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 Europe
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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 Europe
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Partners
Academia
SME
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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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)
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Hosting / installation
Training
Curation workflow software
Data Mgmt software
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Analytics software
Curation support
Standards build and coordination
KM consultancy
– 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
eTRIKS : Linking the Two Worlds
From : Committee on A Framework for Developing a New Taxonomy of
Disease
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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eTRIKS Architecture
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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eTRIKS Study Data Management
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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eTRIKS Curation: Building Contents
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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eTRIKS Data Curation Process
tranSMART-based
eTRIKS Study Data
Management System
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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Use cases
• U-BIOPRED (Unbiased BIOmarkers in PREDiction of respiratory disease
outcomes)
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
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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eTRIKS Ontology Management
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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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
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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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
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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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
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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Standards and terminologies
selection process
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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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
Convergence Meeting:
Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
Semantic Web technology
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Examples
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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Project Information
• www.etriks.org
• Publications
– None yet
• Contact information
– Email: [email protected]
– Website: http://dsg.doc.ic.ac.uk
Convergence Meeting: Semantic
Interoperability for Clinical Research &
Patient Safety in Europe
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