Ontology Based Clinical Trial Builder

Norbert Graf, Fatima Schera, Gabriele Weiler University of the Saarland, Fraunhofer Institute, Germany

Clinical Trial Ontology WorkshopMay 16-17, 2007

" Research and development on innovative ICT systems and services that process, integrate and use all relevant biomedical data for improving health knowledge and processes related to prevention, diagnosis, treatment, and personalisation of health care. "

The ACGT project sees its mission to develop a GRID platform to support and stimulate further exchanges of both clinic and genetic information.

ACGT intends to trigger the emergence of latent clinico-genomic synergies to ensure faster diagnosis and more efficient therapy

ACGT targets two major cancer diseases namely, breast cancer (BRCA) and paediatric nephroblastoma (PN) presented by three (running) clinical trials. In addition, in-silico oncology trial scenarios will be run to assess the utility of tumour-growth simulation on both BRCA and PN.

The ACGT Objective: Fighting Cancer

The Unknown

Reports that sayThat something hasn't happened Are always interesting to me because, As we know, there are known knowns.There are things we know we know.We also knowThere are known unknowns.That is to sayWe know there are some thingsWe do not know.But there are also unknown unknowns,The ones we don't knowWe don't know.

12th February 2002 Press conference

Trial Outline Builder

Repository

CRF-Creator

Trial Builder components

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This is the Ontology build in Protegé

Clinical View of the Ontology

Overview of the Trial Builder

TrialBuilderWill support the design phase of a clinical trialAllows a clinician to capture data definition and further design specifications for a clinical trial in a standardized wayAllows to create all CRFs for a trial, integrating the ACGT master ontology in a way that the data collected with the CRFs can be later queried in terms of the ontology Integrates a CRF repository for reuse of the created CRFs

Clinical Data Management System will be set up by the definitions done in the Trial Builder Web based application that allows to collect the patient data for multicentric clinical trials

Functionality of the Clinical Data Management System

Patient ManagementProviding data in terms of the ontologyStudy ManagementUser ManagementRoles &Rights ManagementSecurity solution

Technical Details

Web ApplicationJakarta Struts (open-source framework to develop Java EE web applications), Java Server Pages,Apache Tomcat Webserver

Backend Spring Framework (Hibernate) Postgres database

XML format for study metadata, clinical data, administrative data and ontology mapping

CDISC ODM (will be extended to comprise ontology mapping)

Show demonstrator

Ontology integration

User friendly GUI Clinician‘s View of the Ontologyby selecting semantic descriptions the items for the ontology will be created automatically on CRFTools are fully functioning without Ontology

databases are independent from ontologydescriptions from ontology are stored in mapping-files

Queries with SPARQL in terms of the ACGT master ontology are possible

Mapping of all relevant data will be done once

Patient

Disease

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Advantages

Enables trial chairmen to create reusable CRFs that allow collection of data that are standardized based on an underlying ontology Enables trial chairmen to create trial databases with comprehensive metadata (automatically generated from designed CRFs)data collected in the generated systems can be directly integrated over the mediator with the data in the ACGT environment (no additional mapping is needed)Systems created in this way have built-in semantic interoperability Inferring new knowledge from data entered in the ontology based clinical data management system may be possible according to relationships, axioms and rules specified in the ACGT master ontology