A corpus-driven approach for design, evolution and alignment of ontologies

Proceedings - Winter Simulation Conference

Volumn , Issue , 2006, Pages 1595-1602

  Wächter, Thomas ^a   Wobst, André ^a   Schroeder, Michael ^a   Tan, He ^b   Lambrix, Patrick ^b  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b LINKÖPING UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

SOFTWARE AGENTS;

DATA SOURCING; EVOLUTION (CO); TEXT CORPORA;

ONTOLOGY;

EID: 46149106171     PISSN: 08917736     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/WSC.2006.322932     Document Type: Conference Paper

References (29)

1. BioPAX, Biological Pathway Exchange. 〈http://www.biopax.org/〉.
2. Chen, B., H. Tan, and P. Lambrix. 2006. Structure-based filtering for ontology alignment. In Proceedings of the IEEE WETICE Workshop on Semantic Technologies in Collaborative Applications.
3. Cilibrasi, R., and P. Vitanyi. 2004. Automatic meaning discovery using Google, 〈http://xxx.lanl.gov/abs/cs.CL/0412098〉.
4. Doms, A., and M. Schroeder. 2005. GoPubMed: exploring PubMed with the gene ontology. Nucleic Acids Research 33:W783-W786.
5. Enzyme Nomenclature. Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). 〈http://www.chem.qmul.ac. uk/iubmb/enzyme/〉.
6. Faure, D., and T. Poibeau. 2000. First experiments of using semantic knowledge learned by ASIUM for information extraction task using INTEX. In Proceedings of the ECAI Workshop on Ontology Learning.
7. The Gene Ontology Consortium. 2000. Gene ontology: tool for the unification of biology. Nature Genetics 25(1):25-29. 〈http://www. geneontology.org/〉.
8. Gomez-Perez, A., and D. Manzano-Macho, editors. 2003. A survey of ontology learning methods and techniques. Onto Web Deliverable 1.5.
9. Hermjakob, H., L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, et al. 2004. The HUPO PSI's Molecular Interaction format - a community standard for the representation of protein interaction data. Nature Biotechnology 22(2):177-183.
10. Hucka, M., A. Finney, H. Sauro, H. Bolouri, J. Doyle, H. Kitano, and the rest of the SBML Forum. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524-531.
11. Lacy, L., and W. Gerber. 2004. Potential modeling and simulation applications of the web ontology language OWL. In Proceedings of the Winter Simulation Conference, 265-270.
12. Lambrix, P. 2004. Ontologies in bioinformatics and systems biology. In Artificial Intelligence Methods and Tools for Systems Biology, ed. Dubitzky and Azuaje, 129-146. Springer.
13. Lambrix, P. 2005. Towards a semantic web for bioinformatics using ontology-based annotation. In Proceedings of the 14th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises, 3-7. Invited talk.
14. Lambrix, P., and H. Tan. 2006. SAMBO - a system for aligning and merging bio-ontologies. Journal of Web Semantics, Special issue on Semantic Web for the Life Sciences 4(3).
15. Lambrix, P., H. Tan, V Jakonienė, and L. Strömbäck. 2006. Biological ontologies. In Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, ed. Baker and Cheung, to appear. Springer.
16. Li, M., X. Chen, X. Li, B. Ma, and B. Vitanyi. 2003. The similarity metric. In Proceedings of the 14th Annual ACM-SIAM Symposium on Discrete Algorithms, 863-872.
17. Maedche, A., and S. Staab. 2000. Discovering conceptual relations from text. In Proceedings of the 14th European Conference on Artificial Intelligence, 21-25.
18. Morin, E. 1999. Automatic acquisition of semantic relations between terms from technical corpora. In Proceedings of the Fifth International Congress on Terminology and Knowledge Engineering, 268-278.
19. Neches, R., R. Fikes, T. Finin, T. Gruber, T. Senator, and W. Swartout. 1991. Enabling technology for knowledge engineering. AI Magazine 12(3):26-56.
20. Ogren, P. V., K. B. Cohen, G. K. Acquaah-Mensah, J. Eberlein, and L. Hunter. 2004. The compositional structure of gene ontology terms. In Proceedings of the Pacific Symposium on Biocomputing, 9:214-225.
21. Orchard, S., L. Montecchi-Palazzi, H. Hermjakob, and R. Apweiler. 2005. The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. In Proceedings of the Pacific Symposium on Biocomputing, 10:186-196.
22. PubMed Central. 〈http://www.pubmedcentral.nih.gov/〉.
23. REWERSE. EU Network of Excellence on Reasoning on the Web with Rules and Semantics, Working group A2. 〈http://rewerse.net/〉.
24. SBML. Systems Biology Markup Language. 〈http://sbml.org〉.
25. Strömbäck, L., D. Hall, and P. Lambrix. 2006a. A review of standards for data exchange within systems biology. Proteomics. Invited contribution, to appear.
26. Strömbäck, L., V. Jakoniené, H. Tan, and P. Lambrix. 2006b. Representing, storing and accessing molecular interaction data: a review of models and tools. Briefings in Bioinformatics. Invited contribution, to appear.
27. Strömbäck, L., and P. Lambrix. 2005 Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX, Bioinformatics 21(24):4401-4407.
28. Tan, H., V. Jakonienė, P. Lambrix, J. Aberg, and N. Shahmehri. 2006. Alignment of biomedical ontologies using life science literature. In Proceedings of the International Workshop on Knowledge Discovery in Life Science Literature, LNBI 3886, 1-17.
29. Takai-Igarashi, T., Y. Nadaoka, and T. Kaminuma. 1998. A database for cell signaling networks. Journal of Computational Biology 5(4):747-754.