RSS-Feed abonnieren
DOI: 10.1055/s-0038-1633938
Grid Requirements for the Integration of Biomedical Information Resources for Health Applications
Publikationsverlauf
Publikationsdatum:
05. Februar 2018 (online)
Summary
Objectives: The goal of this paper is to identify how Grid technology can be applied for the development and deployment of integration systems, bringing together distributed and heterogeneous biomedical information sources for medical applications.
Methods: The integration of new genetic and medical knowledge in clinical workflows requires the development of new paradigms for information management in which the ability to access and relate disparate data sources is essential. We adopt a requirements perspective based on the user needs we have identified in the development of the INFOGENMED system to assess current Grid technology against those requirements.
Results: The gap between Grid features and distributed biomedical information integration needs is characterized. Results from prospective studies are also reported.
Conclusions: Grid infrastructures offer advanced features for the deployment of collaborative computational environments across virtual organizations. New Grid developments are in line with the problem of multiple site information integration. From the INFOGENMED point of view, Grid infrastructures need to evolve to implement structured data access services and semantic content description and discovery.
-
References
- 1 Bayat A. Science, medicine, and the future: Bioinformatics. British Medical Journal (BMJ) 2002; 324 7344 1018-22.
- 2 Human Genome Project Information (online), available at. http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml [Accessed on 2004–04–14].:
- 3 Collins FS, McKusick VA. Implications of the Human Genome Project for medical science. JAMA 2001; 285 (05) 540-4.
- 4 Martin-Sanchez F, Maojo V, Lopez-Campos G. Integrating Genomics into Health Information Systems. Methods Inf Med 2002; 41 (01) 25-30.
- 5 Sarachan BD, Simmons MK, Subramanian P, Temkin JM. Combining Medical Informatics and Bioinformatics toward Tools for Personalized Medicine. Methods Inf Med 2003; 42 (02) 111-5.
- 6 Altman RB. Bioinformatics in Support of Molecular Medicine. In AMIA Annual Symposium. 1998. Orlando: 53-61.
- 7 Martin-Sanchez F, Iakovidis I, Norager S, Maojo V, de Groen P, Van der Lei J, Jones T, Abraham- Fuchs K, Apweiler R, Babic A. Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care. Journal of Biomedical Informatics 2004; 37 (01) 30-42.
- 8 Mitchell JA, McCray AT, Bodenreider O. From phenotype to genotype: issues in navigating the available information resources. Methods Inf Med 2003; 42 (05) 557-63.
- 9 Foster I, Kesselman C, Tuecke S. The Anatomy of the Grid: Enabling scalable virtual organizations. Internation Journal of High Performance Computing Applications 2001; 15 (03) 200-22.
- 10 Maojo V, Iakovidis I, Martin-Sanchez F, Crespo J, Kulikowski C. Medical Informatics and Bioinformatics: European Efforts to Facilitate Synergy. Journal of Biomedical Informatics 2001; 34 (06) 423-7.
- 11 Pereira AS, Maojo V, Martin-Sanchez F, Babic A, Goes S. The INFOGENMED Project. In: Int Congress on Biological and Medical Engineering (ICMBE). Singapore: 2002
- 12 Gupta A Ludäscher, Martone ME. Registering Scientific Information Sources for Semantic Mediation. In. Spaccapietra S, March ST, Kambayashi Y. (eds). Lecture Notes in Computer Science. Springer-Verlag: 2002. 2503 182-98.
- 13 Parent C, Spaccapietra S. Issues and Approaches of Database Integration. Communications of the ACM 1998; 41 (05) 166-78.
- 14 Foster I, Kesselman C, Nick J, Tuecke S. The Physiology of the Grid: An Open Grid Services Architecture for Distributed Systems Integration [online]. Global Grid Forum 2002. Available at. http://www.globus.org/research/papers/ogsa.pdf [Accessed on 2003 10.-09].
- 15 Berti G, Benkner S, Fenner JWJ, Fingberg J Lonsdale, Middleton SE, Surridge M. Medical Simulation Services via the Grid. In 1st European Health GRID Conference. Lyon, France: 2002: 252-63.
- 16 The Biomedical Informatics Research Network [online], available at. http://www.nbirn.net/ [Accessed on 2003 11.-14].
- 17 BioGRID [online], available at. http://biogrid.icm.edu.pl [Accessed on 2003 11-14].
- 18 Stevens RD, Robinson Goble CA. myGrid: personalised bioinformatics on the information grid. Bioinformatics 2003; 19 (Suppl. 01) Supp i302-i304.
- 19 Sloot PMA, van-Albada GD, Zudilova EV, Heinzlreiter P, Kranzlmüller D, Rosmanith H, Volkert J. Grid-based Interactive Visualisation of Medical Images. In: 1st European Health Grid Conference. Lyon, France: 2003: 55-66.
- 20 Hastings S, Gray M, Kurc T, Catalyurek U, Gingrich T, Young D, Saltz S. Grid Support for Collaborative Clinical and Biomedical Research Studies. Arch Pathol Lab Med, July 2003; 127 789-813.
- 21 CLEF Project [online], available at. http://www.clinical-escience.org/ [Accessed on 2004 02.-25].
- 22 Amendolia SR, Brady M, McClatchey R, Mulet- Parada M, Odeh M, Solomonides T. MammoGrid: Large-Scale Distributed Mammogram Analysis. In: Medical Informatics Europe (MIE’2003). France: St Malo; 2003: 194-99.
- 23 Open Grid Services Infrastructure [online], available at. http://www.ggf.org/ogsi-wg/ [Accessed on 2003-10-09].
- 24 Open Grid Services Architecture Data Access and Integration (OGSA DAI) [online], available at. http://www.cs.man.ac.uk/grid-db/ [Accessed on 2003-11-14].
- 25 Malaika S, Hain D. Accessing DB2 Universal Database Using the Globus Toolkitand OGSADAI [online] (2003). IBM Silicon Valley Lab, available at. http://www7b.software.ibm.com/dmdd/library/techarticle/0308malaika/0308malaika.html [Accessed on 2003-11-14].
- 26 Alpdemir MN, Mukherjee A, Gounaris A, Paton NW, Watson P, Fernandes AAA, Smith J. OGSADQP: A Service-Based Distributed Query Processor for the Grid. In 2nd e-Science All Hands Meeting. Nottingham, UK: 2003
- 27 Rector AL, Solomon WD, Nowlan WA, Rush TW, Zanstra Claassen WM. A Terminology Server For Medical Language and Medical Information Systems. Methods Inf Med 1995; 34 1-2 147-57.
- 28 De-Route D, Jennings N, Shadbolt N. The semantic grid: A future e-science infrastructure. In: Grid Computing: Making the Global Infrastructure a Reality. Berman F, Hey A, Fox G. (eds) John Wiley & Sons; 2003: 437-70.
- 29 Breton V, Medina R, Montagnat J. DataGrid, Prototype of a Biomedical Grid. Methods Inf Med 2003; 42 (02) 143-7.
- 30 Ferreira L. Introduction to Grid Computing with Globus [online] (2003). Available at. http://publib-b.boulder.ibm.com/Redbooks.nsf/RedbookAbstracts/sg246895.html?Open [Accessed on 2003-10-09].
- 31 UNICOREpro [online], available at. http://www.pallas.com/e/products/unicore-pro/index.htm [Accessed on 2003-11-14].
- 32 The DataGrid Project [online] (2003). Available at. http://eu-datagrid.web.cern.ch/eu-datagrid/ [Accessed on 2003-11-14].
- 33 IEETA (2003) Prospective study on Grid technology [online], available at. http://www.infogenmed.net/pub/proj-library/lib-index.html [Accessed on 2003-11-14].
- 34 INBIOMED – Red Temática de Investigación Cooperativa de Informática Biomédica [online], available at. http://www.inbiomed.retics.net [Accessed on 2003-10-09].
- 35 Grid Systems [online], available at. http://www.gridsystems.com [Accessed on 2003-10-09].