One Funder’s View for Advancing Open Science

One Funder’s View for Advancing Open Science
Philip E. Bourne, Ph.D., FACMI
Associate Director for Data Science, National Institutes of Health
RWJF/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 systems
and 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
32962
21973
0
5000
10000
15000
20000
25000
30000
35000
2007 2008 2009 2010 2011 2012 2013 2014 2015
Total Approved

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

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

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

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 retrieves
data from the PDB which is
analyzed
3. A composite view of
journal and database
content results
Where Should We Be Going?
1. User clicks on thumbnail
2. 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 has
links 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

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

Support an Open Research Lifecycle
IDEAS – HYPOTHESES – EXPERIMENTS – DATA - ANALYSIS - COMPREHENSION - DISSEMINATION
Authoring
Tools
Lab
Notebooks
Data
Capture
Software
Analysis
Tools
Visualization
Scholarly
Communication
Commercial &
Public Tools
Git-like
Resources
By Discipline
Data Journals
Discipline-
Based Metadata
Standards
Community Portals
Institutional Repositories
New Reward
Systems
Commercial Repositories
Training

Prove there is Intelligent Life on Earth
“So remember, when you're feeling very small
and insecure
How amazingly unlikely is your birth
And 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 Health
philip.bourne@nih.gov
https://datascience.nih.gov/
@pebourne

One Funder’s View for Advancing Open Science

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