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

1. 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 Microbial Research Commons

2. 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

3. 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 Microbial Research Commons

4. Specialized microbial information sources and collections FDLI Webinar

5. 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. Microbial Research Commons

6. Links: 9,113,926 Links: 2,166,612 Links: 721,372 Links: 819,269 Links: 3,593 Links: 7,182 Links: 14,457 Links: 13,477 Links: 1375 Integrating scientific data and information is key to advances Only a few of the interconnected NLM/NCBI scientific databases Links: 3760

7. Integrating information sources: From PubMed Journal Citation. . . Microbial Research Commons

8. To PubMed Central’s Full Text Article Microbial Research Commons

9. Using identifer to link to a clinical research study in ClinicalTrials.gov Microbial Research Commons

10. ClinicalTrials.gov study record Microbial Research Commons

11. Coming full circle: Link back to the scientific literature Microbial Research Commons

12. PubMed 1 Zanamivir Oseltamivir carboxylate RWJ-270201 FIG. 1. Structures of compounds under investigation 3 PubChem RWJ-270201 Further integration with other NLM Resources Chemical Structures in Article 2 4 3-D View of Chemical and Protein RWJ-270201 bound to neuraminidase Microbial Research Commons

13. 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. Microbial Research Commons

14. NIH-wide policies to promote data & information sharing Microbial Research Commons

15. 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? Microbial Research Commons

16. 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 Microbial Research Commons

17. 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: SheehanJR@nlm.nih.gov Microbial Research Commons