eTRIKS - November 2013

eTRIKS: A Knowledge Management Service for Public-Private Partnership Translational ResearchIan Dix, AstraZeneca R&DOn Behalf of eTRIKS

[email protected]: eTRIKS, QMUL, CTMM & RA-Map

Biomarker Discovery

Adapted from CTMM TRAIT

Example Stratified Medicine Consortium

2 Billion €

Partnership

I Billion €

Public

I Billion €

Private

Stratified Medicine:• GAUCHERITE Consortium• Stop HCV• MATURA

• RA-Map• COPD-Map

22 CTMM research projects are active, involving a total of 119 partners and a research budget of 302.7 M€.

Patientobservationdata

Primary DataStorage?

Sample Storage - Biobank Systems

CommoneCRF

400+ patients x up to 6 clinical visits x 6 analyses => >10,000 samples

Patient

Patientdata

Recruiting Hospitals

Local data storage

Proteomics

Metabolomics

Flow cytometry

mRNA

Small RNA

Functional assay

Blood & Urine samples

Sample Distribution

Sample Processing

Newcastle

Glasgow

Leeds

Birmingham

KCL

UCL

Specialist Assay Technology Labs

A Representative Multi-Centre Strat Med Study?

Processed DataStorage

ImageData

X-Ray

Analysis

ABPI/MRC RA-Map

Patientobservationdata

Primary DataStorage?

Sample Storage - Biobank Systems

CommoneCRF

400+ patients x up to 6 clinical visits x 6 analyses => >10,000 samples

Patient

Patientdata

Recruiting Hospitals

Local data storage

Proteomics

Metabolomics

Flow cytometry

mRNA

Small RNA

Functional assay

Blood & Urine samples

Sample Distribution

Sample Processing

Newcastle

Glasgow

Leeds

Birmingham

KCL

UCL

Specialist Assay Technology Labs

A Representative Multi-Centre Strat Med Study?

Processed DataStorage

ImageData

X-Ray

Analysis

ABPI/MRC RA-Map

The Data Management Needs

Clincial DataCapture (EDC)

Sample Tracking

Assays &Local LIMS

Image Data Management

Primary Data Store

IntegratedProcessedData

AnalyticsToolbox Analytics

Reference Knowledge

Study Design, Protocol & Analysis Information

eTRIKS Scope

ETLs / Curation

Study Subject

Sustainability

IT Research £ >> IT Service £

Tsunami of genomic and clinical data

Weak standardsPoor interoperability

Islands of information

Patient DataSecurity

Multiple Partners; Fragmented Platforms

Data Challenges…

Consortia underestimateData Management Effort

The eTRIKS Project

• Service Project: ~80% of project activities driven by demand from supported IMI projects.

• Mandate to support PPP Translational studies with data & KM services:• Open Platform development, enhancement and support• Installation support• Training• Curation ETL support• Standards development• Analytics workflow development• Data hosting• Limited content curation to support studies

• Budget: €23.79m for 5 years (Oct 2012---Sept 2017)

• Members:– 10 Pharma, 3 Academic, 1 standards, 2 Commercial Suppliers

The Consortium…

10 Pharma 6 Partners

+

Projects Engaging eTRIKS

Oncology Safety

InflammationRA-Map

Infection

tranSMART

tranSMART Foundation is a global non-profit organization devoted to realizing the promise of translational biomedical research through development of the tranSMART knowledge management platform.

Community: Large scale KM consortia, AMCs, NFPs, Pharma, Regulators, Biotech service suppliers

PharmaTranSMARTs

UBIOPREDTranSMARTTr

ansl

ation

al

Med

icin

e Pl

atfor

m

RA-MAP TranSMART

Port

al

Publ

ic D

ata

and

Web

Ser

vice

se.

g. G

EO, N

CBI,

PubM

ed,

Gen

eGo

Omic/NGS Data

Extraction Layer – Standardize extracted data formats

Semantic normalisation

Com

plia

nt, A

udita

ble

& T

race

able

Cata

log

of O

ntol

ogy

& T

erm

inol

ogy

Data Checking & Validation

Pseudo-anonymisation Platform

Additional Data Sources Clinical Data

Cohort Selection and Biostatistics

Omics Analysis / Bioinformatics

BiomarkerDiscovery

Nor

mal

ised

Dat

a Sh

arin

g

OncotrackTranSMART

Distinct VirtualMachines (VM)

FutureTranSMARTs

Adapted from Mike Barnes, QMUL

TranSMART Screenshot

eTRIKS Framework Architecture

APIScientific Evidence

Repository

TM Knowledge Base

Study-centric Bio-centric

API

Open Access

Analytics Commons

Genebiomarkers

Collaborative research access platform

External resources

Analysis Results

Clinical dataMolecular ‘omics data

tranSMART-coreData and workflow provenance

support

Research data

Prior knowledge

Delivery through Collaboration…

European Initiative… Dutch National Initiative…

WP 1 Clinical Data

WP 5 Core Infrastructure

WP 6 Deployment

Imaging Data

WP 3Bio-

banking Data

WP 4Experi-mental Data

WP 2 Clinical Imaging

WP 7 Path

Imaging

WP 5 Governance & Business Model

WP7 Ethics

WP1

Service Delivery

Technical Service

Platform Development

Development Service

Standards Research &

DevelopmentStandards

Service

Analytics Research &

Content Curation

Content Service

WP6 Community Engagement and OutreachActive Account Management of eTRIKS Service

WP2 WP3 WP4

KM Groups of support Consortia

QMUL

• Becoming functional – recruitment, op norms, reporting, legal docs, etc

• Production tranSMART v1.1 released in Sept.– Migration to PostgreSQL open platform– 2 x Developer community workshops (with Foundation)

• Support of 5 IMI projects to date:– January: UBIOPRED: server set-up at ICL, 625 patients to date (screening & baseline),

Low density Eicosanoid Lipidomic data, gene expression data, proteomic data and animal model clinical data loaded. Training provided.

– May: Oncotrack, ABIRISK, PredictTB and ABPI/MRC RA-Map: tranSMART installations and training to date.

• Installations at: – Imperial (UBIOPRED), – Liverpool (PredictTB), – Alacris (Oncotrack), – QMUL (RA-Map), – Luxembourg (eTRIKS), and CC-IN2P3 (eTRIKS)

Progress (1)

• Curation of retrospective public content: (Beta URL available 1st Nov) – EBI Atlas gene fold change data (subset): SearchApp– Public Asthma & RA related GEO data: DataSetExplorer App– TCGA Datasets (Clinical and Gene Expression Data):

• Breast invasive carcinoma [BRCA]• Colon adenocarcinoma [COAD]• Uterine Corpus Endometrial Carcinoma [UCEC]• Ovarian serous cystadenocarcinoma [OV]

• Requirements gathering– 2 x User requirement workshops:– Requirements reviewed and consolidated– eTRIKS Product Management WIKI implemented

• Active discussions with 4-5 other projects re requirements and support

Progress (2)

Proposed Future Models?

Patient Stratification

Predicting Therapy Response

Biomarker Discovery: Correlating Signatures to Clinical Outcome

Animal: Human model validation

IMIArchive

DiseaseModelling

COPD -

Local Instance lMI Instance

DataTransfer

ABIRISK

UBIOPRED

StratMed X

Aggregation

SecureFederated

Search(data & samples)

Metadata Query

What Cross-Sectional Arteriosclerosis

studies have been run involving >300 subjects

with genotype information and an age <50 yrs?

Federation

vs

• Accessible Common Infrastructure

• Federation of searchable archives

of translational study information

• Ability to transfer data securely between

organisations within consortia

• Healthy ecosystem of commercial and

NFP service providers supporting projects

and institutions

• Large and diverse innovative

analytics & visualisation toolbox

Ultimately…

Medical CentresAnalytics

Specialists

DiseaseSpecialists

IT Services

CRO

AssaySpecialists

Regulatoryauthorities

Patient organization

P

P

P

Integrated Stratified

Medicine Ecosystem

www.eTRIKS.orgLinked In Discussion Group: eTRIKS Twitter @etriks1

Translational Research Knowledge Management in ActioneTRIKSFriday, January 31, 2014 from 9:30 AM to 4:00 PM (CET)Hospitalet de Llobregat, Barcelona, Spain

Register: https://trekma.eventbrite.com/?ref=ecount

eTRIKS Newsletter: www.etriks.org/newsletter/ eTRIKS Beta-Server: http://public.transmart.etriks.org/transmart/datasetExplorer/index