Transcript Toward a biomedical research commons: A view from NLM-NIH Jerry Sheehan Assistant Director for Policy Development National Library of Medicine – National Institutes of Health Designing.

Toward a biomedical
research commons: A view
from NLM-NIH
Jerry Sheehan
Assistant Director for Policy Development
National Library of Medicine – National Institutes of Health
Designing the Microbial Research Commons
8-9 October 2009, Washington, DC
8 October 2009
Microbial Research Commons
1
National Library of Medicine
More than a Library
•
•
World’s largest medical library (>8 million
artifacts)
Intramural research laboratories
–
–
•
•
Extramural research and training
Information services for various audiences
–
–
–
–
www.nlm.nih.gov
Lister Hill Nat’l Center for Biomed. Comms.
National Center for Biotechnology Information
–
–
–
–
–
–
–
Medline – citations to published literature
PubMed Central – full text journal articles
MedlinePlus – consumer-oriented information
Special Populations - Arctic Health, Native
American, Asian American, Seniors
Genbank – gene sequences
Genetics Home Reference
dbGaP – genome wide associations
PubChem – small molecules database
Hazardous Substances Database
ToxTown - for school children
ClinicalTrials.gov
NLM databases: By the
numbers
• PubMed/Medline
– 16 million citations
– 5300 journals.
– ~ 700K new citations
added per year
– ~ 750M searches per
year
• PubMed Central
– Contains ~1.8M full
text articles
– More than 300K
users per day
8 October 2009
• ClinicalTrials.gov
• ~80,000 registered trials
• 200 results records/month
Microbial Research Commons
3
Specialized microbial information
sources and collections
17 June 2008
FDLI Webinar
4
New Information Service:
Rapid Research Notes
www.ncbi.nlm.nih.gov/rrn
•
•
•
•
•
•
Archives research made available
through emerging online venues
for rapid scientific communication.
Material from participating
publisher programs for immediate
communication.
Stable identifier provided.
Submissions not formally peer
reviewed, but screened by expert
group for suitability.
Initial content from PLoS Currents:
Influenza
<www.ploscurrents.org/influenza>.
Expect to expand over time to
include additional collections in
other high-interest biomedical
fields.
8 October 2009
Microbial Research Commons
5
Integrating scientific data and
information is key to advances
Links: 3760
Links: 9,113,926
Links: 2,166,612
Links: 721,372
Links: 1375
Links: 13,477
Links: 14,457
Links: 7,182
Links: 819,269
Links: 3,593
Only a few of the interconnected NLM/NCBI scientific databases
Integrating information sources:
From PubMed Journal Citation. . .
8 October 2009
Microbial Research Commons
7
To PubMed Central’s Full Text
Article
8 October 2009
Microbial Research Commons
8
Using identifer to link to a clinical
research study in ClinicalTrials.gov
8 October 2009
Microbial Research Commons
9
ClinicalTrials.gov study record
8 October 2009
Microbial Research Commons
10
Coming full circle: Link back to
the scientific literature
8 October 2009
Microbial Research Commons
11
Further integration with other
NLM Resources
1
PubMed
Chemical Structures in Article
2
Zanamivir
Oseltamivir
carboxylate
RWJ270201
FIG. 1. Structures of compounds under
investigation
3
4
PubChem
3-D View of Chemical and Protein
RWJ-270201
RWJ-270201 bound to neuraminidase
8 October 2009
Microbial Research Commons
12
Data and information
sharing a priority for NIH
Francis S. Collins,
M.D., Ph.D.
8 October 2009
• Opportunity -- Apply high-throughput
technologies to understand fundamental biology
and uncover the causes of specific disease
states.
• “[High throughput technologies] provide us with
the opportunity to ask questions that have the
word ‘ALL’ in them. What are ALL the transcripts
in a cell? What are ALL the protein interactions?
• Those kinds of questions are now approachable,
especially if we do the right job of making really
powerful databases publicly accessible to all
those who need them and empower
investigators in small labs as well as big labs to
plunge into that kind of mindset.”
Microbial Research Commons
13
NIH-wide policies to promote
data & information sharing
NIH Data Sharing Policy
 Funded researchers who receive >USD
500,000 from NIH in a single year
 Expected to include with their grant
proposal a plan for making research data
available to other researchers, or explain
why not possible.
 Timely release, not later than acceptance of
manuscript for publication.
NIH Genome Wide
Association Study Policy
 Applies to funded investigators for GWAS.
 Submit de-identified genotypic and
phenotypic data to NLM Database of
Genotype and Phenotype (dbGaP).
 Other investigators may request access to
GWAS data sets for research purposes.
8 October 2009
NIH Public Access Policy
 Applies to all NIH-funded investigators and
NIH researchers.
 Required to submit peer reviewed
manuscripts to PubMed Central upon
acceptance for publication.
 Up to 12-month delay before manuscript is
publicly available.
Clinical Trials Registration
and Results Reporting
 FDA Amendments Act requires registration
of applicable clinical trials of drugs,
biological products, and devices, regardless
of funding source.
 Reporting of results required for products
that have been approved/cleared by FDA.
 Penalties for noncompliance (withhold grant
funds, monetary fines).
Microbial Research Commons
14
Issues to consider
• How to encourage participation
–
–
–
–
–
Incentives for sharing data/information (e.g. recognition for data sharing)
Expectation of scientific community
Requirement of funding agency, publisher
Monitoring compliance
Make it simple
• Policy design
–
–
–
–
–
What information to share (e.g., final, raw)
When to share information (pre/post approval)
Where to share (is infrastructure provided?)
How prescriptive to be
Take into account various stakeholder interests
• Facilitating interoperability
–
–
–
–
Terminologies and vocabularies
Identifiers and their use in the community
Metadata standards, reference standards
Can good data curation practices be embedded in research training?
8 October 2009
Microbial Research Commons
15
The good news
• Progress is being made -- number of
successful data sharing efforts increasing
• Growing interest in and appreciation of
importance of data and information
sharing in biomedical research
• Increasing attention to need for
infrastructure and resources
8 October 2009
Microbial Research Commons
16
Additional information
NIH Data Sharing Policy
http://grants.nih.gov/grants/policy/data_sharing/
NIH Public Access Policy:
http://publicaccess.nih.gov/
PubMed Central:
www.pubmedcentral.nih.gov
National Library of Medicine
www.nlm.nih.gov
Jerry Sheehan: [email protected]
8 October 2009
Microbial Research Commons
17