An ontology for semantic integration of life science web databases

International Journal of Cooperative Information Systems

Volumn 12, Issue 2, 2003, Pages 275-294

  Miled, Zina Ben ^a   Webster, Yue W ^a   Liu, Yang ^a   Li, Nianhua ^b  

^a Purdue School of Engineering and Technology   (United States)

^b Indiana University Purdue University Indianapolis   (United States)

Author keywords

Biology; Integration; Interoperability; Ontology; Query translation; Web databases

Indexed keywords

DATA REDUCTION; DATABASE SYSTEMS; SEMANTICS; WORLD WIDE WEB;

WEB DATABASES;

INFORMATION ANALYSIS;

EID: 0037410033     PISSN: 02188430     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218843003000747     Document Type: Article

References (33)

1. M. Rebhan, V. Chalifa-Caspi, J. Prilusky, and D. Lancet, GeneCards: Encyclopedia for genes, proteins and diseases, Weizmann Institute of Science, Bioinformatics Unit and Genome Center, 1997.
2. B. Eckman, Z. Lacroix and L. Raschid, Biological and chemical information integration system, IEEE Int. Symp. Bioinformatics and Bioengineering (BIBE), Bethesda, Maryland, USA, 2001.
3. Y. Arens, C. Y. Chee, C. N. Hsu and C. A. Knoblock, Retrieving and integrating data from multiple information sources, Int. J. Intelligent and Cooperative Information Systems 2, 2 (1993) 127-158.
4. Z. B. Miled, O. Bukhres, Y. Wang, N. Li, M. Baumgartner and B. Sipes, Biological and chemical information integration system, Network Tools and Applications in Biology, Genoa, Italy, May 2001.
5. G. Wiederhold, Mediators in the architecture of future information systems, IEEE Comput. 25 (1992) 38-49.
6. J. L. Ambite, N. Ashish, G. Barish, C. N. Knoblock, S. Minton, P. J. Modi, I. Muslea, A. Philpot and S. Tejada, ARIADNE: A system for constructing mediators for internet sources, SIGMOD Conf., 1998, 561-563.
7. A. Y. Levy, The information manifold approach to data integration, IEEE Intelligent System 13 (1998) 12-16.
8. Z. Ben-Miled, Y. W. Webster, N. Li, O. Bukres, A. K. Nayar, J. Martin and R. Oppelt, BAO, A biological and chemical ontology for information integration, Online J. Bioinformatics 1 (2002) 60-73.
9. A. Bairoch, SWISS-PROT Protein Knowledgebase User Manual, 2001.
10. http://www.ncbi.nlm.nih.gov/ National Center for Biotechnology Information (NCBI).
11. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P. E. Bourne, The protein data bank, Nucleic Acids Research 28 (2000) 235-242.
12. http://www.geneontology.org/, The Gene Ontology Consortium.
13. http://www.isi.edu/isd/ontosaurus.html, University of Southern California's Information Sciences Institute.
14. D. Brill, Loom Reference Manual for Loom version 2.0, www.isi.edu/isd/LOOM/LOOM-HOME.html, 1993.
15. R. M. MacGregor, H. Chalupsky and E. R. Melz, PowerLoom Manual, 1997.
16. The Gene Ontology Consortium, Gene Ontology: Tool for the unification of biology, 2000.
17. P. Karp and S. Paley, Integrated access to metabolic and genomic data, J. Computational Biology 3 (1996) 191-212.
18. P. D. Karp, M. Riley, M. Saier, I. T. Paulsen, S, Paley and A. Pellegrini-Toole, The Ecocyc Database, 2002.
19. P. D. Karp, EcoCyc: The Resource and the Lessons Learned (Kluwer Academic Publishers, 1999) 47-62.
20. R. Stevens, C. A. Goble and S. Bechhofer, Ontology-based knowledge representation for bioinformatics, 2000.
21. D. Fenser, Relating ontology languages and web standards, 2000.
22. P. D. Karp and S. Paley, Representations of metabolic knowledge: Pathways, Proc. Second Int. Conf. Intelligent Systems for Molecular Biology, 1994.
23. C. A. Goble, Supporting web-based biology with ontologies, Proc. Third IEEE Int. Conf. Information Technology Applications in Biomedicine (ITAB00), Arlington, VA, November 2000, 384-390.
24. N. W. Paton, R. Stevens, P. Baker, C. A. Goble, S. Bechhofer, and A. Brass, Query processing in the TAMBIS bioinformatics source integration system, Int. Conf. Scientific and Statistical Databases (SSDBM) (IEEE Press, 1999) 138-147.
25. S. Bechhofer, R. Stevens, G. Ng, A. Jacoby and C. A. Goble, Guiding the user: An ontology driven interface, UIDIS, Workshop on User Interfaces to Data Intensive Systems, Edinburgh, IEEE Computer Society, 1999, 158-161.
26. T. Etzold and P. Argos, SRS - An indexing and retrieval tool for flat file libraries, Computer Applications in the Biosciences 9, 1, 1993.
27. L. Hass, P. Kodali, P. Schwarz and W. Swope, Integrating life science data - With a little garlic, Proc. IEEE Int. Symp. Bioinformatics and Biomedical Engineering, 2000, 5-12.
28. A. Bouguettaya, Ontology and databases, A Special Issue of Distributed and Parallel Databases, An International Journal 7, 1, January 1999.
29. M. Ouzzani, B. Benatallah and A. Bouguettaya, Ontological approach for information discovery in internet databases, Distributed and Parallel Databases, An International Journal 8, 3, 2000.
30. A. Y. Levy, A. Rajarman and J. J. Ordill, Quering heterogeneous information sources using source descriptions, VLDB 1996, 1996.
31. E. Mena, V. Kashyap, A. Illarramendi and A. Sheth, Domain specific ontologies for semantic information brokering on the global information infrastructure, Int. Conf. Formal Ontology in Information Systems 1998, Treno, Italy, June 1998.
32. S. Decker, M. Erdmann, D. Fensel and R. Studer, Ontobroker: Ontology based access to distributed and semi-structured information, Semantic Issues in Multimedia Systems, Proc. DS'8, Boston, 1999, 351-369.
33. Y. Arene, C. A. Knoblock and W. M. Shen, Query reformulation for dynamic information for dynamic information integration, Int. J. Intelligent and Cooperative Information System, Special Issue on Intelligent Information Integration 6, 2/3 (1996) 99-130.