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The extensible neuroimaging archive toolkit

An informatics platform for managing, exploring, and sharing neuroimaging data

Abstract

The Extensible Neuroimaging Archive Toolkit (XNAT) is a software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data. In particular, XNAT enables qualitycontrol procedures and provides secure access to and storage of data. XNAT follows a threetiered architecture that includes a data archive, user interface, and middleware engine. Data can be entered into the archive as XML or through data entry forms. Newly added data are stored in a virtual quarantine until an authorized user has validated it. XNAT subsequently maintains a history profile to track all changes made to the managed data. User access to the archive is provided by a secure web application. The web application provides a number of quality control and productivity features, including data entry forms, data-type-specific searches, searches that combine across data types, detailed reports, and listings of experimental data, upload/download tools, access to standard laboratory workflows, and administration and security tools. XNAT also includes an online image viewer that supports a number of common neuroimaging formats, including DICOM and Analyze. The viewer can be extended to support additional formats and to generate custom displays. By managing data with XNAT, laboratories are prepared to better maintain the long-term integrity of their data, to explore emergent relations across data types, and to share their data with the broader neuroimaging community.

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References

  • Aarsten, A., Brugali, D., and Menga, G. (1996) Patterns for three-tier client/server applications. In Pattern Languages of Programs (PloP), Monticello, IL.

  • Amer-Yahia, S., Du, F., and Freire, J. (2004) A comprehensive solution to the XML-to-relational mapping problem. WIDM 4, 31–38.

    Google Scholar 

  • Arenas, M. and Libkin, L. (2004) A normal form for XML documents. ACM Trans Database Syst. 29, 195–232.

    Article  Google Scholar 

  • Baru, C., Moore, R., Rajasekar, A., and Wan, M. (1998) The SDS Storage Resource Broker. Proceedings of CASCON'98 Conference, Toronto, Canada.

  • Buckner, R. L., Head, D., Parker, J., et al. (2004) A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume. Neuroimage 23, 724–738.

    PubMed  Article  Google Scholar 

  • Bui, A. A., Weinger, G. S., Barretta, S. J., Dionisio, J. D., and Kangarloo, H. (2002) An XML gateway to patient data for medical research applications. Ann. NY Acad. Sci. 980, 236–246.

    PubMed  Article  Google Scholar 

  • Burns, J. M., Church, J. A., Johnson, D. K., et al. (2005) White matter lesions are prevalent but differentially related with cognition in aging and early Alzheimer Disease. Arch. Neurol. 62, 1870–1876.

    PubMed  Article  Google Scholar 

  • Carminati, B. and Ferrari, E. (2005) AC-XML Documents: Improving the performance of a web access control module. Proceedings of the tenth ACM Symposium on Access Control Models and Technologies, Stockholm, Sweden, pp. 67–76.

    Google Scholar 

  • Chaudhuri, S., Chen, Z., Shim, K., and Wu, Y. (2005) Storing XML (with XSD) in SQL databases: Interplay of logical and physical designs. IEEE Trans. Knowledge Data Eng. 17, 1595–1609.

    Article  Google Scholar 

  • Dolin, R. H., Alschuler, L., Beebe, C., et al. (2001) The HL7 Clinical Document Architecture. J. Am. Med. Inform. Assoc. 8, 552–569.

    PubMed  CAS  Google Scholar 

  • Du, F., Amer-Yahia, S., and Freire, J. (2004) ShreX: Managing XML documents in relational databases. Proceedings of the 30th VLDB Conference, Toronto, Canada, pp. 1297–1300.

  • Fagan, A. M., Younkin, L. H., Morris, J. C., et al. (2000) Differences in the Abeta40/Abeta42 ratio associated with cerebrospinal fluid lipoproteins as a function of apolipoprotein E genotype. Ann. Neurol. 48, 201–210.

    PubMed  Article  CAS  Google Scholar 

  • Fernandez, M., Kadiyska, Y., Suciu, D., Morishima, A., Tan, W. (2002) SilkRoute: A framework for publishing relational data in XML. ACM Trans. Database Syst. 27, 438–493.

    Article  Google Scholar 

  • Fischl, B., Salat, D. H., van der Kouwe, A. J., et al. (2004) Sequence-independent segmentation of magnetic resonance images. Neuroimage 23, S69-S84.

    PubMed  Article  Google Scholar 

  • Fotenos, A. F., Snyder, A. Z., Girton, L. E., Morris, J. C., and Buckner, R. L. (2005) Normative estimates of cross-sectional and longitudinal brain volume decline in aging and AD. Neurology 64, 1032–1039.

    PubMed  CAS  Google Scholar 

  • Gardner, D., Toga, A. W., and Ascoli, G. A. (2003) Towards effective and rewarding data sharing. Neuroinformatics 1(3), 289–295.

    PubMed  Article  Google Scholar 

  • Hartmann, S. and Link, S. (2003) More Functional Dependencies for XML. Lect. Notes Comput. Sci. 2798, 355–369.

    Article  Google Scholar 

  • Hastings, S., Oster, S., Langella, S., et al. (2005) A grid-based image archival and analysis system. J. Am. Med. Inform. Assoc. 12, 286–295.

    PubMed  Article  Google Scholar 

  • Ilioudis, C., Pangalos, G., and Vakali, A. (2001) Security model for XML data. Proceedings of the International Conference on Internet Computing, Las Vegas, NV, pp. 400–406.

  • Keator, D. B., Gadde, S., Grethe, J. S., Taylor, D. V., and Potkin, S. G., FIRST BIRN. (2006) A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinformatics 2, 199–212.

    Article  Google Scholar 

  • Krishnamurthy, R., Kaushik, R., and Naughton, J. F. (2003) XML-to-SQLQuery Translation Literature: The State of the Art and Open Problems. Proceedings of the 1st International XMLDatabase Symposium, Berlin, Germany, pp. 1–18.

  • Lee, M., Ling, T., and Low, W. (2002) Designing functional dependencies for XML, in EDBT 2002, Lecture Notes in Computer Science 2287, pp. 124–141.

  • Leuf, B. and Cunningham, W. (2001) The Wiki Way: Quick Collaboration on the Web. Addison-Wesley, Boston, MA.

    Google Scholar 

  • Marenco, L., Tosches, T., Crasto, C., Shepherd, G., Miller, P. L., and Nadkarni, P. M. (2003) Achieving evolvable web-database bioscience applications using the EAV/CR framework: recent advances. J. Am. Med. Inform. Assoc. 10, 444–453.

    PubMed  Article  Google Scholar 

  • Martone, M. E., Gupta, A., and Ellisman, M. H. (2004) E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat. Neurosci. 7, 467–472.

    PubMed  Article  CAS  Google Scholar 

  • Morris, J. C. (1993) The Clinical Dementia Rating (CDR): current version and scoring rules. Neurology 43, 2412b-2414b.

    Google Scholar 

  • Nadkarni, P. M., Marenco, L., Chen, R., Skoufos, E., Shephard, G., and Miller, P. (1999) Organization of heterogeneous scientific data using the EAV/CR representation. J. Am. Med. Inform. Assoc. 6, 478–493.

    PubMed  CAS  Google Scholar 

  • Nielsen, J. (2000) Designing Web Usability: The Practice of Simplicity. New Riders Publishing, Indianapolis.

  • Noy, N. F., Crubezy, M., Fergerson, R. W., et al. (2003) Protege-2000: an open-source ontology-development and knowledge-acquisition environment. AMIAAnnu. Symp. Proc. 953.

  • Ozyurt, B. I., Wei, D., Keator, D. B., Potkin, S. G., Brown, G. G., and Grethe, J. S., (2004) Webaccessible clinical data management within an extensible neuroimaging database. Program Number 921.10. 2005 Abstract Viewer and Itinerary Planner. Society for Neuroscience, Washington, DC, 2005 Online.

  • Rubin, E. H., Storandt, M., Miller, J. P., et al. (1998) A prospective study of cognitive function and onset of dementia in cognitively healthy elders. Arch. Neurol. 55, 395–401.

    PubMed  Article  CAS  Google Scholar 

  • Scheltens, P., Barkhof, F., Leys, D., et al. (1993) A semiquantative rating scale for the assessment of signal hyperintensities on magnetic resonance imaging. J. Neurol. Sci. 114, 7–12.

    PubMed  Article  CAS  Google Scholar 

  • Shanmugasundaram, J., Gang, H., Tufte, K., Zhang, C., DeWitt, D. J., and Naughton, J. (1999) Relational databases for querying XML documents: limitations and opportunities. Proceedings of VLDB, Edinburgh, Scotland, pp. 302–314.

    Google Scholar 

  • Toga, A. W. (2002) Neuroimage databases: the good, the bad and the ugly. Nat. Rev. Neurosci. 3, 302–309.

    PubMed  Article  CAS  Google Scholar 

  • Van Horn, J. D., Grafton, S. T., Rockmore, D., and Gazzaniga, M. S. (2004) Sharing neuroimaging studies of human cognition. Nat. Neurosci. 7, 473.

    PubMed  Article  CAS  Google Scholar 

  • Varlamis, I. and Vazirgiannis, M. (2001) Bridging XML-schema and relational databases: a system for generating and manipulating relational databases using valid XML documents. Proceedings of ACM Symposium on Document Engineering Atlanta, GA, pp. 105–114.

  • Wang, L., Riethoven, J. J., and Robinson, A. (2002) XEMBL: distributing EMBL data in XML format. Bioinformatics 18, 1147–1148.

    PubMed  Article  CAS  Google Scholar 

  • Westbrook, J., Ito, N., Nakamura, H., Henrick, K., and Berman, H. M. (2005) PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21, 988–992.

    PubMed  Article  CAS  Google Scholar 

  • Zhao, L., Lee, C. P., and Hu, J. (2005) Generating XML schemas for DICOM structured reporting templates. J. Am. Med. Inform. Assoc. 12, 72–83.

    PubMed  Article  Google Scholar 

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Correspondence to Daniel S. Marcus.

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Marcus, D.S., Olsen, T.R., Ramaratnam, M. et al. The extensible neuroimaging archive toolkit. Neuroinform 5, 11–33 (2007). https://doi.org/10.1385/NI:5:1:11

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  • DOI: https://doi.org/10.1385/NI:5:1:11

Index Entries

  • Data sharing
  • database
  • genetics
  • informatics
  • metadata
  • neuroinformatics
  • open
  • source
  • quality control
  • workflow
  • XML schema