Abstract
This paper describes the increasing role of ontologies in the context of Grid computing for obtaining, comparing and analyzing distributed heterogeneous scientific data. In the communities of people committed to a common goal, the management of resources and services becomes very important. We chose the application domain of human disease research and control. A characteristic of the domain is that trusted databases exist but their schemas are often poorly or not documented. The network of biomedical databases forms a loose federation of autonomous, distributed, heterogeneous data repositories ripe for information integration. Grid services will provide a dynamic way to use resources in such a large distributed scientific environment while the use of ontology enables the system to carryout reasoning at 3 levels: a) available information in all Bio-Databases (Grid nodes) worldwide, b) reasoning about the retrievable information from each node, c) reasoning about the retrieved information and presenting it in a meaningful format for users. We adopted the ontology design methodology of DOGMA and developed Generic Human Disease Ontology (GenDO) that contains common general information regarding human diseases. The information is represented in 4 “dimensions”: (a) disease types, (b) causes (c) symptoms and (d) treatments. We illustrate how this GenDO helps to produce Specific Human Disease Ontologies (SpeDO) on request. We show how the combination of two different but complementary techniques, namely Grid computing and ontology, results in a dynamic and intelligent information system. The two approaches together, being complementary, enable the system as a whole.
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References
Altman, R., Bada, M., Chai, X.J., Whirl Carillo, M., Chen, R.O., Abernethy, N.F.: Riboweb: An Ontology Based System for Collaborative Molecular Biology. IEEE Intelligent Systems 14(5), 68–76 (1999)
Barrett, T.B., Hauger, R.L., Kennedy, J.L., Sadovnick, A.D., Remick, R.A., Keck, P.E., McElroy, S.L., Alexander, M., Shaw, S.H., Kelsoe, J.R.: Evidence that a single nucleotide polymorphism in the promoter of the G protein receptor kinase 3 gene is associated with bipolar disorder. Molecular Psychiatry 8, 546–557 (2003)
Bodenreider, O.: The Unified Medical language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32(1), 267–270 (2004)
Craddock, N., Jones, I.: Molecular genetics of bipolar disorder. The British Journal of Psychiatry 178(41), 128–133 (2001)
Deray, T., Verheyden, P.: Towards a semantic integration of medical relational databases by using ontologies: a case study. In: Raś, Z.W., Skowron, A. (eds.) ISMIS 1999. LNCS, vol. 1609, pp. 30–45. Springer, Heidelberg (1999)
Gene Ontology Consortium, Gene Ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2002)
Gruber, T.R.: A Translation Approach to Portable Ontology Specifications. Knowledge Acquisition 5(2), 199–220 (1993)
Halpin, T.: Information modeling and relational databases, 3rd edn. Morgan-Kaufmann, San Francisco (2001)
Hattori, E., Liu, C., Badner, J.A., Bonner, T.I., Christian, S.L., Maheshwari, M., Detera-Wadleigh, S.D., Gibbs, R.A., Gershon, E.S.: Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with bipolar disorder in two independent pedigree series. American Journal of Human Genetics 72(5), 1131–1140 (2003)
Liu, J., Juo, S.H., Dewan, A., Grunn, A., Tong, X., Brito, M., Park, N., Loth, J.E., Kanyas, K., Lerer, B., Endicott, J., Penchaszadeh, G., Knowles, J.A., Ott, J., Gilliam, T.C., Baron, M.: Evidence for a putative bipolar disorder locus on 2p13-16 and other potential loci on 4q31, 7q34, 8q13, 9q31, 10q21-24, 13q32, 14q21 and 17q11-12. Mol. Psychiatry 8(3), 333–342 (2003)
Meersman, R.: Semantic Ontology Tools in Information System Design. In: Raś, Z.W., Skowron, A. (eds.) ISMIS 1999. LNCS, vol. 1609, pp. 30–45. Springer, Heidelberg (1999)
Frank, M.: The importance of formal ontologies: A case study in occupational health. In: Proceedings of the OES-SEO 2001 Rome Workshop. Luiss Publications (2001)
Goble, C.: The Grid Needs you! Enlist Now. In: Meersman, R., Tari, Z., et al. (eds.) CoopIS 2002, DOA 2002, and ODBASE 2002. LNCS, vol. 2519, pp. 589–600. Springer, Heidelberg (2002)
Spyns, P., Meersman, R., Jarrar, M.: Data modelling versus Ontology engineering. SIGMOD Record 31(4), 12–17 (2002)
Stevens, R., Baker, P., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., Brass, A.: TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. Bioinformatics 16(2), 184–186 (2002)
Stevens, R.D., Robinson, A.J., Goble, C.A.: MyGrid: personalised bioinformatics on the information grid. Bioinformatics 19, 302–304 (2003)
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Hadzic, M., Chang, E. (2005). Grid Services Complemented by Domain Ontology Supporting Biomedical Community. In: Herrero, P., Pérez, M.S., Robles, V. (eds) Scientific Applications of Grid Computing. SAG 2004. Lecture Notes in Computer Science, vol 3458. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11423287_8
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DOI: https://doi.org/10.1007/11423287_8
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