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Management of Information in Distributed Biomedical Collaboratories

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Biomedical Informatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 569))

Summary

Organizing and annotating biomedical data in structured ways has gained much interest and focus in the last 30 years. Driven by decreases in digital storage costs and advances in genetics sequencing, imaging, electronic data collection, and microarray technologies, data is being collected at an alarming rate. The specialization of fields in biology and medicine demonstrates the need for somewhat different structures for storage and retrieval of data. For biologists, the need for structured information and integration across a number of domains drives development. For clinical researchers and hospitals, the need for a structured medical record accessible to, ideally, any medical practitioner who might require it during the course of research or patient treatment, patient confidentiality, and security are the driving developmental factors. Scientific data management systems generally consist of a few core services: a backend database system, a front-end graphical user interface, and an export/import mechanism or data interchange format to both get data into and out of the database and share data with collaborators. The chapter introduces some existing databases, distributed file systems, and interchange languages used within the biomedical research and clinical communities for scientific data management and exchange.

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References

  1. Title 45, Volume 1, Parts 1 to 199. 1997. (Accessed at http://www.hhs.gov/foia/45cfr5.html.)

  2. Wu C. Development of a medical informatics data warehouse. AMIA Annu Symp Proc 2006:1148.

    Google Scholar 

  3. Laird AR, Lancaster JL, Fox PT. BrainMap: The social evolution of a human brain mapping database. Neuroinformatics 2005;3(1):65–78.

    Article  PubMed  Google Scholar 

  4. 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.

    Article  PubMed  Google Scholar 

  5. Coiera E, Walther M, Nguyen K, Lovell NH. Architecture for knowledge-based and federated search of online clinical evidence. J Med Internet Res 2005;7(5):e52.

    Article  PubMed  Google Scholar 

  6. Keator DB, Gadde S, Grethe JS, Taylor DV, Potkin SG. A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics 2006;4(2):199–212.

    Article  PubMed  Google Scholar 

  7. Rubin DL, Mongkolwat P, Kleper V, Supekar K, Channin D. Medical Imaging on the Semantic Web: Annotation and Imaging Markup. 2008. AAAI Spring Symposium Series, Semantic Scientific Knowledge Integration 2008.

    Google Scholar 

  8. Mildenberger P, Eichelberg M, Martin E. Introduction to the DICOM standard. Eur Radiol 2002;12(4):920–7.

    Article  PubMed  Google Scholar 

  9. Quinn J. An HL7 overview. J AHIMA 1999;70(7):32–4.

    PubMed  CAS  Google Scholar 

  10. Langlotz CP. RadLex: A new method for indexing online educational materials. Radiographics 2006;26(6):1595–7.

    Article  PubMed  Google Scholar 

  11. Keator DB, Grethe JS, Marcus D, Ozyurt B, Gadde S, Murphy S, Pieper S, Greve D, Notestine R, Bockholt HJ, Papadopoulos P; Function BIRN, Morphometry BIRN, BIRNCoordinating Center. A National Human Neuroimaging Collaboratory Enabled by the Biomedical Informatics Research Network (BIRN). IEEE Trans Inform Technol Biomed Special Bio-Grid edition 2008;12: 162–72.

    Google Scholar 

  12. Satyanarayanan M. Scalable, secure, and highly available distributed file access. IEEE Comput 1990;23(5):9–25.

    Article  Google Scholar 

  13. Braam P. The Coda distributed file system. Linux J 1998;50.

    Google Scholar 

  14. Satyanarayanan M. Coda: A highly available file system for a distributed workstation environment. In: IEEE Workshop on Workstation Operating Systems; Pacific Grove, CA; 1989.

    Google Scholar 

  15. Weil SA, Brandt SA, Miller E, Long D, Maltzahn C. Ceph: A scalable, high-performance distributed file system. In: Conference on Operating Systems Design and Implementation; 2006.

    Google Scholar 

  16. Sinnott R, Gilbert D, Berry D, Hunt E, Atkinson M. Bridges: security focused integration of distributed biomedical data. In: UK e-Science All Hands Meeting; UK; 2003.

    Google Scholar 

  17. Mooney SD, Baenziger PH. Extensible open source content management systems and frameworks: A solution for many needs of a bioinformatics group. Brief Bioinform 2008;9(1):69–74.

    Article  PubMed  Google Scholar 

  18. Ozyurt B, Wei D, Keator D, Potkin S, Brown G, Grethe J. Web-accessible clinical data management within an extensible neuroimaging database. In: Society for Neuroscience; Washington, DC; 2005.

    Google Scholar 

  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(1):11–34.

    PubMed  Google Scholar 

  20. Diercksen K. Cancer Central Clinical Database (C3D) Overview; 2008.

    Google Scholar 

  21. Boiko B. Understanding content management. Am Soc Inf Sci 2001;28(October-November):8–13.

    Google Scholar 

  22. Frost S. Web Content Management Report. London; 2001.

    Google Scholar 

  23. Giles J. Key biology databases go wiki. Nature 2007;445(7129):691.

    Article  PubMed  CAS  Google Scholar 

  24. Rajasekar A, Wan M, Moore R, Schroeder W, Kremenek G, Jagatheesan A, Cowart C, Zhu B, Chen S, Olschanowsky R. Storage Resource Broker-Managing Distributed Data in a Grid. Computer Society of India Journal, Special Issue on San. 2003;33(4):42–54.

    Google Scholar 

  25. Spasojevic M, Satyanarayanan M, An Empirical study of a Wide-Area Distributed File system. ACM Transactions on Computer systems (TOCS). 1996;14(2):200–222.

    Google Scholar 

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Acknowledgment

This work was supported in part by [5 U24 RR021992] to the Functional Imaging Research in Schizophrenia Testbed (FIRST) Biomedical Informatics Research Network (BIRN, http://www.nbirn.net). The author thanks the University of California, Irvine Center for BioMedical Informatics for discussions on clinical information systems and the informatics needs to support clinical translational research.

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Authors and Affiliations

  1. Brain Imaging Center, University of California – Irvine, Irvine, CA, USA

    David B. Keator

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  1. David B. Keator
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Editor information

Editors and Affiliations

  1. Biomedical Informatics Research Network, University of California, San Diego, Gilman Dr. 9500, La Jolla, 92093, U.S.A.

    Vadim Astakhov

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

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Keator, D.B. (2009). Management of Information in Distributed Biomedical Collaboratories. In: Astakhov, V. (eds) Biomedical Informatics. Methods in Molecular Biology™, vol 569. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-524-4_1

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  • DOI: https://doi.org/10.1007/978-1-59745-524-4_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-934115-63-3

  • Online ISBN: 978-1-59745-524-4

  • eBook Packages: Springer Protocols

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