Terminology Development Towards Harmonizing Multiple Clinical Neuroimaging Research Repositories

  • Jessica A. TurnerEmail author
  • Danielle Pasquerello
  • Matthew D. Turner
  • David B. Keator
  • Kathryn Alpert
  • Margaret King
  • Drew Landis
  • Vince D. Calhoun
  • Steven G. Potkin
  • Marcelo Tallis
  • Jose Luis Ambite
  • Lei Wang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9162)


Data sharing and mediation across disparate neuroimaging repositories requires extensive effort to ensure that the different domains of data types are referred to by commonly agreed upon terms. Within the SchizConnect project, which enables querying across decentralized databases of neuroimaging, clinical, and cognitive data from various studies of schizophrenia, we developed a model for each data domain, identified common usable terms that could be agreed upon across the repositories, and linked them to standard ontological terms where possible. We had the goal of facilitating both the current user experience in querying and future automated computations and reasoning regarding the data. We found that existing terminologies are incomplete for these purposes, even with the history of neuroimaging data sharing in the field; and we provide a model for efforts focused on querying multiple clinical neuroimaging repositories.


Neuroimaging Data sharing Clinical scales Assessments Mediation 



SchizConnect is supported by a grant from the National Institutes of Health (NIH/NIMH), 5U01MH097435 to L. Wang, JL. Ambite, S.G. Potkin and J.A.Turner. The work on COINS is also supported by 5P20GM103472 (NIGMS) to V.D. Calhoun. The authors would like to thank Derin Cobia, PhD, for help on constructing the SchizConnect neuropsychological assessment hierarchy.


  1. 1.
    Turner, J.A.: The rise of large-scale imaging studies in psychiatry. GigaScience 3, 29 (2014)CrossRefGoogle Scholar
  2. 2.
    Hall, D., Huerta, M.F., McAuliffe, M.J., Farber, G.K.: Sharing heterogeneous data: the national database for autism research. Neuroinformatics 10, 331–339 (2012)CrossRefGoogle Scholar
  3. 3.
    Keator, D.B., Helmer, K., Steffener, J., Turner, J.A., Van Erp, T.G., Gadde, S., Ashish, N., Burns, G.A., Nichols, B.N.: Towards structured sharing of raw and derived neuroimaging data across existing resources. NeuroImage 82, 647–661 (2013)CrossRefGoogle Scholar
  4. 4.
    Bug, W., Astahkov, V., Boline, J., Fennema-Notestine, C., Grethe, J.S., Gupta, A., Kennedy, D.N., Rubin, D.L., Sanders, B., Turner, J.A., Martone, M.E.: Data federation in the biomedical informatics research network: tools for semantic annotation and query of distributed multiscale brain data. AMIA Annu. Symp. Proc. 1220 6 November 2008Google Scholar
  5. 5.
    Ozyurt, I.B., Keator, D.B., Wei, D., Fennema-Notestine, C., Pease, K.R., Bockholt, J., Grethe, J.S.: Federated Web-accessible clinical data management within an extensible neuroimaging database. Neuroinformatics 8, 231–249 (2010)CrossRefGoogle Scholar
  6. 6.
    Scott, A., Courtney, W., Wood, D., de la Garza, R., Lane, S., King, M., Wang, R., Roberts, J., Turner, J.A., Calhoun, V.D.: COINS: an innovative informatics and neuroimaging tool suite built for large heterogeneous datasets. Front. Neuroinform. 5, 33 (2011)CrossRefGoogle Scholar
  7. 7.
    King, M.D., Wood, D., Miller, B., Kelly, R., Landis, D., Courtney, W., Wang, R., Turner, J.A., Calhoun, V.D.: Automated collection of imaging and phenotypic data to centralized and distributed data repositories. Front. Neuroinform. 8, 60 (2014)CrossRefGoogle Scholar
  8. 8.
    Marcus, D.S., Harwell, J., Olsen, T., Hodge, M., Glasser, M.F., Prior, F., Jenkinson, M., Laumann, T., Curtiss, S.W., Van Essen, D.C.: Informatics and data mining tools and strategies for the human connectome project. Front. Neuroinform. 5, 4 (2011)CrossRefGoogle Scholar
  9. 9.
    Marcus, D.S., Olsen, T.R., Ramaratnam, M., Buckner, R.L.: The extensible neuroimaging archive toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics 5, 11–34 (2007)Google Scholar
  10. 10.
    Wang, L., Kogan, A., Cobia, D., Alpert, K., Kolasny, A., Miller, M.I., Marcus, D.: Northwestern university schizophrenia data and software tool (NUSDAST). Front. Neuroinform. 7, 25 (2013)Google Scholar
  11. 11.
    Wang, L., Alpert, K., Calhoun, V.D., Keator, D.B., King, M.D., Kogan, A., Landis, D., Talllis, M., Potkin, S.G., Turner, J.A., Ambite, J.L.: SchizConnect: Mediating Schizophrenia Neuroimaging Databases for Large-Scale Integration. NeuroImage (Manuscript under review)Google Scholar
  12. 12.
    Jovicich, J., Czanner, S., Han, X., Salat, D., van der Kouwe, A., Quinn, B., Pacheco, J., Albert, M., Killiany, R., Blacker, D., Maguire, P., Rosas, D., Makris, N., Gollub, R., Dale, A., Dickerson, B.C., Fischl, B.: MRI-derived measurements of human subcortical, ventricular and intracranial brain volumes: reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths. NeuroImage 46, 177–192 (2009)CrossRefGoogle Scholar
  13. 13.
    Jovicich, J., Czanner, S., Greve, D., Haley, E., van der Kouwe, A., Gollub, R., Kennedy, D., Schmitt, F., Brown, G., Macfall, J., Fischl, B., Dale, A.: Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. NeuroImage 30, 436–443 (2006)CrossRefGoogle Scholar
  14. 14.
    Glover, G.H., Mueller, B.A., Turner, J.A., van Erp, T.G., Liu, T.T., Greve, D.N., Voyvodic, J.T., Rasmussen, J., Brown, G.G., Keator, D.B., Calhoun, V.D., Lee, H.J., Ford, J.M., Mathalon, D.H., Diaz, M., O’Leary, D.S., Gadde, S., Preda, A., Lim, K.O., Wible, C.G., Stern, H.S., Belger, A., McCarthy, G., Ozyurt, B., Potkin, S.G.: Function biomedical informatics research network recommendations for prospective multicenter functional MRI studies. J. Magn. Reson. Imag. JMRI 36, 39–54 (2012)CrossRefGoogle Scholar
  15. 15.
    Larson, S.D., Martone, M.E.: Ontologies for neuroscience: what are they and what are they good for? Front. Neurosci. 3, 60–67 (2009)CrossRefGoogle Scholar
  16. 16.
    Bug, W.J., Ascoli, G.A., Grethe, J.S., Gupta, A., Fennema-Notestine, C., Laird, A.R., Larson, S.D., Rubin, D., Shepherd, G.M., Turner, J.A., Martone, M.E.: The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics 6, 175–194 (2008)CrossRefGoogle Scholar
  17. 17.
    Larson, S.D., Martone, M.E.: an online framework for neuroscience knowledge. Front. Neuroinform. 7, 18 (2013)CrossRefGoogle Scholar
  18. 18.
    Turner, J.A., Laird, A.R.: The cognitive paradigm ontology: design and application. Neuroinformatics 10, 57–66 (2012)CrossRefGoogle Scholar
  19. 19.
    Poldrack, R.A., Kittur, A., Kalar, D., Miller, E., Seppa, C., Gil, Y., Parker, D.S., Sabb, F.W., Bilder, R.M.: The cognitive atlas: toward a knowledge foundation for cognitive neuroscience. Front. Neuroinform. 5, 17 (2011)CrossRefGoogle Scholar
  20. 20.
    Whetzel, P.L., Team, N.: NCBO technology: powering semantically aware applications. J. Biomed. Semant. 4(Suppl. 1), S8 (2013)CrossRefGoogle Scholar
  21. 21.
    Mejino, J.L., Rubin, D.L., Brinkley, J.F.: FMA-RadLex: an application ontology of radiological anatomy derived from the foundational model of anatomy reference ontology. AMIA Annu. Symp. Proc. 2008, 465–469 (2008)Google Scholar
  22. 22.
    Rubin, D.L.: Creating and curating a terminology for radiology: ontology modeling and analysis. J. Digit. Imag. 21, 355–362 (2008)CrossRefGoogle Scholar
  23. 23.
    Buckler, A.J., Liu, T.T., Savig, E., Suzek, B.E., Rubin, D.L., Paik, D.: Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers. J. Digit. Imag. 26, 630–641 (2013)CrossRefGoogle Scholar
  24. 24.
    Wood, D., King, M., Landis, D., Courtney, W., Wang, R., Kelly, R., Turner, J.A., Calhoun, V.D.: Harnessing modern Web application technology to create intuitive and efficient data visualization and sharing tools. Front. Neuroinform. 8, 71 (2014)CrossRefGoogle Scholar
  25. 25.
    Brinkman, R.R., Courtot, M., Derom, D., Fostel, J.M., He, Y., Lord, P., Malone, J., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S.A., Soldatova, L.N., Stoeckert Jr., C.J., Turner, J.A., Zheng, J., Consortium, O.B.I.: Modeling biomedical experimental processes with OBI. J. Biomed. Semant. 1(1), S7 (2010)CrossRefGoogle Scholar
  26. 26.
    Kong, Y.M., Dahlke, C., Xiang, Q., Qian, Y., Karp, D., Scheuermann, R.H.: Toward an ontology-based framework for clinical research databases. J. Biomed. Inform. 44, 48–58 (2011)CrossRefGoogle Scholar
  27. 27.
    Poline, J.B., Breeze, J.L., Ghosh, S., Gorgolewski, K., Halchenko, Y.O., Hanke, M., Haselgrove, C., Helmer, K.G., Keator, D.B., Marcus, D.S., Poldrack, R.A., Schwartz, Y., Ashburner, J., Kennedy, D.N.: Data sharing in neuroimaging research. Front. Neuroinform. 6, 9 (2012)CrossRefGoogle Scholar
  28. 28.
    Breeze, J.L., Poline, J.B., Kennedy, D.N.: Data sharing and publishing in the field of neuroimaging. Gigascience 1, 9 (2012)CrossRefGoogle Scholar
  29. 29.
    Mejino Jr., J.V., Agoncillo, A.V., Rickard, K.L., Rosse, C.: Representing complexity in part-whole relationships within the foundational model of anatomy. AMIA Annu. Symp. Proc. 2003, 450–454 (2003)Google Scholar
  30. 30.
    Golbreich, C., Grosjean, J., Darmoni, S.J.: The foundational model of anatomy in OWL 2 and its use. Artif. Intell. Med. 57, 119–132 (2013)CrossRefGoogle Scholar
  31. 31.
    Nichols, B.N., Mejino, J.L., Detwiler, L.T., Nilsen, T.T., Martone, M.E., Turner, J.A., Rubin, D.L., Brinkley, J.F.: Neuroanatomical domain of the foundational model of anatomy ontology. J. Biomed. Semant. 5, 1 (2014)CrossRefGoogle Scholar
  32. 32.
    Sim, I., Carini, S., Tu, S.W., Detwiler, L.T., Brinkley, J., Mollah, S.A., Burke, K., Lehmann, H.P., Chakraborty, S., Wittkowski, K.M., Pollock, B.H., Johnson, T.M., Huser, V., Human Studies Database, Project: Ontology-based federated data access to human studies information. AMIA Annu. Symp. Proc. 2012, 856–865 (2012)Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Jessica A. Turner
    • 1
    • 2
    Email author
  • Danielle Pasquerello
    • 1
  • Matthew D. Turner
    • 1
  • David B. Keator
    • 3
  • Kathryn Alpert
    • 4
  • Margaret King
    • 2
  • Drew Landis
    • 2
  • Vince D. Calhoun
    • 2
    • 5
  • Steven G. Potkin
    • 3
  • Marcelo Tallis
    • 6
  • Jose Luis Ambite
    • 6
  • Lei Wang
    • 4
  1. 1.Georgia State UniversityAtlantaUSA
  2. 2.Mind Research NetworkAlbuquerqueUSA
  3. 3.University of CaliforniaIrvineUSA
  4. 4.Northwestern UniversityChicagoUSA
  5. 5.University of New MexicoAlbuquerqueUSA
  6. 6.University of Southern CaliforniaLos AngelesUSA

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