XCEDE: An Extensible Schema for Biomedical Data (original) (raw)

Abstract

The XCEDE (XML-based Clinical and Experimental Data Exchange) XML schema, developed by members of the BIRN (Biomedical Informatics Research Network), provides an extensive metadata hierarchy for storing, describing and documenting the data generated by scientific studies. Currently at version 2.0, the XCEDE schema serves as a specification for the exchange of scientific data between databases, analysis tools, and web services. It provides a structured metadata hierarchy, storing information relevant to various aspects of an experiment (project, subject, protocol, etc.). Each hierarchy level also provides for the storage of data provenance information allowing for a traceable record of processing and/or changes to the underlying data. The schema is extensible to support the needs of various data modalities and to express types of data not originally envisioned by the developers. The latest version of the XCEDE schema and manual are available from http://www.xcede.org/.

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Acknowledgments

The design of XCEDE is informed by valuable input from external collaborators and BIRN-affiliated users of earlier versions of XCEDE. Many thanks to NITRC for hosting development sandboxes for XCEDE and supporting tools.

This research was supported by the National Institutes of Health (NIH) through the following NCRR grants to the Function BIRN [U24-RR021992], Morphometry BIRN [U24-RR021382], BIRN Coordinating Center [U24-RR019701], Neuroimaging Analysis Center (NAC) [P41-RR013218] and Biomedical Informatics Research Network (1 U24 RR025736-01), and the following NIH Roadmap for Medical Research grant to the National Alliance for Medical Imaging Computing (NAMIC) [U54-EB005149].

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Authors and Affiliations

1. Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
   Syam Gadde
2. Surgical Planning Laboratory, Brigham and Women’s Hospital, Boston, MA, USA
   Nicole Aucoin
3. Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
   Jeffrey S. Grethe
4. University of California, Irvine, CA, USA
   David B. Keator
5. Washington University School of Medicine, St. Louis, MO, USA
   Daniel S. Marcus
6. Isomics, Inc., Cambridge, MA, USA
   Steve Pieper

Authors

1. Syam Gadde
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2. Nicole Aucoin
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3. Jeffrey S. Grethe
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4. David B. Keator
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5. Daniel S. Marcus
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6. Steve Pieper
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Consortia

FBIRN, MBIRN, BIRN-CC

Corresponding author

Correspondence toSyam Gadde.

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Gadde, S., Aucoin, N., Grethe, J.S. et al. XCEDE: An Extensible Schema for Biomedical Data.Neuroinform 10, 19–32 (2012). https://doi.org/10.1007/s12021-011-9119-9

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• Published: 09 April 2011
• Issue Date: January 2012
• DOI: https://doi.org/10.1007/s12021-011-9119-9

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