Toward a biomedical research commons: A view from NLM-NIH

8 October 2009 Microbial Research Commons 1

Toward a biomedical research commons: A view from NLM-NIH

Jerry SheehanAssistant Director for Policy DevelopmentNational Library of Medicine – National Institutes of Health

Designing the Microbial Research Commons8-9 October 2009, Washington, DC

National Library of MedicineMore than a Library

• World’s largest medical library (>8 million artifacts)

• Intramural research laboratories– Lister Hill Nat’l Center for Biomed. Comms.

– National Center for Biotechnology Information

• Extramural research and training• Information services for various audiences

– 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

www.nlm.nih.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


• ClinicalTrials.gov• ~80,000 registered trials• 200 results records/month

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.


Integrating scientific data and information is key to advances

Only a few of the interconnected NLM/NCBI scientific databases

Links: 9,113,926

Links: 2,166,612

Links: 721,372

Links: 819,269

Links: 3,593

Links: 7,182Links: 14,457

Links: 13,477

Links: 1375Links: 3760

Integrating information sources: From PubMed Journal Citation. . .


To PubMed Central’s Full Text Article


Using identifer to link to a clinical research study in ClinicalTrials.gov


ClinicalTrials.gov study record


Coming full circle: Link back to the scientific literature



Further integration with other NLM Resources

3-D View of Chemical and Protein4

RWJ-270201 bound to neuraminidase

Chemical Structures in Article2

FIG. 1. Structures of compounds under investigation

Zanamivir Oseltamivir carboxylate

RWJ-270201

PubChem3

RWJ-270201

PubMed1

Data and information sharing a priority for NIH

• 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.”


Francis S. Collins, M.D., Ph.D.

NIH-wide policies to promote data & information sharing


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?


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



Additional information

NIH Data Sharing Policyhttp://grants.nih.gov/grants/policy/data_sharing/

NIH Public Access Policy: http://publicaccess.nih.gov/

PubMed Central: www.pubmedcentral.nih.gov

National Library of Medicinewww.nlm.nih.gov

Jerry Sheehan: [email protected]

Documents

Toward a biomedical research commons: A view from NLM-NIH