The Vision for Data @ the NIH

The Vision for Data @ the NIH
Philip E. Bourne, PhD, FACMI
Associate Director for Data Science
National Institutes of Health
Bio-IT World, Boston
April 21, 2015

Office of Biomedical
Data Science
Mission Statement
To foster an open ecosystem that
enables biomedical research to be
conducted as a digital enterprise that
enhances health, lengthens life and
reduces illness and disability & to
train the next generation of data
scientists
Goals expanded from recommendations in the June 2012 DIWG and
BRWWG reports.

Let Me Give You 4 Examples of What
Drives Us …

1. We are at a Point of Deception …
 Evidence:
– Google car
– 3D printers
– Waze
– Robotics
– Sensors
From: The Second Machine Age: Work, Progress,
and Prosperity in a Time of Brilliant Technologies
by Erik Brynjolfsson & Andrew McAfee

1. We Are At a Point of Deception
The 6D Exponential Framework
Digitization of Basic &
Clinical Research & EHR’s
Deception
We Are Here
Disruption
Demonetization
Dematerialization
Democratization
Open science
Patient centered health care

2. Democratization Will Follow
The Story of Meredith
http://fora.tv/2012/04/20/Congress_Unplugged_
Phil_Bourne
Stephen Friend

47/53 “landmark” publications
could not be replicated
[Begley, Ellis Nature,
483, 2012] [Carole Goble]
3. Disruption Can Occur

4. Demonetization, Democratization?

“And that’s why we’re here today. Because something
called precision medicine … gives us one of the greatest
opportunities for new medical breakthroughs that we
have ever seen.”
President Barack Obama
January 30, 2015

Precision Medicine Initiative
Vision: Build a broad research program to encourage
creative approaches to precision medicine, test them
rigorously, and, ultimately, use them to build the
evidence base needed to guide clinical practice.
Near Term: apply the tenets of precision medicine to a
major health threat – cancer
Longer Term: generate the knowledge base necessary
to move precision medicine into virtually all areas of
health and disease

Precision Medicine Initiative
 National Research Cohort
– >1 million U.S. volunteers
– Numerous existing cohorts (many funded by NIH)
– New volunteers
 Participants will be centrally involved in design and
implementation of the cohort
 They will be able to share genomic data, lifestyle
information, biological samples – all linked to their
electronic health records

National Research Cohort:
What Early Success Might Look Like
 A real test of pharmacogenomics—right drug at the right
dose for the right patient
 New therapeutic targets by identifying loss-of-function
mutations protective against common diseases
– PCSK9 for cardiovascular disease
– SLC30A8 for type 2 diabetes
 Resilience – finding individuals who should be ill but aren’t
 New ways to evaluate mHealth technologies for
prevention/management of chronic diseases

Precision Medicine:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits her
doctor
Now
– Though woman’s glucose control has been suboptimal,
doctor renews her prescription for drug often used for type 2
diabetes
– Continues to monitor blood glucose with fingersticks and
glucometer, despite dissatisfaction with these methods

Precision Medicine:
doctor
Future: + 2 years
– Volunteers for new national research network
• Sample of her DNA, along with her health information,
sent to researchers for sequencing/analysis
• Can view her health/research data via smartphone
– Agrees to researchers’ request to track her glucose levels
via tiny implantable chip that sends wireless signals to her
watch, researchers’ computers
• Using these data, she changes diet,
medicine dose schedule

Other Diseases:
doctor
– Receives word from her doctor about a new drug based
upon improved molecular understanding of type 2 diabetes
– When she enters drug’s name into her smartphone’s Rx
app, her genomic data show she’ll metabolize the drug
slowly
• Her doctor alters the dose accordingly

Other Diseases:
doctor
– Celebrates her 60th birthday and reflects with her family
about how proud she is to be part of cohort study
– Her glucose levels remain well controlled; she’s suffered no
diabetes-related complications
– Her children decide to volunteer for cohort study

EHRsPatient Partnerships
Data Science
GenomicsTechnologies

The BD2K Program is Central
to the Mission
Planned – Black; Available- Green

Elements of The Digital Enterprise
Communities Policies
Infrastructure
• Intersection:
• Sustainability
• Efficiency
• Collaboration
• Training

Elements of The Digital Enterprise
Communities Policies
Infrastructure
• Intersection:
• Sustainability
• Efficiency
• Collaboration
• Training
Virtuous
Research
Cycle

 Big Data: The study involved
MRI images & GWAS data
from over 30,000 people
 Collaboration: Data came
from many different sights
affiliated with the ENIGMA
consortium
 Methods: To homogenize
data from different sites, the
group designed standardized
protocols for image analysis,
quality assessment, genetic
imputation, and association
 Found five novel genetic
variants
 Results provided insight into
the variability of brain
development, and may be
applied to study of
neuropsychiatric dysfunction

 Community – Enigma, BD2K
 Policy
– Improved consent methods
– Cloud accessibility for human subjects data
– Trusted partners
– Data sharing
 Infrastructure
– Standards, compute resources, software

Communities: Thus Far
 Visioning workshop convened 9/3/14
 Launched BD2K ($32M)
– 12 Centers of data excellence
– Data Discovery Index Coordination Consortium
(DDICC)
– Training awards
 First successful consortia meeting 11/3-4
 Workshops to inform future funding
– Software indexing and discoverability
– Gaming

Communities: 2015 Activities
 New FOAs with outreach to new
communities – math, stats, comp science etc.
 Work with e.g GA4GH, RDA, FORCE11,
NDS ….
 IDEAS lab with NSF
 Competition with international funders
 Software carpentry, hackathons, Pi Day

Communities: Questions?
 Societies of the modern age?
 How to enable these groups?
 How to marry the funding of individuals with
the funding of communities?

Policies: Now & Forthcoming
 Data Sharing
– Genomic data sharing announced
– Data sharing plans on all research awards
– Data sharing plan enforcement
• Machine readable plan
• Repository requirements to include grant numbers
http://www.nih.gov/news/health/aug2014/od-27.htm

Policies - Forthcoming
 Data Citation
– Goal: legitimize data as a form of scholarship
– Process:
• Machine readable standard for data citation (done)
• Endorsement of data citation for inclusion in NIH bib
sketch, grants, reports, etc.
• Example formats for human readable data citations
• Slowly work into NLM/NCBI workflow
 dbGaP in the cloud (done!)

BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
DDICC
Software
Standard
s
Infrastructure - The
Commons
Labs
Labs
Labs
Labs

The Commons
Digital Objects
(with UIDs)
Search
(indexed metadata)
Computing
Platform
TheCommons
Vivien Bonazzi
George Komatsoulis

The Commons: Compute Platforms
The Commons
Conceptual Framework
Public Cloud
Platforms
Super Computing
(HPC) Platforms
Other
Platforms ?
 Google, AWS (Amazon)
 Microsoft (Azure), IBM,
other?
 In house compute
solutions
 Private clouds, HPC
– Pharma
– The Broad
– Bionimbus
 Traditionally low access
by NIH

The Commons:
Business Model
[George Komatsoulis]

Infrastructure: Standards
 2013 Workshop on Frameworks for Community-
Based Standards
 August 2014 Input on Information Resources for
Data-Related Standards Widely Used in Biomedical
Science – 30 responses
 Feb 2015 Workshop Community-based Data and
Metadata Standards
 Internal CDE Registry project

Problem: Lack of
Biomedical Data Science Specialists
BD2K T32/T15
BD2K K01
Career path workshops – eg AAU
Challenge
model of
funding

Problem: Limited Access to
Data Science Training
BD2K R25
Metadata
for training
materials
Community-sourced
cataloging and indexing
of training opportunities
Measure utility
NIH Workforce Development Center
RFA-ES-15-004

I not only use all the brains
I have, but all I can borrow.
– Woodrow Wilson

Associate Director for Data Science
Commons BD2K Efficiency
Sustainability Education Innovation Process
• Cloud – Data &
Compute
• Search
• Security
• Reproducibility
Standards
• App Store
• Coordinate
• Hands-on
• Syllabus
• MOOCs
• Community
• Centers
• Training Grants
• Catalogs
• Standards
• Analysis
• Data
Resource
Support
• Metrics
• Best
Practices
• Evaluation
• Portfolio
Analysis
The Biomedical Research Digital Enterprise
Partnerships
Collaboration
rogrammatic Theme
Deliverable
Example Features • IC’s
• Researchers
• Federal
Agencies
• International
Partners
• Computer
Scientists
Scientific Data Council External Advisory Board
Training

NIHNIH……
Turning Discovery Into HealthTurning Discovery Into Health
philip.bourne@nih.gov

The Vision for Data @ the NIH

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