ONTOFUSION: Ontology-based integration of genomic and clinical databases

Computers in Biology and Medicine

Volumn 36, Issue 7-8, 2006, Pages 712-730

  Perez Rey D ^a   Maojo, V ^a   Garcia Remesal M ^a   Alonso Calvo, R ^a   Billhardt, H ^b   Martin Sanchez F ^c   Sousa, A ^d  

^a UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^b UNIVERSIDAD REY JUAN CARLOS   (Spain)

^c INSTITUTO DE SALUD CARLOS III   (Spain)

^d UNIVERSITY OF AVEIRO   (Portugal)

Author keywords

Biomedical informatics; Biomedical ontologies; Database integration; Ontologies; Ontology unification

Indexed keywords

AUTOMATION; BIOMEDICAL ENGINEERING; DATABASE SYSTEMS; GENE TRANSFER;

BIOMEDICAL INFORMATICS; BIOMEDICAL ONTOLOGIES; DATABASE INTEGRATION; ONTOLOGIES; ONTOLOGY UNIFICATION;

GENES;

ARTICLE; BIOINFORMATICS; COMPUTER AIDED DESIGN; DATA BASE; GENE MAPPING; INFORMATION PROCESSING; MEDICAL RESEARCH; METHODOLOGY; PRIORITY JOURNAL;

DATA COLLECTION; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; DATABASES, GENETIC; HUMANS; MEDICAL INFORMATICS; USER-COMPUTER INTERFACE;

EID: 33646832869     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2005.02.004     Document Type: Article

References (31)

1. Lindberg C. The Unified Medical Language System (UMLS) of the National Library of Medicine. J. Am. Med. Record Assoc. 61 5 (1990) 40-42
2. The Gene Ontology Consortium, Gene ontology: tool for the unification of biology, Nat. Genet. 25 (2000) 25-29.
3. Annas G.J. Rules for research on human genetic variation-lessons from Iceland. New England J. Med. 342 (2000) 1830-1833
4. P.C. de Groen, A healthy database, IBM creating a system for millions of Mayo clinic patient files, in: Renee Berg Post-Bulletin, Rochester, MN, 2002.
5. Kimball R., and Ross M. The Data Warehouse Toolkit: The Complete Guide to Dimensional Modeling (2002), Wiley, New York
6. A.S. Lopatenko, Information retrieval in current research information systems, Workshop on Knowledge Markup and Semantic Annotation at K-CAP'2001, 2001.
7. Wiederhold G. Mediators in the architecture of future information systems. IEEE Comput. 25 3 (1992) 38-49
8. S. Chawathe, H. Garcia-Molina, J. Hammer, K. Ireland, Y. Papakonstantinou, J. Ullman, J. Widom, The TSIMMIS project: integration of heterogeneous information sources, In: Proceedings of IPSJ Conference, Tokyo, Japan, 1994, pp. 7-18.
9. Arens Y., Hsu C.N., and Knoblock C.A. Query processing in the SIMS information mediator. In: Huns M.N., and Singh M.P. (Eds). Readings in Agents (1998), Morgan Kauffmann, San Francisco, CA
10. Knoblock C.A., Minton S., Ambite J.L., Ashish N., Muslea I., Philpot A.G., and Tejada S. The Ariadne approach to Web-based information integration. Int. J. Cooperative Inform. Syst. 10 1-2 (2001) 145-169
11. Shan M.C., Ahmed R., Davis J., Du W., and Kent W. Pegasus: a heterogeneous information management system. In: Kim W. (Ed). Modern Database Systems, ACM Press, New York (1994), Addison-Wesley, Reading, MA (Chapter 32)
12. M.J. Carey, L.M. Haas, P.M. Schwarz, M. Arya, W.F. Cody, R. Fagin, M. Flickner, A.W. Luniewski, W. Niblack, D. Petkovic, J. Thomas, J.H. Williams, E.L. Wimmers, Towards heterogeneous multimedia information systems, Proceedings of the IEEE Fifth International Workshop on Research Issues in Data Engineering, Taipei, Taiwan, 1995, p. 124.
13. Haas L.M., Schwarz P.M., Kodali P., Kotlar E., Rice J.E., and Swope W.C. Discoverylink: a system for integrated access to life sciences data sources. IBM Syst. J. 40 2 (2001) 489-511
14. Baker P.G., Brass A., Bechhofer S., Goble C., Paton N., and Stevens R. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics 16 2 (2000) 184-186
15. Z.B. Miled, N. Li, G. Kellett, B. Sipes, O. Bukhres, Complex life science multidatabase queries, in: Proceedings of the IEEE, 90, vol. 11, 2002, pp. 1754-1763.
16. Mena E., Illarramendi A., Kashyap V., and Sheth A.P. OBSERVER: an approach for query processing in global information systems based on interoperation between pre-existing ontologies. Distrib. Parallel Databases 8 2 (2000) 223-271
17. Goasdoué F., Lattes V., and Rousset M.C. The use of CARIN language and algorithms for information integration: the PICSEL project. Int. J. Cooperative Inform. Syst. 9 4 (2000) 383-401
18. C.H. Goh, Representing and reasoning about semantic conflicts in heterogeneous information sources, Ph.D. Dissertation, Massachusetts Institute of Technology, 1997.
19. Wache H., Scholz T., Stieghahn H., and König-Ries B. An integration method for the specification of rule-oriented mediators. In: Kambayashi Y., and Takakura H. (Eds). Proceedings of the International Symposium on Database Applications in Non-Traditional Environments (EFIS 99) (1999), Kühlungsborn, Germany
20. H. Stuckenschmidt, F. van Harmelen, D. Fensel, M. Klein, I. Horrocks, Catalogue integration: a case study in ontology-based semantic translation, Technical Report IR-474, Computer Science Department, Vrije Universiteit Amsterdam, 2000.
21. A. Silvescu, J. Reinoso-Castillo, V. Honavar, Ontology-driven information extraction and knowledge acquisition from heterogeneous, distributed, autonomous biological data sources, Proceedings of the IJCAI2001 Workshop on Knowledge Discovery from Heterogeneous, Distributed, Autonomous, Dynamic Data and Knowledge Sources, 2001.
22. Köhler J., Philippi S., and Lange M. SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 19 18 (2003) 2420-2427
23. http://kaon.semanticweb.org/alphaworld/reverse/
24. C. Bizer, D2R MAP-A database to RDF mapping language, in: Proceedings of the International World Wide Web Conference (WWW2003), Budapest, Hungary, 2003.
25. Gruber T.R. A translation approach to portable ontology specifications. Knowledge Acquisition 5 2 (1993) 199-220
26. Davies J., Fensel D., and van Harmelen F. Towards the Semantic Web: Ontology-Driven Knowledge Management (2003), Wiley, London
27. Gómez-Pérez A., Fernández-López M., and Corcho O. Ontological Engineering (2003), Springer, London
28. The Ontology Web Language. http://www.w3.org/2001/sw/WebOnt/
29. Pisanelli D.M., and Gangemi A. If ontology is the solution, what is the problem?. In: Pisanelli D.M. (Ed). Ontologies in Medicine (2004), IOS Press, Amsterdam 1-19
30. Ceusters W., Smith B., Kumar A., and Dhaen C. Mistakes in medical ontologies: where do they come from and how can they be detected?. In: Pisanelli D.M. (Ed). Ontologies in Medicine (2004), IOS Press, Amsterdam 145-163
31. H. Billhardt, J. Crespo, V. Maojo, F. Martín, J. L. Maté, A new method for unifying heterogeneous databases, in: Proceedings of the ISMDA, 2001, pp. 54-61.