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Presented at the Big Data in Biomedicine Conference at Stanford University May 21, 2014
Citation preview
The Thinking Behind Big Data at the NIHPhilip E. Bourne Ph.D.
Associate Director for Data ScienceNational Institutes of Health
http://www.slideshare.net/pebourne/
Disclaimer: I only started March 3, 2014
…but I and others had been thinking about this prior to my appointment
Let me start with a few examples of what motivates our thinking …
The Story of Meredith
http://fora.tv/2012/04/20/Congress_Unplugged_Phil_Bourne
Stephen Friend
We have Entered An Era of Deinstitutionalize & Democratization
of Science
Daniel Hulshizer/Associated Press
We have Entered An Era of Deinstitutionalize & Democratization
of Science – NIH Should Support This
Daniel Hulshizer/Associated Press
I can’t reproduce research from my own laboratory?
Daniel Garijo et al. 2013 Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome PLOS ONE 8(11) e80278 .
Can you?
But what does it take and does it matter?
47/53 “landmark” publications could not be replicated
[Begley, Ellis Nature, 483, 2012] [Carole Goble]
Reproducibility Studies Are On-going Across the NIH
Expected outcomes:– Improved accessibility to data and software
– Support for workflows
– Closer relationships with publishers
– Metrics for measuring reproducibility
– Closure of the research lifecycle loop
– Rewards for reproducibility
You will notice that so far none of these issues has to do with “Big Data”
per se
“Big Data” has simply bought more attention to these issues
What Worries Me the Most - Sustainability
Source Michael Bell http://homepages.cs.ncl.ac.uk/m.j.bell1/blog/?p=830
We Cant Go On Like This – Some Options
Introduction of business models– The 50% model
– Mergers
– Acquisitions associated with best practices
– Centralization
– Public/private partnerships
– Fee for service
– Archiving
Usage metrics / impact ….
We don’t know enough about how current data
are used!
* http://www.cdc.gov/h1n1flu/estimates/April_March_13.htm
Jan. 2008 Jan. 2009 Jan. 2010Jul. 2009Jul. 2008 Jul. 2010
1RUZ: 1918 H1 Hemagglutinin
Structure Summary page activity forH1N1 Influenza related structures
3B7E: Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir
[Andreas Prlic]
Ironic Since Some Industries Thrive By Asking These Questions
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
Scholarship is broken
I have a paper with 16,000 citations that no one has ever read
I have papers in PLOS ONE that have more citations than ones in PNAS
I have data sets I am proud of few places to put them
I edited a journal but it did not count for much
The reward system is in need of repair
Okay… enough of the problems
What are some solutions?
Approach to Solutions
New policies, e.g. data sharing, blanket consent
Funding where it is most needed– New metrics
– De-identification
– Agile pilots
– Smaller funding for the many, but with appropriate governance
– Competitions
– Coordination across agencies and countries
Shared infrastructure
Support for new reward systems
How We Are Starting to Organize Ourselves
Associate Director for Data Science
CommonsTrainingCenter
BD2KModifiedReview
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
Communication
Collaboration
Programmatic Theme
Deliverable
Example Features • IC’s• Researchers• Federal
Agencies• International
Partners• Computer
Scientists
Scientific Data Council External Advisory Board
* Hires made
Solution: The Power of the Commons
Data
The Long Tail
Core Facilities/HS Centers
Clinical /Patient
The Why:Data Sharing Plans
TheCommons
Government
The How:
DataDiscoveryIndex
SustainableStorage
Quality
Scientific Discovery
Usability
Security/Privacy
Commons == Extramural NCBI == Research Object Sandbox == Collaborative Environment
The End Game:
KnowledgeNIHAwardees
PrivateSector
Metrics/Standards
Rest ofAcademia
Software StandardsIndex
BD2KCenters
Cloud, Research Objects,Business Models
What Does the Commons Enable?
Dropbox like storage
The opportunity to apply quality metrics
Bring compute to the data
A place to collaborate
A place to discover
http://100plus.com/wp-content/uploads/Data-Commons-3-1024x825.png
Commons Timeline
Spring/Summer 2014: DS group are gathering information about activities and needs from ICs (and outside communities).– Shared interests in developing cloud-based biomedical
commons.
– Investigating potential models of sustainability.
– Exploring metrics of usefulness and success.
Fall 2014: Develop possible pilots to explore options in addition to those already being implemented by some ICs.
Associate Director for Data Science
CommonsTrainingCenter
BD2KModifiedReview
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
Communication
Collaboration
Programmatic Theme
Deliverable
Example Features • IC’s• Researchers• Federal
Agencies• International
Partners• Computer
Scientists
Scientific Data Council External Advisory Board
* Hires made
TrainingTraining
Summary of Training Workshop and Request for Information:
– http://bd2k.nih.gov/faqs_trainingFOA.html
– Contact: Michelle Dunn (NCI)
Training Goals:
– develop a sufficient cadre of researchers skilled in the science of Big Data
– elevate general competencies in data usage and analysis across the biomedical research workforce.
BD2K Training RFAsBD2K Training RFAs K01s for Mentored Career Development Awards,
RFA-HG-14-007
Provides salary and research support for 3-5 years for intensive research career development under the guidance of an experienced mentor in biomedical Big Data Science.
R25s for Courses for Skills Development, RFA-HG-14-008
Development of creative educational activities with a primary focus on Courses for Skills Development.
R25 for Open Educational Resources, RFA-HG-14-009
Development of open educational resources (OER) for use by large numbers of learners at all career levels, with a primary focus on Curriculum or Methods Development.
Contemplating CSHL style training center(s)
Associate Director for Data Science
CommonsTrainingCenter
BD2KModifiedReview
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
Communication
Collaboration
Programmatic Theme
Deliverable
Example Features • IC’s• Researchers• Federal
Agencies• International
Partners• Computer
Scientists
Scientific Data Council External Advisory Board
* Hires made
BD2K InnovationBD2K Innovation
Data Discovery Index Coordination Consortium (U24) (closed)
Metadata standards (under development) Targeted Software Development
Development of Software and Analysis Methods for Biomedical Big Data in Targeted Areas of High Need (U01)–RFA-HG-14-020
–Application receipt date June 20, 2014
–Topics: data compression/reduction, visualization, provenance, or wrangling.
–Contact: Jennifer Couch (NCI) and Dave Miller (NCI)
BD2K InnovationBD2K Innovation
BISTI PARs – BISTI: Biomedical Information Science and Technology
Initiative
– Joint BISTI-BD2K effort
– R01s and SBIRs
– Contacts: Peter Lyster (NIGMS) and Jennifer Couch (NCI)
Workshops:– Software Index (Last week)
• Need to be able to find and cite software, as well as data, to support reproducible science.
– Cloud Computing (Summer/Fall 2014)• Biomedical big data are becoming too large to be analyzed on
traditional localized computing systems.
– Contact: Vivien Bonazzi (NHGRI)
BD2K Innovation CentersBD2K Innovation Centers
FY14 Investigator-initiated Centers of Excellence for Big
Data Computing in the Biomedical Sciences (U54) RFA-HG-13-009 (closed)
BD2K-LINCS-Perturbation Data Coordination and Integration Center (DCIC) (U54) RFA-HG-14-001 (closed)
Associate Director for Data Science
CommonsTrainingCenter
BD2KModifiedReview
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
Communication
Collaboration
Programmatic Theme
Deliverable
Example Features • IC’s• Researchers• Federal
Agencies• International
Partners• Computer
Scientists
Scientific Data Council External Advisory Board
* Hires made
Some Thoughts About Process
Machine readable data sharing plans?
Open review?
Micro funding?
Standing data committees to explore best practices?
Crowd sourcing?
Associate Director for Data Science
CommonsTrainingCenter
BD2KModifiedReview
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
Communication
Collaboration
Programmatic Theme
Deliverable
Example Features • IC’s• Researchers• Federal
Agencies• International
Partners• Computer
Scientists
Scientific Data Council External Advisory Board
* Hires made
Where Do We Want to End Up?
Associate Director for Data Science
CommonsTrainingCenter
BD2KModifiedReview
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
Communication
Collaboration
Programmatic Theme
Deliverable
Example Features • IC’s• Researchers• Federal
Agencies• International
Partners• Computer
Scientists
Scientific Data Council External Advisory Board
* Hires made
Components of The Academic Digital Enterprise
Consists of digital assets– E.g. datasets, papers, software, lab notes
Each asset is uniquely identified and has provenance, including access control– E.g. publishing simply involves changing the access control
Digital assets are interoperable across the enterprise
Life in the Academic Digital Enterprise
Jane scores extremely well in parts of her graduate on-line neurology class. Neurology professors, whose research profiles are on-line and well described, are automatically notified of Jane’s potential based on a computer analysis of her scores against the background interests of the neuroscience professors. Consequently, professor Smith interviews Jane and offers her a research rotation. During the rotation she enters details of her experiments related to understanding a widespread neurodegenerative disease in an on-line laboratory notebook kept in a shared on-line research space – an institutional resource where stakeholders provide metadata, including access rights and provenance beyond that available in a commercial offering. According to Jane’s preferences, the underlying computer system may automatically bring to Jane’s attention Jack, a graduate student in the chemistry department whose notebook reveals he is working on using bacteria for purposes of toxic waste cleanup. Why the connection? They reference the same gene a number of times in their notes, which is of interest to two very different disciplines – neurology and environmental sciences. In the analog academic health center they would never have discovered each other, but thanks to the Digital Enterprise, pooled knowledge can lead to a distinct advantage. The collaboration results in the discovery of a homologous human gene product as a putative target in treating the neurodegenerative disorder. A new chemical entity is developed and patented. Accordingly, by automatically matching details of the innovation with biotech companies worldwide that might have potential interest, a licensee is found. The licensee hires Jack to continue working on the project. Jane joins Joe’s laboratory, and he hires another student using the revenue from the license. The research continues and leads to a federal grant award. The students are employed, further research is supported and in time societal benefit arises from the technology.
From What Big Data Means to Me JAMIA 2014 21:194
Some Acknowledgements
Eric Green & Mark Guyer (NHGRI)
Jennie Larkin (NHLBI)
Vivien Bonazzi (NHGRI)
Michelle Dunn (NCI)
Mike Huerta (NLM)
David Lipman (NLM)
Jim Ostell (NLM)
Peter Lyster (NIGMS)
All the over 100 folks on the BD2K team
NIHNIH……Turning Discovery Into HealthTurning Discovery Into Health