Advertisement

Enabling Public Data Sharing: Encouraging Scientific Discovery and Education

  • Christine Fennema-Notestine
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 569)

Summary

To promote scientific discovery and education, the federated Biomedical Informatics Research Network (BIRN) Data Repository (BDR) supports data storage, sharing, querying, and downloading for the biomedical community, enabling the integration of multiple data resources from a single entry point. The BDR encourages data sharing both for investigators requesting assistance with databasing and informatics infrastructure, and for those wishing to extend the reach of existing data resources to be registered with the BDR. Both approaches rely heavily on data integration and knowledge management techniques, ensuring capabilities for intelligent exploration of diverse data resources that make up the BDR’s shared environment. Although the development of the BDR has been driven by BIRN testbeds in the fields of neuroscience and neuroimaging, the infrastructure is flexible and extendable to serve a broad array of disciplines, fueling interdisciplinary studies. For a welcoming environment, the BDR provides simple, straightforward policies and procedures for contributing data and for using available data. Contributing investigators provide information through the BDR Gridsphere-based Portal environment to allow meaningful sharing of their data, and, when relevant, supply documentation for human subjects’ protection. The BDR aims to provide a common resource to increase the availability of, and access to, rare data; complex, sizable data; and existing data sharing structures in support of research and education in the scientific and clinical communities.

Key words

Data sharing Collaborative environment Repository Scientific discovery Data integration BIRN 

Notes

Acknowledgment

The Biomedical Informatics Research Network (BIRN) Data Repository (http://www.nbirn.net/bdr) is supported by grants to the BIRN Coordinating Center (U24-RR019701), Function BIRN (U24-RR021992), Morphometry BIRN (U24-RR021382), and Mouse BIRN (U24-RR021760) Testbeds funded by the National Center for Research Resources at the National Institutes of Health, USA.

References

  1. 1.
    Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: mining tens of millions of expression profiles – database and tools update. Nucleic Acids Res 2007;35:D760–5.PubMedCrossRefGoogle Scholar
  2. 2.
    Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 2007;35:D301–3.PubMedCrossRefGoogle Scholar
  3. 3.
    Bogue MA, Grubb SC, Maddatu TP, Bult CJ. Mouse Phenome Database (MPD). Nucleic Acids Res 2007;35:D643–9.PubMedCrossRefGoogle Scholar
  4. 4.
    Breitkreutz BJ, Stark C, Reguly T, et al. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 2008;36:D637–40.PubMedCrossRefGoogle Scholar
  5. 5.
    Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). 2006. (Accessed at http://www.nitrc.org/.).
  6. 6.
    Internet Analysis Tools Registry (IATR). (Accessed at http://www.cma.mgh.harvard.edu/iatr/.)
  7. 7.
    Grethe JS, Baru C, Gupta A, et al. Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease. Stud Health Technol Inform 2005;112:100–9.PubMedGoogle Scholar
  8. 8.
    NIH Data Sharing Policy and Implementation Guidance. 2003. (Accessed at http://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm.)
  9. 9.
    Van Horn JD, Ishai A. Mapping the human brain: new insights from FMRI data sharing. Neuroinformatics 2007;5:146–53.PubMedCrossRefGoogle Scholar
  10. 10.
    Teeters JL, Harris KD, Millman KJ, Olshausen BA, Sommer FT. Data sharing for computational neuroscience. Neuroinformatics 2008;6(1):47–55.PubMedCrossRefGoogle Scholar
  11. 11.
    Fennema-Notestine C, Gamst AC, Quinn BT, et al. Feasibility of multi-site clinical structural neuroimaging studies of aging using legacy data. Neuroinformatics 2007;5:235–45.PubMedCrossRefGoogle Scholar
  12. 12.
    Butcher J. Alzheimer’s researchers open the doors to data sharing. Lancet Neurol 2007;6:480–1.PubMedCrossRefGoogle Scholar
  13. 13.
    Liu Y, Ascoli GA. Value added by data sharing: long-term potentiation of neuroscience research. A commentary on the 2007 SfN Satellite Symposium on data sharing. Neuroinformatics 2007;5:143–5.PubMedCrossRefGoogle Scholar
  14. 14.
    Martone ME, Tran J, Wong WW, et al. The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J Struct Biol 2008;161(3):220–31.PubMedCrossRefGoogle Scholar
  15. 15.
    Altman M. The clinical data repository: a challenge to medical student education. J Am Med Inform Assoc 2007;14:697–9.PubMedCrossRefGoogle Scholar
  16. 16.
    BIRN Data Repository. 2008. (Accessed at http://nbirn.net/.)
  17. 17.
    Gridsphere Portal Framework. (Accessed at http://www.gridsphere.org/gridsphere/gridsphere.)
  18. 18.
    Martone ME, Gupta A, Ellisman MH. E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci 2004;7:467–72.PubMedCrossRefGoogle Scholar
  19. 19.
    Marcus DS, Olsen TR, Ramaratnam M, Buckner RL. The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics 2007;5:11–34.PubMedGoogle Scholar
  20. 20.
    Ozyurt IB, Brown GG, Grethe JS, Morpho­metry BIRN, FIRST BIRN. A general, extensible system for human brain imaging data retrieval and maintenance. In: Annual Meeting of the Organization for Human Brain Mapping. 2004; Budapest, Hungary.Google Scholar
  21. 21.
    Ozyurt IB, Wei D, Keator DB, et al. A user-friendly, web-accessible system for the management, discovery, retrieval, and analysis of clinical and brain imaging data. In: Human Brain Project Neuro-Informatics meeting. 2004; Bethesda, MD.Google Scholar
  22. 22.
    Turner JA, Fennema-Notestine C, Martone ME, et al. You say potato, I say potahto: ontological engineering applied within the Biomedical Informatics Research Network. In: Society for Neuroscience. 2006; Atlanta, GA.Google Scholar
  23. 23.
    Gupta A, Bean C, Bug W, et al. Creating a community-based knowledge management framework for integrating neuroscience data via ontologies. In: Society for Neuroscience. 2006; Atlanta, GA.Google Scholar
  24. 24.
    Gupta A, Astakhov V, Boline J, et al. Data Federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data. In: Society for Neuroscience. 2007; San Diego, CA.Google Scholar
  25. 25.

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Christine Fennema-Notestine
    • 1
  1. 1.Departments of Psychiatry and RadiologyUniversity of California – San DiegoLa JollaUSA

Personalised recommendations