etriks - november 2013
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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
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Biomarker Discovery
Adapted from CTMM TRAIT
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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€.
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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
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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
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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
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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
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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
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The Consortium…
10 Pharma 6 Partners
+
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Projects Engaging eTRIKS
Oncology Safety
InflammationRA-Map
Infection
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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
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TranSMART Screenshot
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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
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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
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• 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)
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• 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)
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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
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• 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
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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