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Data Integration in the Human Brain Project

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Data Integration in the Life Sciences (DILS 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9162))

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Abstract

The Medical Informatics Platform of the Human Brain Project has the challenging task of organizing and presenting to its users a variety of data originating from different hospitals and hospital systems in a unified way, while protecting patients privacy as imposed by national legislation and institutional ethics. In this paper we view these challenges under the scope of data integration and analyze preliminary steps taken towards realizing the Medical Informatics Platform.

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Notes

  1. 1.

    http://www.vph-share.eu/.

  2. 2.

    http://p-medicine.eu/.

  3. 3.

    http://www.aneurist.org/.

  4. 4.

    CHUV anonymization will be performed by gnúbila, an external subcontractor.

References

  1. Abiteboul, S., Hull, R., Vianu, V.: Foundations of Databases. Addison-Wesley, Boston (1995)

    MATH  Google Scholar 

  2. Ashburner, J., Friston, K.J.: Diffeomorphic registration using geodesic shooting and Gauss-Newton optimisation. NeuroImage 55(3), 954–967 (2011)

    Article  Google Scholar 

  3. Davidson, S.B., Buneman, O.P., Crabtree, J., Tannen, V., Overton, G.C., Wong, L.: Biokleisli: integrating biomedical data and analysis packages. In: Letovsky, S. (ed.) Bioinformatics: Databases and systems, pp. 201–211. Springer, USA (1999)

    Google Scholar 

  4. Centers for Disease Control and Prevention and others: Hipaa privacy rule and public health. Guidance from CDC and the us department of health and human services. MMWR: Morbidity and Mortality Weekly Report, vol. 52, Suppl. 1, pp. 1–17 (2003)

    Google Scholar 

  5. Doan, A., Halevy, A.Y., Ives, Z.G.: Principles of Data Integration. Morgan Kaufmann, San Francisco (2012)

    Google Scholar 

  6. Fagin, R., Kolaitis, P.G., Miller, R.J., Popa, L.: Data exchange: semantics and query answering. Theoret. Comput. Sci. 336(1), 89–124 (2005)

    Article  MathSciNet  Google Scholar 

  7. Forrey, A., et al.: Logical observation identifier names and codes (LOINC) database: a public use set of codes and names for electronic reporting of clinical laboratory test results. Clin. Chem. 42(1), 81–90 (1996)

    Google Scholar 

  8. Garcia-Molina, H., Papakonstantinou, Y., Quass, D., Rajaraman, A., Sagiv, Y., Ullman, J., Vassalos, V., Widom, J.: The tsimmis approach to mediation: Data models and languages. J. Intell. Inf. Syst. 8(2), 117–132 (1997)

    Article  Google Scholar 

  9. Haas, L.M., Kodali, P., Rice, J.E., Schwarz, P.M., Swope, W.C.: Integrating life sciences data-with a little garlic. In: Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering, 2000, pp. 5–12. IEEE (2000)

    Google Scholar 

  10. Hernandez, T., Kambhampati, S.: Integration of biological sources: current systems and challenges ahead. ACM Sigmod Rec. 33(3), 51–60 (2004)

    Article  Google Scholar 

  11. Josifovski, V., Schwarz, P., Haas, L., Lin, E.: Garlic: a new flavor of federated query processing for db2. In: Proceedings of the 2002 ACM SIGMOD International Conference on Management of data, pp. 524–532. ACM (2002)

    Google Scholar 

  12. Karpathiotakis, M., Branco, M., Alagiannis, I., Ailamaki, A.: Adaptive query processing on RAW data. PVLDB 7(12), 1119–1130 (2014)

    Google Scholar 

  13. Klein, A., Tourville, J.: 101 labeled brain images and a consistent human cortical labeling protocol. Front. Neurosci. 6, 101 (2012)

    Article  Google Scholar 

  14. Knoblock, C.A., Minton, S., Ambite, J.L., Ashish, N., Muslea, I., Philpot, A.G., Tejada, S.: The ariadne approach to web-based information integration. Int. J. Coop. Inf. Syst. 10(01n02), 145–169 (2001)

    Article  Google Scholar 

  15. Marnette, B., et al.: ++Spicy: an opensource tool for second-generation schema mapping and data exchange. PVLDB 4(12), 1438–1441 (2011)

    Google Scholar 

  16. Merelli, I., Pérez-Sánchez, H., Gesing, S., D’Agostino, D.: Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. BioMed Res. Int. 2014, 13 (2014)

    Google Scholar 

  17. Organization, W.H., et al.: The ICD-10 Classification of Mental and Behavioural Disorders: Clinical Descriptions and Diagnostic Guidelines. World Health Organization, Geneva (1992)

    Google Scholar 

  18. Peim, M., Franconi, E., Paton, N.W., Goble, C.A.: Query processing with description logic ontologies over object-wrapped databases. In: Proceedings 14th International Conference on Scientific and Statistical Database Management, 2002, pp. 27–36. IEEE (2002)

    Google Scholar 

  19. Sherry, S.T., Ward, M., Sirotkin, K.: dbSNPdatabase for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 9(8), 677–679 (1999)

    Google Scholar 

  20. Stevens, R., Goble, C., Paton, N.W., Bechhofer, S., Ng, G., Baker, P., Brass, A.: Complex query formulation over diverse information sources in tambis. In: Lacroix, Z., Critchlow, T. (eds.) Bioinformatics: Managing Scientific Data. Morgan Kaufmann, San Francisco (2003)

    Google Scholar 

  21. Sweeney, L.: k-anonymity: A model for protecting privacy. Int. J. Uncertainty Fuzziness Knowl. Based Syst. 10(05), 557–570 (2002)

    Article  MathSciNet  MATH  Google Scholar 

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Acknowledgment

Tassos Venetis was funded by the Research Centre of the Athens University of Economics and Business, in the framework of “Research Funding at AUEB for Excellence and Extroversion” and Vasilis Vassalos has received funding from the European Union Seventh Framework Programme (FP7/2007–2013) under grant agreement no.604102 (Human Brain Project).

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Authors and Affiliations

  1. Department of Informatics, Athens University of Economics and Business, Patision 76, 10434, Athens, Greece

    Tassos Venetis & Vasilis Vassalos

Authors
  1. Tassos Venetis
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  2. Vasilis Vassalos
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Corresponding author

Correspondence to Tassos Venetis .

Editor information

Editors and Affiliations

  1. USC Stevens Neuroimaging and Informatics Institute, Los Angeles, California, USA

    Naveen Ashish

  2. USC Information Sciences Institute, Marina del Rey, California, USA

    Jose-Luis Ambite

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Venetis, T., Vassalos, V. (2015). Data Integration in the Human Brain Project. In: Ashish, N., Ambite, JL. (eds) Data Integration in the Life Sciences. DILS 2015. Lecture Notes in Computer Science(), vol 9162. Springer, Cham. https://doi.org/10.1007/978-3-319-21843-4_3

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  • DOI: https://doi.org/10.1007/978-3-319-21843-4_3

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-21842-7

  • Online ISBN: 978-3-319-21843-4

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