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The NIH as a Digital Enterprise:
Implications for PAG
Philip E. Bourne, PhD
Associate Director for Data Science
National I...
What do we mean by the notion of a
Digital Enterprise?
Start by considering how far we have
come in just one researcher’s
career….
Biomedical Research is Becoming
More Digital and FAIR
 Finding
 Accessing
 Integrating
 Reusing
digital research objec...
This move from an observational
science to a more analytical science
is being driven by ever increasing
amounts of digital...
The NIH Fire Hose Slide
And This May Just be the Beginning
 Evidence:
– Google car
– 3D printers
– Waze
– Robotics
From: The Second Machine Age: ...
Further Perturbation:
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]
ADDS Mission
Statement
To foster an open ecosystem that
enables biomedical* research to be
conducted as a digital enterpri...
Some Goals of the Digital Enterprise
 Cost savings through sharing of best
practices
 Sustainability of digital assets
...
Some of Today’s Observations
 Bad News
– We do not yet have a
data sustainability plan
– Global policies define the
why b...
Sustainability 101
Source Michael Bell http://homepages.cs.ncl.ac.uk/m.j.bell1/blog/?p=830
What is the NIH Doing to Fulfill
That Promise?
Elements of The Digital Enterprise
Community
Policy
Infrastructure
• Sustainability
• Collaboration
• Training
Elements of The Digital Enterprise
Community
Policy
Infrastructure
• Sustainability
Collaboration
• Training
Virtuous
Rese...
Policies – Now & Forthcoming
 Data Sharing
– Genomic data sharing announced
– Data sharing plans on all research awards
–...
Policies - Forthcoming
 Data Citation
– Goal: legitimize data as a form of scholarship
– Process:
• Machine readable stan...
BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
BD2K
Center
DDICC
Software
Standard
s
Infrastructure - The
Com...
The Commons
Digital Objects
(with UIDs)
Search
(indexed metadata)
Computing
Platform
TheCommons
Vivien Bonazzi
George Koma...
The Commons: Compute Platforms
The Commons
Conceptual Framework
Public Cloud
Platforms
Super Computing
(HPC) Platforms
Oth...
The Commons:
Business Model
[George Komatsoulis]
How Might PAG’s Participate?
 Consider contributing digital research objects into the
Commons – data, software, standards...
Accelerate This Kind of Study
Pfenning et al 2014 Science 346 1333
Generic Needs
 Homogenization of disparate large unstructured
datasets
 Deriving structure from unstructured data
 Feat...
1) Build an OPEN digital framework for data
science training:
NIH Data Science Workforce Development Center
1) Develop sho...
Associate Director for Data Science
Commons BD2K Efficiency
Sustainability Education Innovation Process
• Cloud – Data &
C...
NIHNIH……
Turning Discovery Into HealthTurning Discovery Into Health
philip.bourne@nih.gov
Potential Outcomes
 Mobility: improve the outcomes of surgeries in
children with cerebral palsy and gait pathology
 Well...
The NIH as a Digital Enterprise: Implications for PAG
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The NIH as a Digital Enterprise: Implications for PAG

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Keynote presentation at the Plant and Animal Genomics meeting in Sad Diego CA on Jan. 11, 2015

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The NIH as a Digital Enterprise: Implications for PAG

  1. 1. The NIH as a Digital Enterprise: Implications for PAG Philip E. Bourne, PhD Associate Director for Data Science National Institutes of Health PAG San Diego January 11, 2015
  2. 2. What do we mean by the notion of a Digital Enterprise?
  3. 3. Start by considering how far we have come in just one researcher’s career….
  4. 4. Biomedical Research is Becoming More Digital and FAIR  Finding  Accessing  Integrating  Reusing digital research objects
  5. 5. This move from an observational science to a more analytical science is being driven by ever increasing amounts of digital data
  6. 6. The NIH Fire Hose Slide
  7. 7. And This May Just be the Beginning  Evidence: – Google car – 3D printers – Waze – Robotics From: The Second Machine Age: Work, Progress, and Prosperity in a Time of Brilliant Technologies by Erik Brynjolfsson & Andrew McAfee
  8. 8. Further Perturbation: The Story of Meredith http://fora.tv/2012/04/20/Congress_Unplugged_ Phil_Bourne Stephen Friend
  9. 9. 47/53 “landmark” publications could not be replicated [Begley, Ellis Nature, 483, 2012] [Carole Goble]
  10. 10. ADDS 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 * Includes biological, biomedical, behavioral, social, environmental, and clinical studies that relate to understanding health and disease.
  11. 11. Some Goals of the Digital Enterprise  Cost savings through sharing of best practices  Sustainability of digital assets  Collaboration through identification of collaborators at the point of data collection not publication  Improved reproducibility through data and methods sharing  Integration of data types and data and literature to accelerate discovery
  12. 12. Some of Today’s Observations  Bad News – We do not yet have a data sustainability plan – Global policies define the why but not the how – We do not know how all the data we currently have are used – We can’t estimate future supply and demand – We need to ramp up training programs in data science  Good news – Genuine willingness to address the problem – Global communities are emerging – Efficiencies can be achieved – BD2K is the beginnings of a plan – We are beginning to quantify the issues
  13. 13. Sustainability 101 Source Michael Bell http://homepages.cs.ncl.ac.uk/m.j.bell1/blog/?p=830
  14. 14. What is the NIH Doing to Fulfill That Promise?
  15. 15. Elements of The Digital Enterprise Community Policy Infrastructure • Sustainability • Collaboration • Training
  16. 16. Elements of The Digital Enterprise Community Policy Infrastructure • Sustainability Collaboration • Training Virtuous Research Cycle
  17. 17. 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
  18. 18. 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
  19. 19. BD2K Center BD2K Center BD2K Center BD2K Center BD2K Center BD2K Center DDICC Software Standard s Infrastructure - The Commons Labs Labs Labs Labs
  20. 20. The Commons Digital Objects (with UIDs) Search (indexed metadata) Computing Platform TheCommons Vivien Bonazzi George Komatsoulis
  21. 21. 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
  22. 22. The Commons: Business Model [George Komatsoulis]
  23. 23. How Might PAG’s Participate?  Consider contributing digital research objects into the Commons – data, software, standards, narrative, course materials …  Initiate your own moves from cylinders of excellence to more integrated and multi-functional data sources  Work to define new business models for the scientific enterprise
  24. 24. Accelerate This Kind of Study Pfenning et al 2014 Science 346 1333
  25. 25. Generic Needs  Homogenization of disparate large unstructured datasets  Deriving structure from unstructured data  Feature mapping and comparison from image data  Visualization and analysis of multi-dimensional phenotypic datasets  Causal modeling of large scale dynamic networks and subsequent discovery  Utilize data that are sparsely and irregularly sampled and noisy BD2K will offer reference datasets and points of domain expertise to explore these questions
  26. 26. 1) Build an OPEN digital framework for data science training: NIH Data Science Workforce Development Center 1) Develop short-term training opportunities: Courses, educational resources, etc. 1) Develop the discipline of biomedical data science and support cross-training – OPEN courseware Community: Training Data Science Training Goals All goals have a diversity component and manate
  27. 27. 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
  28. 28. NIHNIH…… Turning Discovery Into HealthTurning Discovery Into Health philip.bourne@nih.gov
  29. 29. Potential Outcomes  Mobility: improve the outcomes of surgeries in children with cerebral palsy and gait pathology  Wellness: markers derived from constantly monitored eHealth/mobile health devices – apply to smoking cessation, weight loss  Cancer: further personalization of treatment  Mental Health: better identify factors that resist and promote brain disease e.g., schizophrenia, bipolar disorder, major depression, attention deficit hyperactivity disorder (ADHD), obsessive compulsive disorder (OCD), autism  Addiction: utilizing social media to track and treat drug use and addiction

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