8 October 2009Microbial Research Commons1 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

National Library of Medicine More 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

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 2009Microbial Research Commons3 ClinicalTrials.gov ~80,000 registered trials 200 results records/month

Specialized microbial information sources and collections 17 June 2008FDLI Webinar4

New Information Service: Rapid Research Notes 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. Expect to expand over time to include additional collections in other high-interest biomedical fields. 8 October 2009Microbial Research Commons5

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: 7,182 Links: 14,457 Links: 13,477 Links: 1375 Links: 3760

Integrating information sources: From PubMed Journal Citation... 8 October 2009Microbial Research Commons7

To PubMed Central’s Full Text Article 8 October 2009Microbial Research Commons8

Using identifer to link to a clinical research study in ClinicalTrials.gov 8 October 2009Microbial Research Commons9

ClinicalTrials.gov study record 8 October 2009Microbial Research Commons10

Coming full circle: Link back to the scientific literature 8 October 2009Microbial Research Commons11

8 October 2009Microbial Research Commons12 Further integration with other NLM Resources 3-D View of Chemical and Protein 4 RWJ bound to neuraminidase Chemical Structures in Article 2 FIG. 1. Structures of compounds under investigation ZanamivirOseltamivir carboxylate RWJ PubChem 3 RWJ PubMed 1

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 2009Microbial Research Commons13 Francis S. Collins, M.D., Ph.D.

NIH-wide policies to promote data & information sharing 8 October 2009Microbial Research Commons14

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 2009Microbial Research Commons15

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 2009Microbial Research Commons16

8 October 2009Microbial Research Commons17 Additional information NIH Data Sharing Policy NIH Public Access Policy: PubMed Central: National Library of Medicine Jerry Sheehan: