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. 2014 Jul 3:8:65.
doi: 10.3389/fninf.2014.00065. eCollection 2014.

Data dictionary services in XNAT and the Human Connectome Project

Rick Herrick  1 , Michael McKay  1 , Timothy Olsen  1 , William Horton  1 , Mark Florida  1 , Charles J Moore  1 , Daniel S Marcus  1
Affiliations

Data dictionary services in XNAT and the Human Connectome Project

Rick Herrick et al. Front Neuroinform. .

Abstract

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software. We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g., textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as the Resource Description Framework (RDF), JavaScript Object Notation (JSON), and Extensible Markup Language (XML). It also facilitates the conversion of XNAT's native data schema into standard neuroimaging vocabularies and structures.

Keywords: XNAT; human computer interaction; human connectome; ontologies; publishing; translations.

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Figures

Figure 1
Figure 1
HCP subject dashboard.
Figure 2
Figure 2
Access tiers secure subject attribute data based on the level of user data-use agreements.
Figure 3
Figure 3
Dependency injection allows service access while providing flexibility in implementation.
Figure 4
Figure 4
Category, assessment, and attributes are browse-able through the ConnectomeDB dashboard.
Figure 5
Figure 5
Translation of different vocabularies to XNAT entities.
See this image and copyright information in PMC

References

    1. Marcus D. S., Harms M. P., Snyder A. Z., Jenkinson M., Wilson J. A., Glasser M. F., et al. (2013). Human Connectome Project informatics: quality control, database services, and data visualization. Neuroimage 80, 202–219 10.1016/j.neuroimage.2013.05.077 - DOI - PMC - PubMed
    1. Marcus D. S., Olsen T. R., Ramaratnam M., Buckner R. L. (2007). The extensible neuroimaging archive toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics 5, 11–34 10.1385/NI:5:1:11 - DOI - PubMed
    1. Poline J. B., Breeze J. L., Ghosh S., Gorgolewski K., Halchenko Y. O., Hanke M., et al. (2012). Data sharing in neuroimaging research. Front. Neuroinform. 6:9 10.3389/fninf.2012.00009 - DOI - PMC - PubMed
    1. Van Essen D. C., Ugurbil K., Auerbach E., Barch D., Behrens T. E. J., Bucholz R., et al. (2012). The Human Connectome Project: a data acquisition perspective. Neuroimage 62, 2222–2231 10.1016/j.neuroimage.2012.02.018 - DOI - PMC - PubMed

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