An ontology-based approach to support text mining and information retrieval in the biological domain

Journal of Universal Computer Science

Volumn 13, Issue 12, 2007, Pages 1881-1907

  Khelif, Khaled ^a   Dieng Kuntz, Rose ^a   Barbry, Pascal ^b  

^a INRIA   (France)

^b INSTITUT DE PHARMACOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Corese; Life science; NLP; Ontologies; Semantic annotation; Semantic web

Indexed keywords

EID: 40849100338     PISSN: 0958695X     EISSN: 09486968     Source Type: Journal    
DOI: None     Document Type: Article

References (38)

1. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.. Nature Genet, 25, 25-29, (2000).
2. Bourigault D. and Fahre C., Approche linguistique pour l'analyse syntaxique de corpus. Cahiers de grammaire, Vol.25, 131-151, (2000).
3. Briscoe E. and Carroll J., Robust accurate statistical annotation of general text. In Proceedings of the Third IC LR E, Las Palmas, Gran Canaria. 1499-1504 (2002).
4. Clark J., XSL Transformations (XSLT) Version. 1.0, W3C Recommendation, http://www.w3.org/TR/xslt, (1999).
5. Corby O., Dieng-Kuntz R. and Faron-Zucker C., Querying the Semantic Web with the CORESE engine. In R. Lopez de Mantaras and L. Saitta eds, Proceedings of the 16th European Conference on Artificial Intelligence (ECAI'2004), Valencia, Spain, IOS Press, p.705-709, (2004).
6. Corby O., Dieng-Kuntz R., Gandon F. and Faron-Zucker C., Searching the Semantic Web: Approximate Query Processing Based on Ontologies. In IEEE Intelligent Systems Vol.21 No.1 pp. 20-27, (2006).
7. Cunningham H., Maynard D., Bontcheva K. and Tablan V., GATE: A Framework and Graphical Development Environment for Robust NLP Tools and Applications. ACL'02, (2002).
8. Gaizauskas R., Demetriou G., Artymiuk P., and Willett P., Bioinformatics applications of information extraction from journal articles. Journal of Bioinformatics, 19(1), pp. 135-143, (2003).
9. Gandon F., Lo M., Corby O. and Dieng-Kuntz R., Managing enterprise applications as dynamic resources in corporate semantic webs: an application scenario for semantic web services. In W3C Workshop on Frameworks for Semantics in Web Services, http://www.w3.org/2005/04/FSWS/, (2005).
10. Golebiowska J., Dieng-Kuntz R., Corby O. and Mousseau D., Building and Exploiting Ontologies for an Automobile Project Memory. Proc. of the First International Conference on Knowledge Capture (K-CAP), Victoria, October 23-24, (2001).
11. Ghoula, N., Khelif, K., and Dieng-Kuntz, R., Supporting patent mining by using ontology-based semantic annotations. In IEEE/WIC/ACM International Conference on Web Intelligence, Silicon Valley, USA (2007).
12. Handschuh S., Staab S. and Ciravegna F., S-CREAM - Semiautomatic CREAtion of Metadata. In Gómez-Pérez, A., and Benjamins R. (eds.), Knowledge Engineering and Management: Ontologies and the Semantic Web, 13th International Conference, EKAW 2002, Siguenza, Spain Springer Verlag, LNAI2473, 358-372 (2002).
13. Hoang H.H. and Tjoa A., The State of the Art of Ontology-based Query Systems: A Comparison of Existing Approaches, In Proc. of ICOCI06, (2006).
14. Humphreys B. and Lindberg D., The UMLS project: making the conceptual connection between users and the information they need. Bulletin of the Medical Library Association 81(2): 170, (1993).
15. Kashyap V., Borgida A., Representing the UMLS Semantic Network using OWL: (Or "What's in a Semantic Web link?"). In ISWC'2003. Heidelberg: Springer-Verlag; 1-16, (2003).
16. Khelif K., Dieng-Kuntz R., Barbry P., Semantic web technologies for interpreting DNA microarray analyses: the MEAT system. Proc. of WISE'05, 20-22/11 New York, (2005).
17. Khelif K., Web sémantique et mémoire d'expériences pour l'analyse du transcriptome. Phd thesis, Nice Sophia Antipolis University, (2006).
18. Lassila O. and Swick R., W3C Resource Description framework (RDF) Model and Syntax Specification, http://www.w3.org/TR/REC-rdf-syntax/, (2001).
19. Lomax J. and McCray A., Mapping the Gene Ontology into the Unified Medical Language System. Comparative and Functional Genomics, 5:354-361, (2004).
20. McBride B., "RDF Vocabulary Description Language 1.0: RDF Schema", W3C Recommendation, http://www.w3.org/TR/rdf-schema/, (2004).
21. McCray A., An upper level ontology for the biomedical domain. Comp Functional Genomics; 4: 80-84, (2003).
22. McGuinness D.L. and Van Harmelen F., OWL Web Ontology Language Overview, http://www.w3.org/TR/owl.-features/, (2004).
23. Mrabet, Y., Khelif, K., and Dieng-Kuntz, R., Recognising professional-activity groups and web usage mining for web browsing personalisation. In IEEE/WIC/ACM International Conference on Web Intelligence, Silicon Valley, USA (2007).
24. Muller H.M. and Kenny E.E. and Sternberg P.W., Textpresso: an ontology-based information retrieval and extraction system for biological literature PLoS Biol, 2, E309, (2004).
25. Nédellec C., Bibliographical Information Extraction in Genomics. IEEE Intelligent Systems & their Applications, N. Shadbolt (ed.), Trends & Controversies - Mining Information for Functional Genomics, 76-80, May-June (2002).
26. Ohlbach H.J. and Schaffen S., eds Workshop on Principles and Practice of Semantic Web Reasoning at the 20th ICLP, St Malo, France, (2004).
27. Popov B., Kiryakov A., Ognyanoff D., Manov D. and Kirilov A., KIM - a semantic annotation platform for information extraction and retrieval. Natural Language Engineering, 10, Issues 3-4, 375-392, (2004).
28. Rector A., Rogers J.E. and Pole P., The GALEN High Level Ontology. Fourteenth International Congress of the European Federation for Medical Informatics, MIE96, Copenhagen, Denmark, (1996).
29. Rzhetsky A., Iossifov I., Koike T., Krauthammer M., Kra P., GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inf 37: 43-53, (2004).
30. Séguéla P. and Aussenac-Gilles N., Extraction de relations sémantiques entre termes et enrichissement de modèles du domaine. In Proc. of IC'99, Paris, 79-88, (1999).
31. Schmid H., Probabilistic part-of-speech tagging using decision trees. In proceedings of International Conference on New Methods in Language Processing. Manchester, (1994).
32. Shatkay H., Edwards S., and Boguski M., Information Retrieval Meets Gene Analysis. IEEE Intelligent Systems 17, 2, 45-53, (2002).
33. Shatkay H. and Feldman R., Mining the biomedical literature in the genomic era: an overview, Journal of Computational Biology, 10, 821-855, (2003).
34. Staab S., Mining Information for Functional Genomics. IEEE Intelligent Systems & their Applications, March-April, 66-80, (2002).
35. Uren V., Cimiano P., Iria J., Handschuh S., Vargas-Vera M., Motta E. et Ciravegna F., Semantic annotation for knowledge management: Requirements and a survey of the state of the art. In Web Semantics, Volume 4, Issue 1, 14-28, 2006.
36. Vargas-Vera M., Motta E., Domingue J., Lanzoni M., Stutt A. and Ciravegna F., MnM: Ontology Driven Semi-Automatic and Automatic Support for Semantic Markup, In Gómez-Pérez A. and Benjamins R. eds, Knowledge Engineering and Management: Ontologies and the Semantic Web, 13th International Conference, EKAW 2002, Siguenza, Spain, Springer Verlag LNAI2473, 379-391, (2002).
37. Summary Report - W3C Workshop on Semantic Web for Life Sciences. http://www.w3.org/2004/10/swls-workshop-report.html, (2004).
38. Zweigenbaum P., MENELAS: an access system for medical records using natural language. Comput Methods Programs Biomed. Oct;45(1-2):117-20, (1994).