitis NEC        Hepatitis E    070.5      Hepatitis NEC

                                          Viral Hepatitis Mortality


The “Will Rodgers Phenomenon”:
                                                                           070.1
  During the Great Dust Bowl Era, when
                                                                           070.3
  Oakies moved to California, the IQ in
                                                                           070.5
  both states increased.
                                                                           070.4
                                          1994      1995      1996
    Available Terminology: CPT

• Current Procedural Terminology
• Developed and owned by AMA
• Required for procedure reimbursement
• Required for physician visit reimbursement
  (E&M Coding)
• Licensing fee per application, per seat
                  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
     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)
         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
539   Respiratory disease, other respiratory system operating procedure and major
      complication or comorbidity
540 Respiratory infection with major complication or comorbidity
631   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
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
 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)
     Coding the Data

Allergies: “Bufferin”

Medications: “Activated Charcoal”,
 “Enteric-Coated Aspirin”

Coding: NDC
  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
     National Drug Codes: Example

0000003412| 0071|0569|0.3|MG|R|TAB|0039994|NITROSTAT TABLETS

0000003412|24|100|BOT

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?)
http://www.fda.gov/cder/ndc/database/default.htm
           RxNorm

• Food and Drug Administration

• Veterans Health Administration

• National Library of Medicine

• Drug knowledge base vendors
                            RxNorm
                         C1249939:
                          Diazepam Oral Capsule




             C1256450:                   C0976327:
              Valium Oral Capsule         Diazepam 5 MG Oral Capsule




C0350474:                              C0697435:
 Diazepam 5 MG Oral Capsule [Valium]    Diazepam 5 MG Oral Capsule [Solis]
   Synonym: Valium 5 MG Oral Capsule




                                                          C0991533:
 C0699187:                   C0992254:
                                                           Oral Capsule
  Valium                      Diazepam 5 MG
                 LOINC

• HL7 Message:
   OBX|…|Observation|…|Result|…|
• Observation = Code^Name^Coding System
• Logical Objects, Identifiers, Names and
  Codes
• Self-defining names for lab tests
       LOINC - Structure

•   Component.subspecies^challenge
•   Property
•   Timing
•   System
•   Scale (Precision)
•   Method
•   Related names
•   Other codes
               LOINC - Examples

4764-5 | GLUCOSE^3H POST 100 G GLUCOSE PO | SCNC | PT | SER/PLAS
  | QN|

1530-5 | GLUCOSE^3H POST 100 G GLUCOSE PO | MCNC | PT | SER/PLAS
  | QN |

5955-0 | COAGULATION THROMBIN INDUCED | TIME | PT | PPP^CONTROL
  | 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 |
 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
    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
    Coding Nursing Concepts

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

          Diagnoses Interventions Outcomes   Goals
  NANDA       X
   NIC                   X
  NOC                               X
  GHHCC       X          X          X
  PCDS        X          X                    X
  Omaha       X          X          X
  AORN        X          X          X
  ICNP        X          X          X         X
 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 patient’s physical exam

Reusing the data:
  Epidemiologic studies
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
   Semantic Representation in
      SNOMED-RT/CT
                                  Bacterial
            Tularemia
                                 Pneumonia
                          is-a

                        Pulmonary
                        Tularemia


                 associated-
  Lung           morphology                   Francisella
Structure                                     tularensis
                     Inflammation
http://nciterms.nci.nih.gov/NCIBrowser/Startup.do
http://snomed.vetmed.vt.edu/sct/menu.cfm
 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
Available Terminology: MeSH

  • Medical Subject Headings

  • National Library of Medicine

  • Indexing the medical literature
             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
http://www.nlm.nih.gov/mesh/MBrowser.html
 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
               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
    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
http://fme.biostr.washington.edu:8089/FME/index.html
          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
                          GO Example
id: GO:0043234 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."
[GO:curators] 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: GO:0005575 ! cellular_component

id: GO:0000214 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."
    [EC:3.1.27.9]
is_a: GO:0043234 ! protein complex
relationship: part_of GO:0005634 ! nucleus
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
          UMLS History


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


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

               2004      2005      2006      2008      2009


• Sources       115       132      134       145       152

• Strings    3,295,308 4,673,237 6,177,437 7,781,500 8,006,171

• Concepts   1,020,866 1,179,179 1,341,487 1,553,638 2,125,395
          Metathesaurus
              Concept

                   String

                   String



Concept                     Concept

     String                      String
     String                      String
                    SUIs and CUIs
“Heart”
String Unique Identifier S0047194
Concept Unique Identifier C0018787
Terminologies: MeSH:D006321; Read:Xa8SM; SNOMED:T-32000;
      SNOMED:U000438(hierarchy); AIR:MFHRT; LCH:U002104; PSY:22460;
      UWDA:7088; ICD10:C38.0; ICD10:D15.1

“HEART”
String Unique Identifier: S0375948
Concept Unique Identifier: C0018787
Terminologies: SNOMED-Int:T-32000 (Hierarchy); CCPSS:U000039

“heart”
String Identifier: S0419735
Concept Unique Identifier: C0018787
Terminologies: AOD:0000002498; CSP:1390-0233
                          SUIs and CUIs
                                ICD-10:
                                . Malignant neoplasms [C00-C97.9]
“Heart”                         . . Malignant neoplasms of respiratory and
                                        intrathoracic organs [C30-C39.9]
String Unique Identifier S0047194 . . Malignant neoplasm of heart, mediastinum
                                .
Concept Unique Identifier C0018787         and pleura [C38]
                                  . . . Heart [C38.0]
Terminologies: MeSH:D006321; .Read:Xa8SM; SNOMED:T-32000;
      SNOMED:U000438(hierarchy); AIR:MFHRT; LCH:U002104; PSY:22460;
      UWDA:7088; ICD10:C38.0; ICD10:D15.1

“HEART”
String Unique Identifier: S0375948
Concept Unique Identifier: C0018787
Terminologies: SNOMED-Int:T-32000 (Hierarchy); CCPSS:U000039
 ICD-10:
 . Benign neoplasms [D10-D36.9]
“heart”
 . . Benign neoplasm of other and unspecified
String Identifier: S0419735[D15]
          intrathoracic organs
 . . . Heart [D15.1]
Concept Unique Identifier: C0018787
Terminologies: AOD:0000002498; CSP:1390-0233
                                  Canonical Clinical Problem Statement System:
                                  . HEART [1390-0233]
                     SUIs and CUIs
“Heart”                            “Heart”
String Unique Identifier S0047194  String Unique Identifier S0047194
Concept Unique Identifier C0018787 Concept Unique Identifier C0153500
Terminologies: MeSH:D006321; Read:Xa8SM; SNOMED:T-32000;
                                   Terminologies: ICD10:C38.0
      SNOMED:U000438(hierarchy); AIR:MFHRT; LCH:U002104; PSY:22460;
      UWDA:7088; ICD10:C38.0; ICD10:D15.1
                                    “Heart”
“HEART”
                                    String Unique Identifier S0047194
String Unique Identifier: S0375948
                                    Concept Unique Identifier C0153957
Concept Unique Identifier: C0018787
                                    Terminologies: ICD10:D15.1
Terminologies: SNOMED-Int:T-32000 (Hierarchy); CCPSS:U000039

“heart”
String Identifier: S0419735         “HEART”
Concept Unique Identifier: C0018787 String Unique Identifier: S0375948
                                    Concept Unique Identifier: C0795691
Terminologies: AOD:0000002498; CSP:1390-0233
                                    Terminologies: CCPSS:U000039
     Metathesaurus - MRCONSO
C0153957|ENG|P|L0180790|PF|S1084242|Y|A1141630||||MTH|PN|U001287
   |benign neoplasm of heart|0|N||
C0153957|ENG|P|L0180790|VC|S0245316|N|A0270815||||ICD9CM|PT|
   212.7|Benign neoplasm of heart|0|N||
C0153957|ENG|P|L0180790|VC|S0245316|N|A0270817||||RCD|SY|B727.|
   Benign neoplasm of heart|3|N||
C0153957|ENG|P|L0180790|VO|S1446737|Y|A1406658||||SNMI|PT|
   D3-F0100|Benign neoplasm of heart, NOS|3|N||
C0153957|ENG|S|L0524277|PF|S0599118|N|A0654589||||RCDAE|PT|B727.
   |Benign tumor of heart|3|N||
C0153957|ENG|S|L0524277|PF|S0599118|Y|A2996703|1218640014|
   92132009||SNOMEDCT|SY|92132009|Benign tumor of heart|4|N||
C0153957|ENG|S|L0524277|VO|S0599510|N|A0654975||||RCD|PT|B727.|
   Benign tumour of heart|3|N||
C0153957|ENG|S|L0018787|PF|S0047194|Y|A0066366||||ICD10|PS|D15.1
   |Heart|3|Y||
C0153957|ENG|S|L0018787|VO|S0900815|Y|A0957792||||MTH|MM|U003158
   |Heart <3>|0|Y||
C0153957|ENG|S|L1371329|PF|S1624801|N|A1583056|||10004245|MDR|LT
   |10004245|Benign cardiac neoplasm|3|N||
C0153957|GER|P|L1258174|PF|S1500120|Y|A1450314||||DMDICD10|PT|
   D15.1|Gutartige Neubildung: Herz|1|N||
C0153957|SPA|P|L2354284|PF|S2790139|N|A2809706||||MDRSPA|LT|
   10004245|Neoplasia cardiaca benigna|3|N||
     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]
         Metathesaurus - MRREL
C0153957|A0066366|AUI|PAR|C0348423|A0876682|AUI||R06101405||ICD1
   0|ICD10|||N||
C0153957|A0066366|AUI|RQ|C0153957|A0270815|AUI|default_mapped_
   from|R03575929||NCISEER|NCISEER|||N||
C0153957|A0066366|AUI|SY|C0153957|A0270815|AUI|uniquely_mapped_
   to|R03581228||NCISEER|NCISEER|||N||
C0153957|A0270815|AUI|RQ|C0810249|A1739601|AUI|classifies|
   R00860638||CCS|CCS|||N||
C0153957|A0270815|AUI|SIB|C0347243|A0654158|AUI||R06390094||
   ICD9CM|ICD9CM||N|N||
C0153957|A0270815|CODE|RN|C0685118|A3807697|SCUI|mapped_to|
   R15864842||SNOMEDCT|SNOMEDCT||Y|N||
C0153957|A1406658|AUI|RL|C0153957|A0270815|AUI|mapped_from|
   R04145423||SNMI|SNMI|||N||
C0153957|A1406658|AUI|RO|C0018787|A0357988|AUI|location_of|
   R04309461||SNMI|SNMI|||N||
C0153957|A2891769|SCUI|CHD|C0151241|A2890143|SCUI|isa|R19841220|
   47189027|SNOMEDCT|SNOMEDCT|0|Y|N||
C0153957|A3807333|SCUI|RO|C0086692|A3579828|SCUI|associated_
   morphology_of|R13712546|907149029|SNOMEDCT|SNOMEDCT|1|N|N||
        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
  UMLS Semantic Network - Event
Activity                                Phenomenon or Process
 Behavior                                 Injury or Poisoning
    Social Behavior                       Human-caused Phenomenon or Process
    Individual Behavior                     Environmental Effect of Humans
 Daily or Recreational Activity           Natural Phenomenon or Process
 Occupational Activity                      Biologic Function
    Health Care Activity                       Physiologic Function
      Laboratory Procedure                       Organism Function
      Diagnostic Procedure                          Mental Process
      Therapeutic or Preventive Procedure        Organ or Tissue Function
    Research Activity                            Cell Function
      Molecular Biology Research                 Molecular Function
                Technique                           Genetic Function
    Governmental or Regulatory Activity        Pathologic Function
    Educational Activity                         Disease or Syndrome
 Machine Activity                                   Mental or Behavioral Dysfunction
                                                    Neoplastic Process
                                                 Cell or Molecular Dysfunction
                                                 Experimental Model of Disease
  UMLS Semantic Network - Entity
                                       Conceptual Entity
Physical Object                         Organism Attribute
 Organism +                                Clinical Attribute
 Anatomical Structure                   Finding
   Embryonic Structure                     Laboratory or Test Result
   Fully Formed Anatomical Structure       Sign or Symptom
      Body Part, Organ, or              Idea or Concept +
                Organ Component         Occupation or Discipline
      Tissue                               Biomedical Occupation or Discipline
      Cell                              Organization
      Cell Component                       Health Care Related Organization
      Gene or Genome                       Professional Society
   Anatomical Abnormality                  Self-help or Relief Organization
      Congenital Abnormality            Group
      Acquired Abnormality                 Professional or Occupational Group
 Manufactured Object                       Population Group
   Medical Device                          Family Group
      Drug Delivery Device                 Age Group
   Research Device                         Patient or Disabled Group
   Clinical Drug                        Group Attribute
 Substance                              Intellectual Product
   Body Substance                          Regulation or Law
   Chemical+                               Classification
   Food                                 Language
UMLS Semantic Network - Entity
Organism
   Plant
      Alga                   Idea or Concept
   Fungus                        Temporal Concept
   Virus                         Qualitative Concept
   Rickettsia or Chlamydia       Quantitative Concept
   Bacterium                     Spatial Concept
   Animal                           Body Location or Region
      Invertebrate                  Body Space or Junction
      Vertebrate                    Geographic Area
         Amphibian                  Molecular Sequence
         Bird                         Nucleotide Sequence
         Fish                         Amino Acid Sequence
         Reptile                      Carbohydrate Sequence
         Mammal                  Functional Concept
            Human                   Body System
    Archaeon
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
   Semantic Network - SRDEF

STY|T191|Neoplastic Process|B2.2.1.2.1.2|A 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
lymphoepithelioma|All neoplasms are assigned to
this type. Do not also assign a type from the
'Anatomical Abnormality' hierarchy.||neop||
     Metathesaurus - MRSTY



C0153957|T191|B2.2.1.2.1.2|Neoplastic
  Process|AT08223379||
        Specialist Lexicon

• A lexicon, not a terminology

• Provides syntactic, morphological, and
  graphemic information - but not
  semantic information
Specialist Lexicon


 {base=beer
   entry=E0012226
   cat=noun
   variants=uncount
   variants=reg}
http://www.nlm.nih.gov/research/umls/
    The UMLS is not a Terminology!



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

• Reconstructing source terminologies

• Finding additional synonyms for source
  terms (mapping)

• Automated translation
         Data Types

                                           Standard
Numeric               Coded
                                            Coded
                    NLP

    Text              Structured           Symbols

 Interpretation

Signal            Image

                                   Blobs
              Choice of Terminologies
                         HPI    PMH Exam Labs          Diag    Dx         Rx    Tx
          ICD$                                         +      ++                ++
          CPT$                                    +     +                       +
          DRG                                                  +
          NDC                                                             +++
          RxNorm                                                          +++
          LOINC                                  +++    +
          Nursing                                                         ++
          SNOMED        +++    +++    +++        ++    ++     +++         ++    ++
          MeSH           +       +      +        +     ++      ++         ++    ++
          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
                  Coding the Case
1)Go to:
  http://miproject.mbl.edu/terminology/terminologylab/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/TermsBrowser/
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., don’t 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!)
     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
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)
Reusing Data: Summary Reports

• Lab summaries typically aggregate codes

• Hardcoded aggregations are hard to maintain

• Use a high-quality controlled terminology…
  Reusing Data: Summary Reports



              Lab Test                            Lab Display


     Intravascular Glucose Test                 Chem20 Display


Fingerstick Glucose Test   Serum Glucose Test


                Plasma Glucose Test
Lab Result Summary 1990
Lab Result Summary: 1995
What are the blood glucose test results?

        Eclipsys Summary
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
Reuse of Data: “DXplain Button”


                  Serum Potassium Test


 Serum Specimen
                          Abnormalities of
                          Serum Potassium

           Potassium
  Serum
                                   Hypokalemia
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
Reusing the Data: Infobuttons
Translations to Support Infobuttons

                 Clinical Data


   Serum                              Injectable
 Gentamicin                          Gentamicin
   Level

                  Gentamicin                 Decision
                                              Rule


   Gentamicn                         Gentamicin
   Sensitivity                        Toxicity
     Test
                     Drug
                 Information
                                 Expert
                                 System
 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?
       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

                   Aspirin Preparations          has-ingredient
                                                                  Aspirin


        Bufferin             Enteric-Coated Aspirin
 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 (>140)?
f) If the patient has criteria for the for the diagnosis of
    myocardial infarction (any two of: chest pain, elevated
    cardiac enzymes (CK>200 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?
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




                                           MI
                                           MI+Aspirin




           2000 2001 2002 2003 2004 2005
                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)
                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)
                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)
      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
                    Additional Reading
Cimino JJ. Desiderata for controlled medical vocabularies in the Twenty-First Century.
   Methods of Information in Medicine; 1998;37(4-5):394-403.
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. In defense of the Desiderata. J Biomed Inform. 2006 Jun;39(3):299-306.
Humphreys BL, Lindberg DA, Schoolman HM, Barnett GO. The Unified Medical
  Language System: an informatics research collaboration. JAMIA. 1998;5(1):1-11.
Lindberg DAB, Humphreys BL, McCray AT. The Unified Medical Language System.
   Meth Inform Med. 1993;32:281-291.
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-Jun;13(3):277-88.
Wang AY, Sable JH, Spackman KA. The SNOMED clinical terms development
  process: refinement and analysis of content. Proc AMIA Symp. 2002;:845-9.

				
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