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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
8 October 2009 Microbial Research Commons 3
• ClinicalTrials.gov• ~80,000 registered trials• 200 results records/month
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
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. . .
8 October 2009 Microbial Research Commons 7
Using identifer to link to a clinical research study in ClinicalTrials.gov
8 October 2009 Microbial Research Commons 9
Coming full circle: Link back to the scientific literature
8 October 2009 Microbial Research Commons 11
8 October 2009 Microbial Research Commons 12
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.”
8 October 2009 Microbial Research Commons 13
Francis S. Collins, M.D., Ph.D.
NIH-wide policies to promote data & information sharing
8 October 2009 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
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8 October 2009 Microbial Research Commons 17
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]