Translating Medical Research for Patient Findability

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Translating Medical Research for Patient FindabilityMichael Panzer | Mike Hatton

Taxonomy Boot Camp 2016, Washington D.C.14 November 2016

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Professional Background

• Large-scale classification systems• Semantic web technology• Long-time involvement with the

Dewey Decimal Classification• Editor-in-Chief until 2015• Notorious linked data evangelist

• Currently• Manager-Ontologist at Mayo Clinic• 9 person team of (Sr) Ontologists

dewey.info

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Mayo ClinicLocations

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Outline

1. Situation/Background• Status quo ante for the publication of

clinical trials

2. Designing a metadata framework• Leveraging standard clinical vocabularies• Developing a clinical study ontology

3. Evaluating outcomes• Findability, interoperability• Desiderata

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What is a Clinical Trial (Clinical Study)?

• “A research study using human subjects to evaluate biomedical or health-related outcomes. Two types of clinical studies are Interventional studies (or clinical trials) and Observational studies.”

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Publication of Clinical Trials

• Situation: People couldn’t find trials, study coordinators couldn’t find them either!

• Background: Antiquated browse system based on tags assigned by developers

• Focus on benefactors, not study purpose• Started using MeSH (only UF)• Trial summary was written for specialists

• Clinical trial management part of larger reworking of comprehensive research management

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External Web

epiCenterCore Study Data

Mayo sponsored studies -More information to populate registration, including SNOMED terms

Clinicaltrials.gov

Sponsored studies

Ontologist

Core Study Data Capture Process Flow

KCMS

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Outline

1. Situation/Background• Status quo ante for the publication of

clinical trials

2. Designing a metadata framework• Developing a clinical study ontology• Leveraging standard clinical vocabularies

3. Evaluating outcomes• Findability, interoperability• Desiderata

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Career Opportunity

isLocatedIn LocationisLocationOf Research

Study

Organization

Person

Information Resource

Clinicial Trial

Subclass of

isLocationOf

isLocatedIn

isLocationOf

isLocatedIn

conducts

isRelatedResourceOf

relatedResource

conductedBy

offersisOfferedBy

Research Web Domain Model

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Clinicial TrialprimaryCondition

secondaryConditionintervention

SNOMED Concept

skos:closeMatch

Consumer Health

Vocabulary Concept

associatedBodySystem Anatomical Structure

Medical Specialty

associatedMedicalSpecialty

OrganizationisConductedBy

associatedProcedureassociatedCondition

RxNorm Concept

investigatesDrugIntervention

Annotation Design

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Annotation Design

Annotation Property Required

Repeatable

Vocabulary Provide to

epiCenter?

SNOMED synonyms needed?

Primary Condition N Y SNOMED CT

Y Y

Secondary Condition N Y SNOMED CT

Y Y 

Intervention N Y SNOMED CT

Y Y 

Drug Intervention N Y RxNorm Y YAssociated Condition

N Y CHV Y N

Associated Procedure

N Y CHV Y N

Medical Specialty N Y SNOMED > Healthcare specialty

Y N

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Vocabulary selection

• SNOMED CT• Comprehensive clinical health terminology• ~300,000 concepts• Synonymy• Mappings to CHV

• CHV (Consumer Health Vocabulary)• Set of consumer-oriented concepts of

conditions, procedures, symptoms, devices, anatomy

• ~5,000 concepts, rich set of relationships

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Vocabulary selection

• RxNorm• Normalized names for clinical drugs and

links to many drug vocabularies• Generic and branded drugs• Part of UMLS, edited by NLM

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Vocabulary application

• Primary subject captures the primary condition the study is researching to finest granularity

• Secondary subject captures other conditions• “Diabetic neuropathy in patients with

untreated diabetes”

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Questions that can be answered by the design• What SNOMED codes are annotated to this study?• What CHV terms are annotated to this study?• What organizations are associated to this study?• What medical specialty terms are associated to this

study?• What body systems are associated to this study?• What are the SNOMED synonyms associated with

this study?

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Outline

1. Situation/Background• Status quo ante for the publication of

clinical trials

2. Designing a metadata framework• Leveraging standard clinical vocabularies• Developing a clinical study ontology

3. Evaluating outcomes• Findability, interoperability• Desiderata

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Interoperability benefits

• Integration for trials with health information content

• Condition and procedure topic pages• Search

• Clinical study header service• Integration with clinical departments

• Emphasis on recall rather than precision• Example: Endocrinology

• Integration with research centers

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mayoclinic.org mayo.edu

Integration overview

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Examples

• mayoclinic.org: Condition• mayoclinic.org: Procedure• mayoclinic.org: Department• mayo.edu/research: Research organization

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Outcomes

• Cancer Center saw increase from 3500 inquiries a year to 5000 after improvements went live

• Inquiry volume continues to increase• Deeper dive into a random sample of calls from

Mar. 2015–Mar. 2016• 1921 inquiries• 20% resulted in appointments• 25% of those resulted in signed consents (5%

overall)

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Questions & Discussion

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Translating Medical Research for Patient FindabilityMichael Panzer

Taxonomy Boot Camp 2016, Washington D.C.14 November 2016