Toward a Diagnosis Driven (Dental) Profession through Controlled...
Transcript of Toward a Diagnosis Driven (Dental) Profession through Controlled...
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Toward a Diagnosis Driven (Dental) Profession through
Controlled Terminology
James J. Cimino, MD
Director, Informatics Institute University of Alabama at Birmingham
Birmingham, Alabama, USA
Los Angeles, CA March 19, 2016
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What I will cover in this talk
Why bother?
Some history from the medical domain
Some formal tactics to consider
Looking ahead
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Everyday Controlled Terminologies
C:\> _
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Controlled Terminologies in Biohealth
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Common Terminology Features
Preferred name
Code
Hierarchy
Synonyms
Cross-mappings
Definitions
Formal semantics
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Value in capturing data with controlled terminology
Capturing what the clinician wants to say
Interoperability
Reuse
Maintenance
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A little history
Cimino JJ. Desiderata for controlled medical vocabularies in the Twenty-First Century. Methods of Information in Medicine; 1998;37(4-5):394-403.
1994
1997
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Desiderata 101
Content: synonyms, structural considerations
Concept oriented: nonvague, unambiguous, nonredundant
Concept permanence: minor name changes only
Meaningless identifiers: no mnemonics or code hierarchy
Multiple hierarchy
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ICD-10-CM: 51 Tuberculosis Codes + 10 hierarchy codes) A15 0 Respiratory tuberculosis A15.0 1 Tuberculosis of lung A15.4 1 Tuberculosis of intrathoracic lymph nodes A15.5 1 Tuberculosis of larynx, trachea and bronchus A15.6 1 Tuberculous pleurisy A15.7 1 Primary respiratory tuberculosis A15.8 1 Other respiratory tuberculosis A15.9 1 Respiratory tuberculosis unspecified A17 0 Tuberculosis of nervous system A17.0 1 Tuberculous meningitis A17.1 1 Meningeal tuberculoma A17.8 0 Other tuberculosis of nervous system A17.81 1 Tuberculoma of brain and spinal cord A17.82 1 Tuberculous meningoencephalitis A17.83 1 Tuberculous neuritis A17.89 1 Other tuberculosis of nervous system A17.9 1 Tuberculosis of nervous system, unspecified A18 0 Tuberculosis of other organs A18.0 0 Tuberculosis of bones and joints A18.01 1 Tuberculosis of spine A18.02 1 Tuberculous arthritis of other joints A18.03 1 Tuberculosis of other bones A18.09 1 Other musculoskeletal tuberculosis A18.1 0 Tuberculosis of genitourinary system A18.10 1 Tuberculosis of genitourinary system, unspecified A18.11 1 Tuberculosis of kidney and ureter A18.12 1 Tuberculosis of bladder A18.13 1 Tuberculosis of other urinary organs A18.14 1 Tuberculosis of prostate A18.15 1 Tuberculosis of other male genital organs A18.16 1 Tuberculosis of cervix
A18.17 1 Tuberculous female pelvic inflammatory disease A18.18 1 Tuberculosis of other female genital organs A18.2 1 Tuberculous peripheral lymphadenopathy A18.3 0 Tuberculosis of intestines, peritoneum and
mesenteric glands A18.31 1 Tuberculous peritonitis A18.32 1 Tuberculous enteritis A18.39 1 Retroperitoneal tuberculosis A18.4 1 Tuberculosis of skin and subcutaneous tissue A18.5 0 Tuberculosis of eye A18.50 1 Tuberculosis of eye, unspecified A18.51 1 Tuberculous episcleritis A18.52 1 Tuberculous keratitis A18.53 1 Tuberculous chorioretinitis A18.54 1 Tuberculous iridocyclitis A18.59 1 Other tuberculosis of eye A18.6 1 Tuberculosis of (inner) (middle) ear A18.7 1 Tuberculosis of adrenal glands A18.8 0 Tuberculosis of other specified organs A18.81 1 Tuberculosis of thyroid gland A18.82 1 Tuberculosis of other endocrine glands A18.83 1 Tuberculosis of digestive tract organs, NEC A18.84 1 Tuberculosis of heart A18.85 1 Tuberculosis of spleen A18.89 1 Tuberculosis of other sites A19 0 Miliary tuberculosis A19.0 1 Acute miliary tuberculosis of a single specified
site A19.1 1 Acute miliary tuberculosis of multiple sites A19.2 1 Acute miliary tuberculosis, unspecified A19.8 1 Other miliary tuberculosis A19.9 1 Miliary tuberculosis, unspecified
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B90 0 Sequelae of tuberculosis B900 1 Sequelae of central nervous system tuberculosis B901 1 Sequelae of genitourinary tuberculosis B902 1 Sequelae of tuberculosis of bones and joints B908 1 Sequelae of tuberculosis of other organs B909 1 Sequelae of respiratory and unspecified tuberculosis O980 0 Tuberculosis compl preg/chldbrth O9801 0 Tuberculosis complicating pregnancy O98011 1 Tuberculosis complicating pregnancy, first trimester O98012 1 Tuberculosis complicating pregnancy, second trimester O98013 1 Tuberculosis complicating pregnancy, third trimester O98019 1 Tuberculosis complicating pregnancy, unspecified trimester O9802 1 Tuberculosis complicating childbirth
J65 1 Pneumoconiosis associated with tuberculosis P370 1 Congenital tuberculosis Z8611 1 Personal history of tuberculosis
13 Other Tuberculosis Codes + 3 more hierarchy codes)
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What if ICD-10-CM was a Polyhierarchy?
disease
cholera meningitis
infectious disease lung disease
tuberculosis
tuberculosis in pregnancy
infectious disease in pregnancy
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Desiderata 101
Content: synonyms, structural considerations
Concept oriented: nonvague, unambiguous, nonredundant
Concept permanence: minor name changes only
Meaningless identifiers: no mnemonics or code hierarchy
Multiple hierarchy
Formal definitions
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Narrative definition: Serum Potassium Test: “a test that measures potassium ion concentration in the serum”
Formal definition: Serum Potassium Test: is_a: Test has_specimen: Serum Specimen measures_substance: Potassium Ion
Formal Definitions
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Serum Potassium Test
Specimen
is_a
Substance
is_a
Test
is_a
Serum Specimen
has_specimen
Potassium Ion
measures_substance
Formal Definitions
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Desiderata 101
Content: synonyms, structural considerations
Concept oriented: nonvague, unambiguous, nonredundant
Concept permanence: minor name changes only
Meaningless identifiers: no mnemonics or code hierarchy
Multiple hierarchy
Formal definitions
Avoid “other” terms (NEC) NEC
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Used for concepts without explicit codes
Can never have a formal definition
Terminology changes induce semantic drift
Reject “Not Elsewhere Classified”
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2007 2008
Diagnosis ICD9-CM Code
ICD9-CM Name
Cardiogenic Shock
785.51 Cardiogenic
Shock Septicemic
Shock 785.52
Septic Shock
Hypovolemic Shock
785.59 Shock without
Mention of Trauma, NEC
Diagnosis ICD9-CM Code
ICD9-CM Name
Cardiogenic Shock
785.51 Cardiogenic
Shock
Septicemic Shock
785.59 Shock without
Mention of Trauma, NEC
Hypovolemic Shock
785.59 Shock without
Mention of Trauma, NEC
Annual Incidence of Shock (Normalized)
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2007 2008
Diagnosis ICD9-CM Code
ICD9-CM Name
Cardiogenic Shock
785.51 Cardiogenic
Shock Septicemic
Shock 785.52
Septic Shock
Hypovolemic Shock
785.59 Shock without
Mention of Trauma, NEC
Diagnosis ICD9-CM Code
ICD9-CM Name
Cardiogenic Shock
785.51 Cardiogenic
Shock
Septicemic Shock
785.59 Shock without
Mention of Trauma, NEC
Hypovolemic Shock
785.59 Shock without
Mention of Trauma, NEC
The “Will Rodgers Phenomenon”: During the Great Dust Bowl Era, when Oakies moved to California, the IQ in both states increased.
05
1015202530354045
2006 2007 2008 2009 2010 2011 2012
785.5785.51785.59785.52
Annual Incidence of Shock (Normalized)
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Desiderata 101
Content: synonyms, structural considerations
Concept oriented: nonvague, unambiguous, nonredundant
Concept permanence: minor name changes only
Meaningless identifiers: no mnemonics or code hierarchy
Multiple hierarchy
Formal definitions
Avoid “other” terms (NEC)
Evolve gracefully
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Handling Retired Concepts
Viral Hepatitis
Hepatitis A Hepatitis B Non-A, Non-B Hepatitis
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Handling Retired Concepts
Viral Hepatitis
Hepatitis C
Hepatitis A Hepatitis B Non-A, Non-B Hepatitis
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Terminology Maintenance
Adding a new lab system 2533 test terms 5291 new terms 6 weeks to go-live
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Automated Classification
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Terminology Maintenance
Adding a new lab system 2533 test terms 5291 new terms 6 weeks to go-live
Maintaining a pharmacy formulary 2091 drugs ~914 new drugs per year (~3 per day) Classification by ingredient, AHFS, DEA, allergy, etc.
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Automated Allergy Coding
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Terminology Maintenance
Adding a new lab system 2533 test terms 5291 new terms 6 weeks to go-live
Maintaining a pharmacy formulary 2091 drugs ~914 new drugs per year (~3 per day) Classification by ingredient, AHFS, DEA, allergy, etc. 211 drugs found to be missing allergy codes
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Desiderata 101
Content: synonyms, structural considerations
Concept oriented: nonvague, unambiguous, nonredundant
Concept permanence: minor name changes only
Meaningless identifiers: no mnemonics or code hierarchy
Multiple hierarchy
Formal definitions
Avoid “other” terms (NEC)
Evolve gracefully
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1998
1997
1994
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Semantic Representation in SNOMED-CT
is-a
Bacterial Pneumonia Tularemia
Pulmonary Tularemia
Francisella tularensis
Lung Structure Inflammation
associated- morphology
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LOINC (Logical Objects, Identifiers, Names and Codes)
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 |
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RxNorm
C0350474: Diazepam 5 MG Oral Capsule [Valium] Synonym: Valium 5 MG Oral Capsule
C0697435: Diazepam 5 MG Oral Capsule [Solis]
C0991533: Oral Capsule
C0699187: Valium
C0992254: Diazepam 5 MG
C0976327: Diazepam 5 MG Oral Capsule
C1256450: Valium Oral Capsule
C1249939: Diazepam Oral Capsule
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1998
1997
1994
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Suggest some formal tactics
Concept-oriented approach Interface terminology follows Interoperability follows Render unto Cesar what is Cesar’s
Strive for semantic modeling Improves concept-oriented approach Reuse for research follows Supports maintenance
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Looking ahead
Diagnostic terminologies differ based on perspective
Multiple terminologies can peacefully co-exist
Getting things by their right names is the first step
Formal definitions will allow…
…humans to understand each other
…computers to help with maintenance and translation