Transcript Using Ontology and Controlled Vocabulary in A Clinical Trial

Javed Mostafa
Jane Greenberg
Rahul Deshmukh
Lina Huang
Outline
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Clinical Trials
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SPIROMICS

Application of Ontologies and Controlled Vocabularies

Use Cases - Ontologies in Clinical Trials

SPIRO-V : Role of Ontology and Controlled Vocabularies in
SPIROMICS

SPIRO-V: Where We Are Now
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Controlled Vocabulary Management - The Road Ahead
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Demo
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Questions?
Clinical Trials
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Conducted by Government Organizations,
Pharmaceutical Companies, Academic Research Centers
etc.
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Mostly to assess safety and effectiveness of new
medication or device
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Types

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Treatments - Combination of drugs
Diagnostics
Quality of Life - For patients with chronic illness
Clinical Trials (Contd.)
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Phases
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Phase 0 - Protocol , Patient Identification
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Phase 1 – Small Group (20-80) safety & side – effects of drug/treatment
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Phase II – Larger Group (100-300)

Phase III – Large Group (1000-3000)
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Phase IV – Drug’s Risks, Benefits and Optimal Uses
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Duration – 6 to 8 years
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Cost for pharmaceutical companies between $100 - $800 Million

In 2005, 8000 Clinical Trials, $24 Billion Invested
SPIROMICS
Subpopulations and intermediate outcome measures in
COPD study (SPIROMICS)

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Primary Goals
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Identify and validate markers of disease severity

Identify disease subpopulations
Secondary Goals

Clarify the natural history of COPD

Develop bioinformatics infrastructure

Generate clinical, radiographic and genetic data that can be
used for future multisite clinical trials
Application of Ontologies and
Controlled Vocabularies
Ontology , Controlled
Vocabulary
Communication
For people to talk
the same language
Indexing
To improve
retrieval and
analysis of data
Functions
Retrieval
Browsing
Visualization
Use Cases - Ontologies in Clinical
Trials


Locating eligible patients for clinical trials – IBM, Columbia
University

Matched patient data to SNOMED-CT ontology
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Semantic gulf between raw data and clinician’s interpretation
Structural representation of a disease ontology – Influenza
Infectious Disease Ontology

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Coverage of Infectious Disease Domain
Clinical Trial Data Management System – CancerGrid

Model of study OR Dataset  Forms, Services, Metadata Registry etc
SPIRO-V: Vision
SPIRO-V Clinical Trial Application
Ontology
Visualization
SPIROMICS
Knowledge Base
Ontology
SPIROMICS
Controlled
Vocabularies
Patient
Identification
Mapping
Specimen
Tracking
Clinical Trial
DBMS
Controlled Vocabularies
Editing/ Management
Where We Are Now
Controlled Vocabularies Harvesting
Goal - A COPD Vocabulary set to accurately describe all
the SPIROMICS cohorts, phenotypes, and outcome
measures.
Two Approaches
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Manual

Automatic
Manual Approach

Manual approach to collect vocabularies from authoritative
sources on COPD
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Domain experts conduct quality control
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Downside:
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Low efficiency
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communication, coordination takes time
Consolidated Excel Spreadsheet
Automatic Approach

A relational database back end to store the terms, definitions
and associations
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Incorporation of VCGS automatic metadata generation
system for rapid harvesting
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Provide human review functionality to control the quality of
terms and associations generated.
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Manage controlled vocabularies development process
VCGS
Manage Controlled Vocabulary
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Visualize vocabulary set and make it browsable,
searchable, and editable.
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Vocabulary gathering workflow:
Suggest candidates -> review -> release/reject
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Collaborative initiatives: co-authoring and discussion
Demo
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Database
•
Physical database in MySQL
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VCGS
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TemaTres
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SPIRO-V
Questions?
References
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http://clinicaltrials.gov/ct2/home
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http://www.cscc.unc.edu/spir/
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http://iswc2007.semanticweb.org/papers/809.pdf
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http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/
Main_Page
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http://www.cancergrid.org/
Collaborative thesaurus editing
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Level of user privileges
•
Common users can suggest a candidate term, an
association or a definition and provide feedback
•
Authorized users can reject/accept the suggestions.
• Document changes and comments from different
users.
Ontology, Thesaurus, Controlled
Vocabularies
Ontology
Thesaurus
Where We Are
Controlled Vocabularies