one funder’s view for advancing open science

One Funder’s View for Advancing Open SciencePhilip E. Bourne, Ph.D., FACMI

Associate Director for Data Science, National Institutes of HealthRWJF/SPARC October 19, 2015

[Thanks to Francis Collins for Some Slides]

Conversation Cards From where has the NIH come?

Where should we be going?

What is needed to get there?

“Science in pursuit of fundamental knowledge about the nature and behavior of living systemsand the application of that knowledge to extend healthy life and reduce illness and disability.”

...

NIH: Steward of Medical and Behavioral Research for the United States

Laying the Foundation for Open Access:HGP, Bermuda, 1996

“The HGP changed the norms around data sharing in biomedical research.”

Data Sharing: An Essential Component

A Culture of Sharing

1999 20042003 2007 20142008

Research Tools Policy

NIH Data Sharing Policy

Model Organism Policy

Genome-wide Association (GWAS) Policy

2012

NIH Public Access Policy (Publications)

Big Data to Knowledge (BD2K) Initiative

Genomic Data Sharing (GDS) Policy

Modernization of NIH Clinical Trials

White House Initiative

(2013 “Holdren Memo”)

Guiding Principle of NIH GWAS Policy

The greatest public benefit will be realized if data from GWAS are made available, under terms and conditions consistent with the informed consent provided by individual participants, in a timely manner to the largest possible number of investigators.

NIH expectation that data would be shared in the NIH database of Genotype and Phenotype (dbGaP)

Data Access Requests Per Year 2007–September 2015

2007 2008 2009 2010 2011 2012 2013 2014 20150

5000

10000

15000

20000

25000

30000

35000 32962

21973

Total Approved


1999 20042003 2007 20142008





2012







NIH Public Access Policy for Publications

Ensures public access to published results of all research funded by NIH since 2008– Recipients of NIH funds required to submit final peer-reviewed

journal manuscripts to PubMed Central (PMC) upon acceptance for publication

– Papers must be accessible to the public on PMC no later than 12 months after publication


1999 20042003 2007 20142008





2012







Harnessing Data to Improve Health: BD2K (Big Data to Knowledge)NIH’s 6-year initiative to use data science to foster an open digital ecosystem that will accelerate efficient, cost-effective biomedical research to enhance health, lengthen life, and reduce illness and disability

Programs and activities: Advance discovery for biomedical research Facilitate use and re-use of biomedical data Develop analytical methods and software Enhance biomedical data science training


1999 20042003 2007 20142008





2012







NIH Genomic Data Sharing (GDS) Policy

Purpose– Sets forth expectations, responsibilities that ensure broad,

responsible sharing of genomic research data in a timely manner

Scope– All NIH-funded research generating large-scale human or non-

human genomic data – and their use for subsequent research• Data to be submitted to NIH-designated data repositories

(e.g., dbGaP, GEO, GenBank, WormBase, FlyBase, Rat Genome Database)

– Applies to all funding mechanisms (grants, contracts, intramural support) with no minimum threshold for cost

Released August 2014; effective January 25, 2015

gds.nih.gov


1999 20042003 2007 20142008





2012







Modernizing NIH Clinical Trials Activities:The Need NIH-Funded trials published within 100 months of completion

Less than 50% published within 30 months of completion

BMJ 2012;344:d7292

1. A link brings up figures from the paper

0. Full text of PLoS papers stored in a database

2. Clicking the paper figure retrievesdata from the PDB which is

analyzed

3. A composite view ofjournal and database

content results

Where Should We Be Going?

1. User clicks on thumbnail2. Metadata and a

webservices call provide a renderable image that can be annotated

3. Selecting a features provides a database/literature mashup

4. That leads to new papers

4. The composite view haslinks to pertinent blocks

of literature text and back to the PDB

1.

2.

3.

4.

PLoS Comp. Biol. 2005 1(3) e34

What is Needed to Get There?Value the Right Things

Diffuse the hypercompetitive environment– Collaboration– Data sharing– Quality data– Quality software– Standards

development– Value FAIR– Reproducibility

What is Needed to Get There?How?

Educate stakeholders Make funder and

publisher data sharing plans consistent

Make DMPs with teeth

Encourage data and software citation

Encourage the use of preprint servers

What is Needed to Get There?Support an Open Research Lifecycle

IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION

AuthoringTools

Lab Notebooks

DataCapture

Software

Analysis Tools

Visualization

ScholarlyCommunication

Commercial &Public Tools

Git-likeResources

By Discipline

Data JournalsDiscipline-Based Metadata

Standards

Community Portals

Institutional Repositories

New Reward Systems

Commercial Repositories

Training

What is Needed to Get There?Prove there is Intelligent Life on Earth

“So remember, when you're feeling very small and insecureHow amazingly unlikely is your birthAnd pray that there's intelligent life somewhere up in space'Cause there's bugger all down here on Earth”

Monty Python - Galaxy Song Lyrics | MetroLyrics

NIH… Turning Discovery Into [email protected]

https://datascience.nih.gov/@pebourne

mailto:[email protected]

https://datascience.nih.gov/

one funder’s view for advancing open science

Education