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

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

Partners

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe3

Academia

SME

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

eTRIKS : Linking the Two Worlds

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe5

From : Committee on A Framework for Developing a New Taxonomy of Disease

eTRIKS Architecture

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Interoperability for Clinical Research & Patient Safety in Europe

eTRIKS Study Data Management

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe7

eTRIKS Curation: Building Contents

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Patient Safety in Europe8

eTRIKS Data Curation Process

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe9

tranSMART-based eTRIKS Study Data Management System

• 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

eTRIKS Ontology Management

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe11

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 Europe13

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 Europe14

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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Patient Safety in Europe15

Standards and terminologies selection process

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Patient Safety in Europe16

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

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe17

Examples

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe18

Project Information• www.etriks.org• Publications

– None yet

• Contact information – Email: y.guo@imperial.ac.uk– Website: http://dsg.doc.ic.ac.uk

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe19