@neurIST: Infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services

IEEE Transactions on Information Technology in Biomedicine

Volumn 14, Issue 6, 2010, Pages 1365-1377

  Benkner, Siegfried ^a   Arbona, Antonio ^b   Berti, Guntram ^c   Chiarini, Alessandro ^d   Dunlop, Robert ^e   Engelbrecht, Gerhard ^a   Frangi, Alejandro F ^f   Friedrich, Christoph M ^g   Hanser, Susanne ^h   Hasselmeyer, Peer ^c   Hose, Rod D ^j   Iavindrasana, Jimison ^l   Khler, Martin ^a   Iacono, Luigi Lo ^c   Lonsdale, Guy ^c   Meyer, Rodolphe ^l   Moore, Bob ⁱ   Rajasekaran, Hariharan ^c   Summers, Paul E ^k   Whrer, Alexander ^a   Wood, Steven ^j   more..

^a UNIVERSITY OF VIENNA   (Austria)

^b GridSystems SA   (Spain)

^c NEC LABORATORIES EUROPE   (Germany)

^d B3C BioComputing Competence Centre   (Italy)

^e Infermed Ltd   (United Kingdom)

^f UNIVERSITAT POMPEU FABRA   (Spain)

^g FRAUNHOFER INSTITUTE FOR ALGORITHMS AND SCIENTIFIC COMPUTING SCAI   (Germany)

^h UNIVERSITY OF FREIBURG   (Germany)

ⁱ IDAC Ireland Limited   (Ireland)

^j UNIVERSITY OF SHEFFIELD   (United Kingdom)

^k UNIVERSITY OF OXFORD   (United Kingdom)

^l GENEVA UNIVERSITY HOSPITALS   (Switzerland)

more..

Author keywords

Aneurysms; architecture; biomechanical simulation; biomedical grid; ontology

Indexed keywords

ANEURYSMS; BIOMECHANICAL SIMULATION; BIOMEDICAL GRID; BIOMEDICAL RESEARCH; CEREBRAL ANEURYSMS; CLINICAL CARE; COMPLEX PROCESSING; COMPUTING RESOURCE; COMPUTING SERVICES; CRITICAL MASS; DISEASE MANAGEMENT; DISTRIBUTED INFORMATION SOURCES; GRID INFRASTRUCTURES; HETEROGENEOUS DATA; HUMAN DISEASE; MEDICAL RESEARCHERS; PATIENT DATA; SYSTEMS ARCHITECTURE; TREATMENT PLANNING;

ARCHITECTURE; BIOMECHANICS; HOSPITAL DATA PROCESSING; INDUSTRIAL RESEARCH; KNOWLEDGE BASED SYSTEMS; ONTOLOGY;

DISEASES;

ANEURYSM; ARTICLE; COMPUTER NETWORK; COMPUTER SECURITY; DATA BASE; DISEASE MANAGEMENT; EUROPE; HUMAN; INFORMATION DISSEMINATION; MEDICAL INFORMATICS; MEDICAL RESEARCH; METHODOLOGY;

ANEURYSM; BIOMEDICAL RESEARCH; COMPUTER COMMUNICATION NETWORKS; COMPUTER SECURITY; DATABASE MANAGEMENT SYSTEMS; DISEASE MANAGEMENT; EUROPE; HUMANS; INFORMATION DISSEMINATION; MEDICAL INFORMATICS;

EID: 78249262585     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/TITB.2010.2049268     Document Type: Article

References (51)

1. M. Tsiknakis, M. Brochhausen, J. Nabrzyski, J. Pucacki, S. G. Sfakianakis, G. Potamias, C. Desmedt, and D. Kafetzopoulos, "A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of postgenomic clinical trials on cancer," IEEE Trans. Inf. Technol. Biomed., vol. 12, no. 2, pp. 205-217, Mar. 2008.
2. J. Freund, D. Comaniciu, Y. Ioannis, P. Liu, R. McClatchey, E. Morley-Fletcher, X. Pennec, G. Pongiglione, and X. Zhou, "Health-e-Child: An integrated biomedical platform for grid-based paediatrics," in Studies in Health Technology and Informatics. Amsterdam, The Netherlands: IOS Press, 2006, pp. 259-270.
3. S. Oster, S. L. Hastings, S. Langella, T. Kurc, and J. H. Saltz, "Data management and exchange in the cancer grid," presented at the Advancing Practice, Instruction and Innovation Through Informatics (APIII), Frontiers in Oncology and Pathology Informatics, Pittsburgh, PA, 2004.
4. Biomedical Informatics Research Network. [Online]. Available: http://www.nbirn.net/
5. @neurIST: European initiative to integrate biomedical informatics in the management of cerebral aneurysms, Tirana, Albania. [Online]. Available: http://www.aneurist.org
6. A. Arbona, S. Benkner, G. Engelbrecht, J. Fingberg, M. Hofmann, K. Kumpf, G. Lonsdale, and A. Woehrer, "A service-oriented grid infrastructure for biomedical data and compute services," IEEE Trans. Nanobiosci., vol. 6, no. 2, pp. 136-141, Jun. 2007.
7. H. Rajasekaran, L. L. Iacono, P. Hasselmeyer, J. Fingberg, P. Summers, S. Benkner, G. Engelbrecht, A. Arbona, A. Chiarini, C. M. Friedrich, M. Hofmann-Apitius, K. Kumpf, B. Moore, P. Bijlenga, J. Iavindrasana, H. Mueller, R. D. Hose, R. Dunlop, and A. F. Frangi, "@neurIST-Towards a system architecture for advanced disease management through integration of heterogeneous data, computing, and complex processing services," in Proc. 21st IEEE Int. Symp. Comput.-based Med. Syst., 2008, pp. 361-366.
8. S. C. Johnston, C. B. Wilson, V. V. Halbach, R. T. Higashida, C. F. Dowd, M. W. McDermott, C. B. Applebury, T. L. Farley, and D. R. Gress, "En-dovascular and surgical treatment of unruptured cerebral aneurysms: Comparison of risks," Ann. Neurol., vol. 48, no. 1, pp. 11-19, Jul. 2000.
9. Y. B. Roos, M. G. Dijkgraaf, K. W. Albrecht, L. F. Beenen, R. J. Groen, R. J. de Haan, and M. Vermeulen, "Direct costs of modern treatment of aneurysmal subarachnoid hemorrhage in the first year after diagnosis," Stroke, vol. 33, no. 6, pp. 1595-1599, Jun. 2002.
10. International Subarachnoid Aneurysm Trial (ISAT) Collaborative Group. "International Subarachnoid Aneurysm Trial (ISAT) of neurosurgical clipping versus endovascular coiling in 2143 patients with ruptured intracra-nial aneurysms: A randomised trial," Lancet, vol. 360, pp. 1267-1274, 2002.
11. A. J. Molyneux, R. S. C. Kerr, L. M. Yu, M. Clarke, M. Sneade, J. A. Yarnold, and P. Sandercock, "International subarachnoid aneurysm trial (ISAT) of neurosurgical clipping versus endovascular coiling in 2143 patients with ruptured intracranial aneurysms: A randomised comparison of effects on survival, dependency, seizures, rebleeding, subgroups and aneurysm occlusion," Lancet, vol. 366, pp. 809-817, 2005.
12. A. Camp, N. Ramzi, A. J. Molyneux, P. E. Summers, R. S. C. Kerr, M. Snead, J. A. Yarnold, J. Rischmiller, and J. V. Byrne, "Retreatment of ruptured cerebral aneurysms in patients randomized by coiling or clipping in the International Subarachnoid Aneurysm Trial (ISAT)," Stroke, vol. 38, no. 5, pp. 1538-1544, May 2007. [Epub 29 March, 2007].
13. D. O. Wiebers, J. P. Whisnant, J. Huston, III, I. Meissner, R. D. Brown, Jr, D. G. Piepgras, G. S. Forbes, K. Thielen, D. Nichols, W. M. O'Fallon, J. Peacock, L. Jaege, N. F. Kassell, G. L. Kongable-Beckma, and J. C. Torner, "Unruptured intracranial aneurysms-Risk of rupture and risks of surgical intervention. International Study of Unruptured Intracranial Aneurysms Investigators," N. Engl. J. Med., vol. 339, no. 24, pp. 1725-1733, Dec. 1998.
14. Digital Imaging and Communications in Medicine (DICOM). [Online]. Available: http://medical.nema.org/
15. C. M. Friedrich, H. Dach, T. Gattermayer, G. Engelbrecht, S. Benkner, and M. Hofmann-Apitius, "@neuLink: A service-oriented application for biomedical knowledge discovery," in Proc. HealthGrid 2008. Amsterdam, The Netherlands: IOS Press, pp. 165-172.
16. R. Aragues, D. Jaeggi, and B. Oliva, "PIANA: Protein interactions and network analysis," Bioinformatics, vol. 22, no. 8, pp. 1015-1017, 2006.
17. M. Berthold., (2009). KNIME (Konstanz Information Miner) Webpage: last accessed 2009-02-26 [Online]. Available: http://www.knime.org/
18. C. M. Friedrich, M. Hofmann-Apitius, R. Dunlop, I. Chronakis, M. C. J. M. Sturkenboom, R. Risselada, B. Oliva, and F. Sanz, "Initial results on knowledge discovery and decision support for intracranial aneurysms," in Proc. HEALTHINF 2008, INSTICC, pp. 265-272.
19. M. Hofmann-Apitius, J. Fluck, L. I. Furlong, O. Fornes, C. Kolarik, S. Hanser, M. Boeker, S. Schulz, F. Sanz, R. Klinger, H.-T. Mevissen, T. Gattermayer, B. Oliva, and C. M. Friedrich, "Knowledge environments representing molecular entities for the virtual physiological human," Philos. Trans. R. Soc. A, vol. 1878, no. 366, pp. 3091-3110, 2008.
20. openMAF [Online]. Available: http://www.openmaf.org/maf/doc/maf-2-0- documentation/
21. P. K. Singh, A. Marzo, S. Coley, G. Berti, P. Bijlenga, P. Lawford, M. C. Villa-Uriol, D. A. Rufenacht, K. M. McCormack, A. F. Frangi, U. J. Patel, and D. R. Hose, "The role of computational fluid dynamics in the management of unruptured intracranial aneurysms: A clinicians' view," Comput. Intell. Neurosci., vol. 2009, p. 2, 2009, Article ID 760364, 1. DOI: 10.1155/2009/760364.
22. A. Geers, I. Larrabide, A. G. Radaelli, H. Bogunovic, H. A. F. Gratama van Andel, C. B. Majoie, and A. F. Frangi, "Reproducibility of image-based computational hemodynamics in intracranial aneurysms: Comparison of CTA and 3DRA," in Proc IEEE Int. Symp. Biomed. Imag., 2009, pp. 610-613.
23. Simulation Software version 12.0, ANSYS, Inc., Canonsburg, PA. [Online]. Available: www.ansys.com/products
24. M. Kim, I. Larrabide, M. C. Villa-Uriol, and A. F. Frangi, "Hemodynamic alterations of a patient-specific intracranial aneurysm induced by virtual deploymentofstents in various axial orientation," in Proc. IEEE Int. Symp. Biomed. Imag., 2009, pp. 1215-1218.
25. I. Larrabide, A. G. Radaelli, and A. F. Frangi, "Fast virtual stenting with deformable meshes: Application to intracranial aneurysms," in Proc. Med. Image Comput. Comput.-Assisted Intervention, Lect. Notes Comput. Sci., vol. 5247, 2008, pp. 790-797.
26. J. Fox and R. Thomson, "Decision support and disease management: A logic engineering approach," IEEE Trans. Inf. Technol. Biomed., vol. 2, no. 4, pp. 217-228, Dec. 1998.
27. J. Fox, D. Glasspool, D. Grecu, S. Modgil, M. South, and V. Patkar, "Argumentation-based inference and decision-making-A medical perspective," IEEE Intell. Syst., vol. 22, no. 6, pp. 34-41, Nov./Dec. 2007.
28. Arezzo Technical White Paper, InferMed Limited, London, U.K. [Online]. Available: http://www.infermed.com/assets/infermed/docs/
29. Fura. [Online]. Available: http://fura.sourceforge.net/
30. S. Benkner, G. Berti, G. Engelbrecht, J. Fingberg, G. Kohring, S. E. Mid-dleton, and R. Schmidt, "GEMSS: Grid-infrastructure for medical service provision," presented at the HealthGRID, Clermont-Ferrand, France, Jan. 2004.
31. S.Benkner,I. Brandic,G.Engelbrecht, andR. Schmidt, "VGE-A service-oriented grid environment for on-demand supercomputing," presented at the 5th IEEE/ACM Int. Workshop Grid Comput. (Grid), Pittsburgh, PA, Nov. 2004.
32. S. Benkner, G. Engelbrecht, M. Köhler, and A. Wöhrer, "Virtualizing scientific applications and data sources as grid services," in Cyberinfras-tructure Technologies and Applications, J. Cao, Ed. New York: Nova Science Publishers, 2009, ISBN: 978-1-60692-063-3.
33. A. Woehrer, P. Brezany, and A. M. Tjoa, "Novel mediator architectures for Grid information systems," J. Future Gen. Comput. Syst.-Grid Comput.: Theory, Methods Appl., vol. 21, pp. 107-114, Jan. 2005.
34. M. Antonioletti, M. Atkinson, R. Baxter, A. Borley, N. P. Chue Hong, B. Collins, N. Hardman, A. C. Hume, A. Knox, M. Jackson, A. Krause, S. Laws, J. Magowan, N. W. Paton, D. Pearson, T. Sugden, P. Watson, and M. Westhead, "The design and implementation of grid database services in OGSA-DAI," Concurr. Comput.: Pract. Exp., vol. 17, no. 2-4, pp. 357-376, Feb. 2005.
35. M. N. Alpdemir, A. Mukherjee, A. Gounaris, N. W. Paton, P. Watson, A. A. A. Fernandes, and D. J. Fitzgerald, "OGSA-DQP: A service for distributed querying on the grid," in Proc. 9th Int. Conf. Extending Database Technol., LNCS, vol. 2992, 2004, pp. 858-861.
36. G. Wiederhold, "Mediators in the architecture of future information systems," IEEE Comput., vol. 25, no. 3, pp. 38-49, Mar. 1992.
37. K. Kumpf, A. Woehrer, S. Benkner, G. Engelbrecht, and J. Fingberg, "A semantic mediation architecture for a clinical data grid," in Grid Computing for Bioinformatics and Computational Biology. New York: Wiley, 2007.
38. M. Boeker, H. Stenzhorn, K. Kumpf, P. Bijlenga, S. Schulz, and S. Hanser, "The @neurIST ontology of intracranial aneurysms: Providing terminological services for an integrated IT infrastructure," presented at the AMIA 2007 Annu. Symp., Chicago, IL.
39. C. Qu, F. Zimmermann, K. Kumpf, R. Kamuzinzi, V. Ledent, and R. Her-zog, "Semantics-enabled service discovery framework in the SIMDAT pharma grid," IEEE Trans. Inf. Technol. Biomed., vol. 12, no. 2, pp. 182-190, Mar. 2008.
40. B. V. Aduna and Sirma AI Ltd. (2006). User Guide for Sesame. [Online]. Available: http://www.openrdf.org/doc/sesame/users/index.html
41. A. Kiryakov, D. Ognyanov, and D. Manov, "OWLIM-A pragmatic semantic repository for OWL," in Proc. Int. Workshop Scalable Semantic Web Knowl. Base Syst. (SSWS), WISE (LNCS series), LNCS 3807. New York: Springer-Verlag, Nov. 2005, pp. 182-192.
42. T. Mason and R. Lawrence, "Dynamic database integration in a JDBC driver," in Proc. 7th Int. Conf. Enterprise Inf. Syst., 2005, pp. 326-333.
43. Protégé. [Online]. Available: http://protege.stanford.edu
44. Web Ontology Language-Description Logic (OWL-DL). (2004). [Online]. Available: http://www.w3.org/TR/owl-features/
45. RacerPro. [Online]. Available: http://www.racer-systems.com
46. Pellet. [Online]. Available: http://pellet.owldl.com
47. Descriptive Ontology for Linguistic and Cognitive Engineering (DOLCE). [Online]. Available: http://www.loa-cnr.it/DOLCE.html
48. Foundational Model of Anatomy (FMA). [Online]. Available: http://sig.biostr.washington.edu/projects/fm
49. O. Bodenreider, "The Unified Medical Language System (UMLS): Integrating biomedical terminology," Nucl. Acids Res., vol. 32, pp. D267-D270, 2004, [Online]. Available: http://www.nlm.nih.gov/research/umls
50. OASIS WS-Trust Specification. [Online]. Available: http://docs.oasis- open.org/
51. OASIS. Security Assertion Markup Language. [Online]. Available: http://www.oasis-open.org/