Clinical Terminologies for Research

Clinical Terminologies for Clinical Terminologies for ResearchResearch

S. Trent Rosenbloom, MD MPHS. Trent Rosenbloom, MD MPHAssistant Professor, Department of Biomedical InformaticsAssistant Professor, Department of Biomedical InformaticsAssistant Professor in Clinical Nursing, School of NursingAssistant Professor in Clinical Nursing, School of Nursing

Adjunct Faculty, Departments of Internal Medicine & PediatricsAdjunct Faculty, Departments of Internal Medicine & PediatricsVanderbilt University Medical Center, Nashville, TN, USAVanderbilt University Medical Center, Nashville, TN, USA

Pithy QuotePithy Quote

Water, water, everywhere, Water, water, everywhere, and all the boards did shrink;and all the boards did shrink;

Water, water, everywhere,Water, water, everywhere,nor any drop to drink.nor any drop to drink.

Samuel Taylor Coleridge, The Rime of the Ancient Mariner, 1798Samuel Taylor Coleridge, The Rime of the Ancient Mariner, 1798

SignificanceSignificance

There is a lot of patient data in clinical There is a lot of patient data in clinical documents (i.e., Water, water, everywhere)documents (i.e., Water, water, everywhere)

Most data is difficult to extract for research Most data is difficult to extract for research or automation of routine operational tasks or automation of routine operational tasks (i.e., nor any drop to drink)(i.e., nor any drop to drink)

Terminologies may improve the accessibility Terminologies may improve the accessibility of clinical data.of clinical data.

What is a Terminology?What is a Terminology?

In In mymy research database: research database: – ““Myocardial Infarction”Myocardial Infarction”– ““Heart Attack”Heart Attack”

In In anotheranother researcher’s database researcher’s database– ““Myocardial Infarct”Myocardial Infarct”

This leads to problems of This leads to problems of ambiguityambiguity and and with with interoperabilityinteroperability


The problem is not just theoretical:The problem is not just theoretical:– At our institution, At our institution, weightweight is stored in at least is stored in at least

ten formats within the same EHR systemten formats within the same EHR system– WizOrder (>3)WizOrder (>3)– StarPanelStarPanel– StarNotesStarNotes– StarForms (?n)StarForms (?n)– Quill (can reuse data, user does not always opt for this)Quill (can reuse data, user does not always opt for this)– DictationsDictations– Research intake forms (?n)Research intake forms (?n)– Others?Others?

How do I perform efficient HSR and QA?How do I perform efficient HSR and QA?


Morning Star Evening Star

The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days at a mean distance of approximately 108.2 million kilometers (67.2 million miles).


Morning Star Evening Star

The second planet from the sun, having an average radius of 6,052 kilometers (3,761 miles), a mass 0.815 times that of Earth, and a sidereal period of revolution about the sun of 224.7 days at a mean distance of approximately 108.2 million kilometers (67.2 million miles).

Physical Entity

Conceptual ExperienceRepresentative Terms

Venus

Adapted from Campbell, ‘Representing thoughts, words, and things in the UMLS’, 1998.


Venus

Mercury

Earth

Jupiter

Saturn

Neptune

Planets of the Solar System

inside outside


Terminologies are formal representations Terminologies are formal representations of of entitiesentities and their interrelationships. and their interrelationships.– Embodied asEmbodied as concepts concepts andand terms terms

ConceptsConcepts are universal definitional meanings are universal definitional meanings

TermsTerms are evocative words or phrases. are evocative words or phrases.

What is a Terminology?What is a Terminology?ConceptConcept: Myocardial Infarction : Myocardial Infarction CUI: C0027051 CUI: C0027051 Semantic Type: Disease or Syndrome Semantic Type: Disease or Syndrome

EntityEntity: Gross necrosis of the myocardium, as a result of interruption of the blood supply : Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area. (Dorland, 27th ed) to the area. (Dorland, 27th ed)

Representative Terms (synonyms)Representative Terms (synonyms): : Myocardial Infarction Myocardial Infarction Attack coronary Attack coronary Cardiac infarction Cardiac infarction Heart attack Heart attack Infarction of heart Infarction of heart MI MI MI - Myocardial infarction MI - Myocardial infarction Myocardial Infarct Myocardial Infarct Myocardial infarction (disorder) Myocardial infarction (disorder) Myocardial infarction syndrome Myocardial infarction syndrome myocardium; infarction myocardium; infarction

More Specific Concepts (children):Acute myocardial infarction Old myocardial infarction Microinfarct of heart True posterior wall infarction Aborted myocardial infarction Other specified anterior myocardial infarction Silent myocardial infarction Subsequent myocardial infarction Postoperative myocardial infarction First myocardial infarction Myocardial infarction with complication Non-Q wave myocardial infarction

Adapted from the UMLS Metathesaurus.


Best terminology practices can help Best terminology practices can help improve research data in terms of:improve research data in terms of:

InteroperabilityInteroperabilityClarity Clarity ConsistencyConsistencyQuery-ability (accuracy and precision)Query-ability (accuracy and precision)ManipulabilityManipulability


Terminology DesiderataTerminology DesiderataStatement of purpose, scope, and comprehensivenessStatement of purpose, scope, and comprehensivenessComplete coverage of domain specific contentComplete coverage of domain specific contentUse of concepts rather than terms, phrases and words (concept orientation)Use of concepts rather than terms, phrases and words (concept orientation)Concepts do not change with time, view or use (concept consistency)Concepts do not change with time, view or use (concept consistency)Concepts must evolve with change in knowledgeConcepts must evolve with change in knowledgeConcepts identified through nonsense identifiers (context-free identifier)Concepts identified through nonsense identifiers (context-free identifier)Representation of concept context consistently from multiple hierarchiesRepresentation of concept context consistently from multiple hierarchiesConcepts have single explicit formal definitionsConcepts have single explicit formal definitionsSupport for multiple levels of concept detailSupport for multiple levels of concept detailAbsence of or methods to identify duplication, ambiguity, and synonymyAbsence of or methods to identify duplication, ambiguity, and synonymyIntegration with other terminologiesIntegration with other terminologiesMapping to administrative terminologiesMapping to administrative terminologies

Bottom line: Bottom line: comprehensively represents a medical domain with all comprehensively represents a medical domain with all

the concepts it contains, called the concepts it contains, called CompletenessCompleteness

Adapted from Cimino, ‘Desiderata for controlled medical vocabularies in the twenty-first century’, 1998.


Completeness achieved by one of two waysCompleteness achieved by one of two ways

Post-coordinationPost-coordination - complex concepts from different - complex concepts from different levels of detail are composed as needed from levels of detail are composed as needed from fundamental concepts fundamental concepts

(e.g., ‘chest pain’ composed from the concepts ‘chest’ and (e.g., ‘chest pain’ composed from the concepts ‘chest’ and ‘pain’ when needed) ‘pain’ when needed)

Pre-coordinationPre-coordination - all levels of detail are modeled - all levels of detail are modeled with distinct concepts with distinct concepts

(e.g., ‘chest pain’, ‘substernal chest pain’, and ‘crushing (e.g., ‘chest pain’, ‘substernal chest pain’, and ‘crushing substernal chest pain’ are all in the terminology) substernal chest pain’ are all in the terminology)


Completeness measured by Completeness measured by CoverageCoverage::

coverage calculated as the proportion of concepts coverage calculated as the proportion of concepts covered by a terminologycovered by a terminology

multiple studies: multiple studies: post-coordinatedpost-coordinated terminologies terminologies generally have better coverage than pre-generally have better coverage than pre-coordinated terminologiescoordinated terminologies


ConsequencesConsequences of post-coordination: of post-coordination:

Inefficient post-coordination: “too cumbersome for Inefficient post-coordination: “too cumbersome for complex problem entry”complex problem entry”

Nonsensical ConceptsNonsensical Concepts

Concept duplicationConcept duplication

D5-46210 01 Acute appendicitis, NOS G-A231 01 Acute D5-46100 01 Appendicitis, NOS

M-41000 01 Acute inflammation, NOSG-CO06 01 InT-59200 01 Appendix, NOS

G-A231 01 AcuteM-40000 01 inflammation, NOSG-CO06 01 InT-59200 01 Appendix, NOS

Table. Duplication due to compositionality: four ways to compose ‘Appendicitis’ in SNOMED, from the CANON Group


Terminologies come in different flavorsTerminologies come in different flavors

Adapted from Chute, Layers of Terminology Processing, in ‘Desiderata for a Clinical Terminology Server’, 1999.

Interface Terminology

The ProblemThe Problem

My colleagues down the hall have a grant to My colleagues down the hall have a grant to pay for data extraction from clinical records:pay for data extraction from clinical records:– ““The patient has The patient has MRMR””– ““LADLAD disease was noted by the referring doc” disease was noted by the referring doc”

Data extraction usually isolated from patient Data extraction usually isolated from patient care episodescare episodesDocumentation often performed without Documentation often performed without considering subsequent data extraction considering subsequent data extraction

Encounters between patients and healthcare providers are Encounters between patients and healthcare providers are typically recorded in clinical documents. typically recorded in clinical documents.

clinic notes, clinic notes, procedural narratives, procedural narratives, comprehensive history and physical reports, comprehensive history and physical reports, periodic assessments, periodic assessments, progress notes, consultation notes, progress notes, consultation notes, hospital discharge summaries hospital discharge summaries

Clinical documentation creates an objective record of Clinical documentation creates an objective record of physical findings, medical reasoning, and delivered care physical findings, medical reasoning, and delivered care

Many additional demands are imposed on clinical Many additional demands are imposed on clinical documentation by third partiesdocumentation by third parties

Clinical DocumentationClinical Documentation


The federal government and major stakeholders in The federal government and major stakeholders in healthcare emphasize the importance of rapidly healthcare emphasize the importance of rapidly deploying electronic health record systems to all sites deploying electronic health record systems to all sites of health care.of health care.

increase patient safetyincrease patient safetyreduce errorsreduce errorsimprove efficiencyimprove efficiencyreduce costsreduce costs

Capturing structured information from clinical notes Capturing structured information from clinical notes can improve healthcare and research, but remains a can improve healthcare and research, but remains a major challenge.major challenge.

Medical documents have long served as Medical documents have long served as legallegal treatises, treatises, recounting the care and procedures that individual patients recounting the care and procedures that individual patients receive for the purposes of potential future arbitration.receive for the purposes of potential future arbitration.Insurers use the quality and quantity of documentation to Insurers use the quality and quantity of documentation to justify the level of justify the level of reimbursementreimbursement for given services. for given services. Elements of medical records may be used as markers for Elements of medical records may be used as markers for the the qualityquality of care provided to patients. of care provided to patients. Clinical documentation content may be used as a substrate Clinical documentation content may be used as a substrate for for decision supportdecision support systems. systems.

Each of these forces defines additional components that must Each of these forces defines additional components that must be included in medical documents.be included in medical documents.


Current state of the artCurrent state of the artPaper based / ImpermanentPaper based / ImpermanentAsynchronousAsynchronousRedundantRedundantExpensiveExpensiveIllegible (or inefficient to transcribe)Illegible (or inefficient to transcribe)Location-BoundLocation-BoundLimited functionalityLimited functionality

Unchanged in 5000+ yearsUnchanged in 5000+ years



Clinical Note circa 3000 BCEClinical Note circa 3000 BCE

Clinical DocumentationClinical DocumentationClinical Note circa 2000 CEClinical Note circa 2000 CE

Chief Complaint

History of Present Illness

Past Medical History

Family History

Social History

Review of Systems

Physical Exam

To date, most CNCTs described in the literature To date, most CNCTs described in the literature serve only isolated domains or single problemsserve only isolated domains or single problems

Workup of febrile neonates,Workup of febrile neonates,Evaluation of providers who have had blood and body fluid Evaluation of providers who have had blood and body fluid exposures,exposures,Generation of progress notes in the neonatal and medical Generation of progress notes in the neonatal and medical intensive care units, intensive care units, Enhancing compliance with standards of diabetes care, Enhancing compliance with standards of diabetes care, Documenting pediatric care based on national guidelines, Documenting pediatric care based on national guidelines, Construction of obstetric databasesConstruction of obstetric databasesDocumentation of endoscopy proceduresDocumentation of endoscopy procedures

Only a few general purpose CNCT have been Only a few general purpose CNCT have been described, although they may be increasingdescribed, although they may be increasing



Clinical Documentation – currentClinical Documentation – current

Real-time documentation using categorical Real-time documentation using categorical information is called information is called Structured EntryStructured Entry

Structured Entry can improve patient care Structured Entry can improve patient care by generating data in real timeby generating data in real time

Structured Entry can generate data to Structured Entry can generate data to support clinical researchsupport clinical research– Requires an “Requires an “Interface TerminologyInterface Terminology””


BackgroundBackground

A Structured Entry toolA Structured Entry tool


Structured entryStructured entry of clinical notes currently poorly of clinical notes currently poorly adopted in healthcareadopted in healthcare

Reasons for poor adoption not well characterizedReasons for poor adoption not well characterizedInefficient to useInefficient to useComplicated interfacesComplicated interfacesInflexible in face of unforeseen clinical problemsInflexible in face of unforeseen clinical problemsDifficulty finding what you want to sayDifficulty finding what you want to say

The The terminologiesterminologies supporting structured entry supporting structured entry tools may play a significant roletools may play a significant role

TerminologiesTerminologies

There currently exist many terminologiesThere currently exist many terminologies

In 2003, the National Committee on Vital Health In 2003, the National Committee on Vital Health and Statistics (NCVHS) recommended a subset of and Statistics (NCVHS) recommended a subset of existing terminologies as:existing terminologies as:

““uniform data standards for patient medical uniform data standards for patient medical record information (PMRI) and the electronic record information (PMRI) and the electronic exchange of such information”exchange of such information”


PMRI standards:PMRI standards:– SNOMED CTSNOMED CT (as licensed by the National Library of (as licensed by the National Library of

Medicine) - for the exchange, aggregating, and analysis Medicine) - for the exchange, aggregating, and analysis of patient medical information.of patient medical information.

– Logical observation Identifiers Names and CodesLogical observation Identifiers Names and Codes - for - for the representation of individual laboratory teststhe representation of individual laboratory tests

– Federal Drug TerminologiesFederal Drug Terminologies:: RxNorm;RxNorm; The representations of the mechanism of action and The representations of the mechanism of action and physiologic effect of drugs from NDF-RT; physiologic effect of drugs from NDF-RT; Ingredient name, manufactured dosage form and package Ingredient name, manufactured dosage form and package type form the FDAtype form the FDA


PMRI recommended mapping priorities:PMRI recommended mapping priorities:– Priority 1Priority 1: Terminologies previously designated : Terminologies previously designated

as HIPAA medical code sets:as HIPAA medical code sets: CPT-4CPT-4 (Current Procedural Terminology) (Current Procedural Terminology) CDTCDT (Current Dental Terminology) (Current Dental Terminology)ICD-9-CMICD-9-CM (International Classification of Diseases – (International Classification of Diseases – Clinical Modification)Clinical Modification) NDCNDC (National Drug Codes) (National Drug Codes)


PMRI recommended mapping priorities:PMRI recommended mapping priorities:– Priority 2Priority 2: Terminologies in common use as : Terminologies in common use as

enablers of important healthcare functions.enablers of important healthcare functions.DSM-IVDSM-IV (diagnosis codes for mental disorders) (diagnosis codes for mental disorders)ISBT 128ISBT 128 (coding system for describing blood (coding system for describing blood products and tissues)products and tissues) MedcinMedcin (codes for structured entry of clinical notes) (codes for structured entry of clinical notes) MedDRAMedDRA (international code set for use by drug (international code set for use by drug regulatory agencies)regulatory agencies) Nursing terminologiesNursing terminologies not otherwise included in not otherwise included in SNOMED CTSNOMED CT


What about the UMLS?What about the UMLS?(Unified Medical Language System)(Unified Medical Language System)

– The UMLS is a terminology collectionThe UMLS is a terminology collection– Concepts are unique and may fit the best Concepts are unique and may fit the best

practices desideratapractices desiderata– No formal relationships among concepts No formal relationships among concepts

present, per sepresent, per se


Using the UMLS:Using the UMLS:– Semantics and relationshipsSemantics and relationships from source from source

terminologies lost (or worse, implied)terminologies lost (or worse, implied)– May mix up May mix up different levelsdifferent levels of detail from of detail from

different terminologiesdifferent terminologies– Can loose link with Can loose link with source terminologysource terminology, ,

which can hinder maintenance.which can hinder maintenance.

ConclusionConclusion

Clinical terminologies Clinical terminologies – are formal arrangements of terms, concepts are formal arrangements of terms, concepts

and their interrelationshipsand their interrelationships– can represent knowledge and data if can represent knowledge and data if

generated according to best practicesgenerated according to best practices

Challenges remainChallenges remain– Getting data from narrativesGetting data from narratives– Creating flexible structured entry toolsCreating flexible structured entry tools– Picking the right terminology to fit the intended usePicking the right terminology to fit the intended use

AcknowledgementAcknowledgement

Assistance in developing this work:Assistance in developing this work:Steven H. BrownSteven H. BrownKevin B. JohnsonKevin B. JohnsonPeter L. ElkinPeter L. ElkinTed Speroff Ted Speroff Randolph A. MillerRandolph A. MillerJudy G. OzboltJudy G. Ozbolt

supported by NIH 1 K22 LM08576-01supported by NIH 1 K22 LM08576-01

DiscussionDiscussion

Questions?Questions?

[email protected]@vanderbilt.edu

Thank You!Thank You!

mailto:[email protected]

Clinical Terminologies for Research

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