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XCEDE: An Extensible Schema for Biomedical Data

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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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Notes

  1. http://www.saxproject.org/

  2. http://www.cdisc.org/

  3. http://www.cdisc.org/models/odm/v1.1/

  4. http://medical.nema.org/

  5. http://teem.sourceforge.net/nrrd/

  6. http://www.nitrc.org/projects/bxh_xcede_tools

  7. https://xwiki.nbirn.org:8443/xwiki/bin/view/%20BIRN-OTF-Public/Home

References

  • Blackburn, K., Lazzarini, A., et al. (1999). XSIL: Extensible Scientific Interchange Language. 7th International Conference of High-Performance Computing and Networking, Springer.

  • Bray, T., Hollander, D., et al. (2006a). Namespaces in XML 1.0 (2nd edition), W3C.

  • Bray, T., Paoli, J., et al. (2006b). Extensible Markup Language (XML) 1.0 (4th edition), W3C.

  • Clark, J. (1999). XSL Transformations (XSLT), version 1.0, W3C.

  • Clark, J., DeRose, S. (1999). XML Path Language (XPath), version 1.0, W3C.

  • Clunie, D. (2000). DICOM structured reporting. Bangor: PixelMed.

    Google Scholar 

  • Dolin, R. H., Alschuler, L., et al. (2006). HL7 clinical document architecture, release 2. Journal of the American Medical Informatics Association, 13(1), 30–39.

    Article  PubMed  Google Scholar 

  • Fenstermacher, D., Street, C., et al. (2005). The Cancer Biomedical Informatics Grid (caBIG™). Conf Proc IEEE Eng Med Biol Soc.

  • Fischl, B., Salat, D. H., et al. (2002). Whole brain segmentation. Automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3), 341–355.

    Article  PubMed  CAS  Google Scholar 

  • Gering, D. T., Nabavi, A., et al. (1999). An integrated visualization system for surgical planning and guidance using image fusion and interventional imaging. Conf Med Image Comput Comput Assist Interv (MICCAI), Cambridge, England.

  • Hors, A. L., Hégaret, P. L., et al. (2004). Document Object Model (DOM) level 3 core specification, version 1.0, W3C.

  • ISO/IEC (2006). Document Schema Definition Languages (DSDL)—part 3: rule-based validation—Schematron. ISO/IEC19757-3:2006.

  • Keator, D. B., Gadde, S., et al. (2006). A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics, 4(2), 199–211.

    Article  PubMed  Google Scholar 

  • Keator, D. B., Grethe, J. S., et al. (2008). A national human neuroimaging collaboratory enabled by the biomedical informatics research network. IEEE Transactions on Information Technology in Biomedicine, 12(2), 162–172.

    Article  PubMed  Google Scholar 

  • Kunze, J., Baker, T. (2007). The Dublin core metadata element set. RFC 5013, from http://www.ietf.org/rfc/rfc5013.txt.

  • Lohrey, J. M., Killeen, N. E. B., et al. (2009). An integrated object model and method framework for subject-centric e-Research applications. Frontiers in Neuroinformatics, 3, 19.

    Article  PubMed  Google Scholar 

  • Marcus, D. S., Olsen, T. R., et al. (2007). The extensible neuroimaging archive toolkit (XNAT): an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics, 5, 11–34.

    PubMed  Google Scholar 

  • Myers, J. D., Chappell, A. R., et al. (2003). Re-integrating the research record. Computing in Science and Engineering.

  • Oldfield, R. C. (1971). The assessment and analysis of handedness: the Edinburgh inventory. Neuropsychologia, 9(1), 97–113.

    Article  PubMed  CAS  Google Scholar 

  • Ozyurt, I. B., Keator, D. B., et al. (2010). Federated web-accessible clinical data management within an extensible neuroimaging database. Neuroinformatics, 8(4), 231–249.

    Article  PubMed  Google Scholar 

  • Rubin, D. L, Mongkolwat, P., et al. (2008). Medical imaging on the semantic web: Annotation and image markup. 2008 AAAI Spring Symposium Series, Semantic Scientific Knowledge Integration. Stanford University.

  • Sufi, S., Mathews, B. (2004). CCLRC scientific metadata model: version 2. CCLRC Technical Report DL-TR-2004-001 Retrieved Feb 25, 2011, from http://epubs.cclrc.ac.uk/work-details?w=30324.

  • Talairach, J., & Tournoux, P. (1988). Co-planar stereotaxic atlas of the human brain. New York: Thieme Medical Publishers.

    Google Scholar 

  • Thompson, H. S., Beech, D., et al. (2004). XML schema 1.0, W3C.

Download references

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

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  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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FBIRN, MBIRN, BIRN-CC

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Correspondence to Syam 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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