How can we build a strong and thriving open source / open data community around FAIR principles?
PERSONAL HEALTH TRAIN WORKSHOP, UTRECHT, NOVEMBER 10, 2016
Kees van Bochove, CEO & Founder, The Hyve
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Agenda
u Introduction
u Flash updates from The Hyve – 4 example health trains
u TraIT/BBMRI: mapping clinical studies into tranSMART
u cBioPortal: mapping cancer genomics data into cBioPortal
u EMIF: mapping 50 million EU patients into OMOP
u RADAR: import wearable sensor data into hospital patient records
u Future directions for FAIR infrastructure & community
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The Hyve
u Professionalsupportforopensourceso*wareforbioinforma1csandtransla1onal
researchso5ware,suchastranSMART,cBioPortal,i2b2,Galaxy,ADAMandOHDSI
MissionEnablepre-compe11vecollabora1oninlifescienceR&Dbyleveragingopensourceso*ware
Corevalues ShareReuseSpecialize
OfficeLoca5onsUtrecht,NetherlandsCambridge,MA,UnitedStates
ServicesSo5waredevelopmentDatascienceservicesConsultancyHos1ng/SLAs
Fast-growingStartedin201240peoplebynow
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Open Source in Precision Medicine
Data management / Study design:
Biobanking:
Scientific compute:
Data visualisation:
Workflow / NGS:
Datawarehousing:
Imaging:
Clinical / Healthcare:
Interdisciplinary team
so5ware engineers, data scien1sts, project managers & staff; exper1se inbioinforma1cs,medicalinforma1cs,so5wareengineering,biosta1s1csetc.
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Offices at the Arthur van Schendelstraat in Utrecht
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PI: Prof. Gerrit Meijer, Netherlands Cancer Institute
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TranSMART Platform: Scientific Function
CLINICAL GENETICS SENSORS IMAGING
DATA
UNDER STANDING BIOLOGY MEDICINE
Contributors
TraIT data workflow Hospital (IT) Translational Research (IT)
data domains
clinical data
imaging data
experimental data
biobanking
integrated data translational analytics
workbench
HIS
PACS
LIS
Galaxy
tranSMART/ cohort explorer
R tranSMART/i2b2 datawarehouse
CBM-NL
OpenClinica
NBIA + AIM
e.g. PhenotypeDB, Annai Systems
e.g. Galaxy, Chipster
Samples (IT)
Pseudonymization
Public Data
BIMS
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TranSMART: working with clinical data
2.
TRANSLATIONAL RESEARCH DATA
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cBioPortal for Cancer Genomics current community a.o.
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POPULATION HEALTH DATA
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OMOP Common Data Model v5.0
v OMOP =
Observational
Medical
Outcomes
Partnership
v CDM = Common
Data Model
v SQL Tables
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Overview of ontologies used in OMOP
over 80 healthcare vocabularies mapped
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ATLAS: Individual Patient Profile
>40
mill
ion
MAAS
SDR
EGCUT
PEDIANET
SCTS
IMASIS
HSD
AUH
IPCI
ARS
SIDIAP
PHARMO
THIN
100 1,000 10,000 100,000 1,000,000 10,000,000 100,000,000
Ap
pro
xim
ate
tota
l (c
umul
ativ
e)
num
be
r of s
ubje
cts
Available data sources in EMIF
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EMIF-Platform
EMIF-Available Data Sources; EXAMPLES
1K
2K
52K
400K
475K
2.8M
2.3M
10M
Status Jan 2016
3.6M
1.6M
1M
12M
6M
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PI: Prof. Matthew Hotopf, King’s College London
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RADAR-CNS: Focus areas from diagnose & treat ! predict & pre-empt
u Epilepsy
u Monitoring and predicting epileptic seizures
u Multiple Sclerosis
u Monitoring exacerbations and disease state
u Depression
u Monitoring for possible relapses, plan timely interventions
u Predict bipolar state transitions
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Continuous Patient Assessment
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Preliminary Technology Stack
Analytics Cloud data endpoints
Mobile data streams
Direct data streams
- Feedback to mobile apps - Streaming analytics
- Translational analytics
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Software development RADAR platform
Developing Core RADAR-CNS Platform
Freiburg Epilepsy
Study
King’s Epilepsy
Study
Gathering requirements & steering platform development through supporting actual studies
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Conclusion u What’s ‘the core’ in FAIR?
u Digital (data) interoperability standards
u Use existing open standards which are adopted: e.g. the OMOP data model
u Aspects of the FAIR community
u Software community: DTL (wiki etc.) for now, but need to expand
u Data community: positioning via e.g. ELIXIR
u Science community: contribute to scientific conferences
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Training is needed for: u Research scientists & labs generating data
u Care providers that are required to share data to their patients
u Medical informatics researchers looking for data
u Patients looking for sound medical advice
u Patients that want to share their data with friends & family
u Citizens looking for nutritional / behaviour advice
u Citizens looking for data to do citizen science
u Physicians need access to medical records (including patient-recorded outcomes) of their patients
u Epidemiologists & medical outcome researchers at pharma companies looking for ‘real world data’
u …
Where is the most urgent need?
