european translational research information and km services (etriks) prof yike guo department of...
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European Translational Research Information and KM Services
(eTRIKS)Prof Yike Guo
Department of Computing Imperial College London
Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe
Convergence Meeting: Semantic Interoperability for Clinical Research &
Patient Safety in Europe1
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Goals & Objectives
• Objective: – Provision of a sustainable KM Platform and Service to support
Private/Public Translational Research (TR) in IMI and beyond– Single access point to standardised curated TR study information
• Scope:– Cloud Hosting, KM Platform, Data & Service Standards, Analytics,
Curation, and Training– Potentially support for any IMI Project involving translational research
• Budget: €23.98m for 5 years (Oct/2012---Sept/2017)
Convergence Meeting: Semantic Interoperability for Clinical Research &
Patient Safety in Europe2
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Partners
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Patient Safety in Europe3
Academia
SME
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ETRIKS Deliverable • KM support for IMI (and other PPP) projects
– Access to fit-for-purpose, secure, easy-access, standardised TR KM services (for ongoing cross-organisation TR study support)
• Hosting / installation• Training• Curation workflow software• Data Mgmt software
– Single point of access to curated historic TR study data on the cloud
– Sustainable, interoperable, collaborative, re-usable, open source TR platform, based on open, agreed standards, used and contributed to by global research community.
• Development of an active TR analytics & informatics community
TR Informatics Standard and Centralized Data Cloud
• Analytics software• Curation support• Standards build and coordination• KM consultancy
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eTRIKS : Linking the Two Worlds
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Patient Safety in Europe5
From : Committee on A Framework for Developing a New Taxonomy of Disease
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eTRIKS Architecture
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Interoperability for Clinical Research & Patient Safety in Europe
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eTRIKS Study Data Management
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Patient Safety in Europe7
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eTRIKS Curation: Building Contents
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eTRIKS Data Curation Process
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Patient Safety in Europe9
tranSMART-based eTRIKS Study Data Management System
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• U-BIOPRED (Unbiased BIOmarkers in PREDiction of respiratory disease outcomes)
Use cases
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Interoperability for Clinical Research & Patient Safety in Europe
1. Reaching international consensus on diagnostic criteria 2. Creating adult/pediatric cohorts and biobanks 3. Creating novel biology ‘handprints’ by combining molecular, histological, clinical and patient-reported data 4. Validating such ‘handprints’ in relation to exacerbations and disease progression 5. Refining the ‘handprints’ by using preclinical and human exacerbation models 6. Predicting efficacy of gold-standard and novel interventions 7. Refining the diagnostic criteria and phenotypes 8. Establishing a platform for exchange, education and dissemination
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eTRIKS Ontology Management
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Semantic Resources• Based on NCBO (BioPortal Ontologies)
• eTRIKS Possible focus:– UMLS ( Vocabularies include: CPT®, ICD-10-CM, LOINC®, MeSH®,
RxNorm, and SNOMED CT®)– CTSA – NCBO Human related Phenotype ontologies – Omics ontologies
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Adoption of standards•CDISC Data Model
– SDTM : Study Data Tabulation Model – ADaM : Analysis Data Model – SEND: Standard for Exchange of Nonclinical Data – CDASH Clinical Data Acquisition Standards Harmonization– PR: Protocol Representation– TDM: Study/Trial Design Model– ODM: Operational Data Model – LAB: Laboratory Data Model– BRIDG Model
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Patient Safety in Europe14
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Quality assurance of the semantic resources
•All tools used based on open source community based building•Continuous interfacing with developing community and regular standards updates will ensure quality•WP3 dedicated to ontologies and standards, led by CDISC •Large collaboration with projects across EU/USA
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Standards and terminologies selection process
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Semantic interoperability issues•Legacy data for certain projects / studies– Possible Solution: Development of custom ETL procedures.
•Diverse EHR systems in clinics : not a problem now but EHR will be an ideal addtion to CTMS
– Working closely with projects like EHR4CR/Euroca /Open Phacts
• Too many standards and mappings – Committing to some widely adopted systems (by IMI projects)
•Cross projects mapping – Need terminology mapping services : learning Semantic Web
technology
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Patient Safety in Europe17
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Examples
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Patient Safety in Europe18
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Project Information• www.etriks.org• Publications
– None yet
• Contact information – Email: [email protected]– Website: http://dsg.doc.ic.ac.uk
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