AMIA 2014

NIH as a Digital EnterprisePhilip E. Bourne Ph.D.

Associate Director for Data ScienceNational Institutes of Health

http://www.slideshare.net/pebourne/

http://bd2k.nih.gov/addsup_meeting.html#sthash.lS6Kw3jH.WbCnnPMq.dpbshttps://docs.google.com/document/d/12V3icSNfwOgykIkrmfq8hGu6Mm_1RbZ0kgDfwInTEwk/edit#heading=h.iwxmy5mfh114

http://bd2k.nih.gov/addsup_meeting.html#sthash.lS6Kw3jH.WbCnnPMq.dpbs

What Do we Mean by the Digital Enterprise?

http://bd2k.nih.gov/addsup_meeting.html#sthash.lS6Kw3jH.WbCnnPMq.dpbs

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

I know you are interested in the policies and funding opportunities

that are coming but I think it helps to first get a sense of some things that

are motivating 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

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

Scholarship is broken

I have a paper with 17,000 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?

General Approach to Solutions …

New policies – Data sharing

– Blanket consent

– Data citation

Funding where it is most needed– New metrics

– De-identification

– Agile commons pilots

Smaller funding for the many, but with appropriate governance– Competitions

– Coordination across disciplines, agencies and countries

General Approach to Solutions

Shared infrastructure– Commons

– Standards framework

– CDE homogenization

Support for new reward systems

Lets Dig Down Based on How We Are Starting to Organize Ourselves

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

Programmatic Theme

Deliverable

Example Features • IC’s• Researchers• Federal

Agencies• International

Partners• Computer

Scientists

Scientific Data Council External Advisory Board

Training


Commons BD2K Efficiency

Sustainability Education Innovation Process







• Metrics• Best


Analysis


Partnerships

Collaboration

Programmatic Theme

Deliverable




Scientists


Training

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

Sustainability - the Commons

Compare Cancer Genomics Data Commons

dBGaP in the cloud

New business model

http://100plus.com/wp-content/uploads/Data-Commons-3-1024x825.png

[Adapted from George Komatsoulis]

Commons Business Model

HPC, Institution …

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

Pilots Around A Virtuous CycleExpect a Funding Call


CommonsTrainingCenter

BD2KModifiedReview

Sustainability* Education* Innovation* Process







• Metrics• Best


Analysis


Communication

Collaboration

Programmatic Theme

Deliverable




Scientists


* Hires made

Training & EducationTraining & Education

– Awards

– Metadata description of courses (virtual and physical)

– Cross-training

– VP training (with NSF)

– With libraries around curation etc.

http://bd2k.nih.gov/pdf/Documents_for_ADDS_Data_Science_Meeting_draft_edu_training_workforce_dev.pdf

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.



BD2KModifiedReview








• Metrics• Best


Analysis


Communication

Collaboration

Programmatic Theme

Deliverable




Scientists


* Hires made

Data Discovery Index Coordination Consortium (Awards Sept)

Targeted Software Development (under review)

Investigator-initiated Centers of Excellence for Big Data (Awards Sept)

BD2K-LINCS-Perturbation Data Coordination and Integration Center (Award Fall)

BD2K Innovation FY 14 BD2K Innovation FY 14 (Jennie Larkin and Mark (Jennie Larkin and Mark

Guyer)Guyer)

Relevant Workshops

– ELSI for research use of clinical data Spring 2015 Lyn Hardy and Ajay Pillai

– Private Sector Capacities Relevant to Advancing Research Use of Clinical Data Spring 2015 Nancy Miller and Valerie Florance, Jerry Sheehan and Leslie Derr

– Think Tank: Using EHRs for outcomes research and to identify risk factors/etiology of diseases. Fall 2014 Jerry Sheehan, Leslie Derr, Gina Wei, and Weinu Gan

– Think Tank: Inspiring the Game Developer Community to Engage in and Enhance Biomedical Research, Fall 2014 David Miller, Jennifer Couch

Others?

BD2K Innovation FY 15 BD2K Innovation FY 15 (Jennie Larkin and Mark (Jennie Larkin and Mark

Guyer)Guyer)



BD2KModifiedReview








• Metrics• Best


Analysis


Communication

Collaboration

Programmatic Theme

Deliverable




Scientists


* Hires made

Process Current Efforts

– Clinical data harmonization

– Data citation

– Machine readable data sharing plans

– New review models, audiences etc.

• Open review

• Micro funding

• Standing data committees to explore best practices

• Crowd sourcing



BD2KModifiedReview








• Metrics• Best


Analysis


Communication

Collaboration

Programmatic Theme

Deliverable




Scientists


* Hires made

Collaboration Current Efforts

Joint public – private partnership workshop with NOAA?

2 joint workshops with NSF + Dear Colleague letter

OSTP – Open Data 2.0

HIRO’s big data meeting

NIHNIH……Turning Discovery Into HealthTurning Discovery Into Health

[email protected]