Managing Provenance for Medical Datasets - An Example Case for Documenting the Workflow for Image Processing

Ajinkya Prabhune, Rainer Stotzka, Michael Gertz, Lei Zheng, Jürgen Hesser

2017

Abstract

In this paper, we present a novel data repository architecture that is capable of handling the complex image processing workflows and its associated provenance for clinical image data. This novel system has unique and outstanding properties versus existing systems. Among the most relevant features are a flexible and intuitively usable data and metadata management that includes the use of a graph-based provenance management strategy based on a standard provenance model. Annotation is supported to allow for flexible text descriptors as being widespread found for clinical data when structured templates are not yet available. The architecture presented here is based on a modern database and management concepts and allows to overcome the limitations of current systems namely limited provenance support, lacking flexibility, and extensibility to novel requests. To demonstrate the practical applicability of our architecture, we consider a use case of automated image data processing workflow for identifying vascular lesions in the lower extremities, and describe the provenance graph generated for this workflow. Although presented for image data, the proposed concept applies to more general context of arbitrary clinical data and could serve as an additional service to existing clinical IT systems.

References

  1. Allcock, W., Bresnahan, J., Kettimuthu, R., et al. (2005). The globus striped gridftp framework and server. In Proceedings of the 2005 ACM/IEEE conference on Supercomputing, page 54. IEEE Computer Society.
  2. Bian, J., Topaloglu, U., and Lane, C. (2009). Eir: Enterprise imaging repository, an alternative imaging archiving and communication system. In 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pages 2168-2171.
  3. Brockmann, C., Jochum, S., Hesser, J., et al. (2010). Graphmatching-based computed tomography angiography in peripheral arterial occlusive disease. Clinical Imaging, 34(5):367 - 374.
  4. Davidson, S. B., Boulakia, S. C., Eyal, A., Ludäscher, B., McPhillips, T. M., Bowers, S., Anand, M. K., and Freire, J. (2007). Provenance in scientific workoflw systems. IEEE Data Eng. Bull., 30(4):44-50.
  5. Dolin, R. H., Alschuler, L., Boyer, S., Beebe, C., Behlen, F. M., Biron, P. V., and Shabo (Shvo), A. (2006). Hl7 clinical document architecture, release 2. Journal of the American Medical Informatics Association, 13(1):30-39.
  6. Estrella, F., Hauer, T., McClatchey, R., Odeh, M., Rogulin, D., and Solomonides, T. (2007). Experiences of en-
  7. 7www.pcornet.org 8www.miracum.de 9www.helmholtz-lsdma.de gineering grid-based medical software. International Journal of Medical Informatics, 76(8):621 - 632.
  8. Goland, Y., Whitehead, E., Faizi, A., Carter, S., and Jensen, D. (1999). Http extensions for distributed authoringwebdav. Technical report.
  9. Kifor, T., Varga, L. Z., Vazquez-Salceda, J., Alvarez, S., Willmott, S., Miles, S., and Moreau, L. (2006). Provenance in agent-mediated healthcare systems. IEEE Intelligent Systems, 21(6):38-46.
  10. Liu, Y. and Wang, J. (2010). PACS and digital medicine: essential principles and modern practice. CRC Press.
  11. Maksimov, D., Hesser, J., Brockmann, C., Jochum, S., Dietz, T., et al. (2009). Graph-matching based cta. IEEE Transactions on Medical Imaging, 28(12):1940-1954.
  12. Marcheschi, P., Ciregia, A., Mazzarisi, A., Augiero, G., and Gori, A. (2009). A new approach to affordable and reliable cardiology pacs architecture using open-source technology. In 2009 36th Annual Computers in Cardiology Conference (CinC), pages 537-540.
  13. Matthews, B. (2015). Csmd: the core scientific metadata model. Online http://icatprojectcontrib.github.io/CSMD/csmd-4.0.html.
  14. Mildenberger, P., Eichelberg, M., and Martin, E. (2002). Introduction to the DICOM standard. European Radiology, 12(4):920-927.
  15. OASIS (2007). Standard, O.A.S.I.S: Web services business process execution language version 2.0. Online http://docs.oasis-open.org/wsbpel/2.0/OS/wsbpel-v2.
  16. Prabhune, A., Stotzka, R., Jejkal, T., Hartmann, V., Bach, M., Schmitt, E., Hausmann, M., and Hesser, J. (2015). An optimized generic client service api for managing large datasets within a data repository. In Big Data Computing Service and Applications (BigDataService), 2015 IEEE First International Conference on, pages 44-51.
  17. Prabhune, A., Zweig, A., Stotzka, R., Gertz, M., and Hesser, J. (2016). Prov2ONE: An Algorithm for Automatically Constructing ProvONE Provenance Graphs, pages 204-208. Springer Publishing.
  18. Sanderson, R., Ciccarese, P., Van de Sompel, H., Bradshaw, S., Brickley, D., a Castro, L. J. G., et al. (2013). Open annotation data model. W3C community draft.
  19. Sandoval, J. (2009). Restful java web services: Master core rest concepts and create restful web services in java. Packt Publishing Ltd.
  20. Zeilinger, G., Montgomery, O., Evans, D., et al. (2010). The dcm4che project. Online Sourceforge project https://sourceforge.net/projects/dcm4che/.
  21. Zhang, J., Lu, X., Nie, H., Huang, Z., and van der Aalst, W. M. P. (2009). Radiology information system: a workflow-based approach. International Journal of Computer Assisted Radiology and Surgery, 4(5):509- 516.
  22. Zhao, Y., Wilde, M., and Foster, I. (2006). Applying the Virtual Data Provenance Model, pages 148-161. Springer Berlin Heidelberg, Berlin, Heidelberg.
  23. Zhu, N. Q. (2013). Data visualization with D3. js cookbook. Packt Publishing Ltd.
Download


Paper Citation


in Harvard Style

Prabhune A., Stotzka R., Gertz M., Zheng L. and Hesser J. (2017). Managing Provenance for Medical Datasets - An Example Case for Documenting the Workflow for Image Processing . In Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, (BIOSTEC 2017) ISBN 978-989-758-213-4, pages 236-243. DOI: 10.5220/0006109402360243


in Bibtex Style

@conference{healthinf17,
author={Ajinkya Prabhune and Rainer Stotzka and Michael Gertz and Lei Zheng and Jürgen Hesser},
title={Managing Provenance for Medical Datasets - An Example Case for Documenting the Workflow for Image Processing},
booktitle={Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, (BIOSTEC 2017)},
year={2017},
pages={236-243},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0006109402360243},
isbn={978-989-758-213-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, (BIOSTEC 2017)
TI - Managing Provenance for Medical Datasets - An Example Case for Documenting the Workflow for Image Processing
SN - 978-989-758-213-4
AU - Prabhune A.
AU - Stotzka R.
AU - Gertz M.
AU - Zheng L.
AU - Hesser J.
PY - 2017
SP - 236
EP - 243
DO - 10.5220/0006109402360243