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Ontology Based Clinical Trial Builder

Ontology Based Clinical Trial Builder. Norbert Graf, Fatima Schera, Gabriele Weiler University of the Saarland, Fraunhofer Institute, Germany Clinical Trial Ontology Workshop May 16-17, 2007.

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Ontology Based Clinical Trial Builder

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  1. Ontology Based Clinical Trial Builder Norbert Graf, Fatima Schera, Gabriele Weiler University of the Saarland, Fraunhofer Institute, Germany Clinical Trial Ontology Workshop May 16-17, 2007

  2. " 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. "

  3. The ACGT Objective: Fighting Cancer • The ACGT project sees its mission to developa 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-silicooncology trial scenarios will be run to assess the utility of tumour-growth simulation on both BRCA and PN.

  4. The Unknown Reports that say That 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 know There are known unknowns. That is to say We know there are some things We do not know. But there are also unknown unknowns, The ones we don't know We don't know. 12th February 2002 Press conference

  5. Trial Outline Builder CRF-Creator Repository Trial Builder components

  6. SIOP 2001 / GPOH Report / output P P P P stop P AV AV-1 P P AV-2 P randomisation P AVD irradiation P HR P P P AVD Diagnosis stratification pathology stratification clinic laboratory imaging registration imaging Follow-up surgery P P AV / AVD SAEs / SUSARs Patient diary C timeline

  7. Report / output P P P P stop P AV S AV-1 S P P S AV-2 P randomisation P AVD irradiation C C P HR P P P AVD Diagnosis stratification pathology stratification clinic laboratory imaging registration imaging surgery Follow-up C P P AV / AVD timeline Patient diary SIOP 2001 / GPOH

  8. This is the Ontology build in Protegé

  9. Clinical View of the Ontology

  10. Overview of the Trial Builder • TrialBuilder • Will support the design phase of a clinical trial • Allows a clinician to capture data definition and further design specifications for a clinical trial in a standardized way • Allows 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

  11. Functionality of the Clinical Data Management System • Patient Management • Providing data in terms of the ontology • Study Management • User Management • Roles &Rights Management • Security solution

  12. Technical Details • Web Application • Jakarta 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)

  13. Show demonstrator

  14. Ontology integration • User friendly GUI  Clinician‘s View of the Ontology • by selecting semantic descriptions the items for the ontology will be created automatically on CRF • Tools are fully functioning without Ontology • databases are independent from ontology • descriptions 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

  15. Disease S R Personal Data S R Tumor S R Patient Therapeutic Procedure S R Measurements S R Symptom S R

  16. Disease S R Personal Data S R Tumor S R Patient Therapeutic Procedure S R S R Measurements Pharmacotherapy S R Symptom S R Surgical Proc. S R Radiotherapy S R

  17. Disease S R Personal Data S R Tumor S R Patient Therapeutic Procedure S R Measurements S R Pharmacotherapy S R Symptom S R Surgical Proc. S R Radiotherapy S R Radiotherapy of Lung S R Abdominal Radiotherapy S R

  18. Disease S R Personal Data S R Tumor S R Patient Therapeutic Procedure S R Measurements S R Pharmacotherapy S R Symptom S R Surgical Proc. S R Radiotherapy S R A Begin End A Duration A SingleDose A Radiotherapy of Lung S R TotalDose A S R Device Field A

  19. Disease S R Personal Data S R Tumor S R Patient Therapeutic Procedure S R Measurements S R Pharmacotherapy S R Symptom S R Surgical Proc. S R Radiotherapy S R Begin A End A Duration A SingleDose A Radiotherapy of Lung S R TotalDose A S R Device Field A

  20. Disease S R Personal Data S R Tumor S R Patient Therapeutic Procedure S R Measurements S R Pharmacotherapy S R Symptom S R Surgical Proc. S R Radiotherapy S R Begin A End A Duration A SingleDose A Radiotherapy of Lung S R TotalDose A S R Device Field A

  21. 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

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