Query expansion with a medical ontology to improve a multimodal information retrieval system

Computers in Biology and Medicine

Volumn 39, Issue 4, 2009, Pages 396-403

  Diaz Galiano M C ^a   Martín Valdivia, M T ^a   Urena Lopez L A ^a  

^a UNIVERSITY OF JAÉN   (Spain)

Author keywords

Information retrieval system; Knowledge integration; MeSH ontology; Natural language processing; Query expansion

Indexed keywords

BIOMEDICAL INFORMATIONS; BIOMEDICAL RESOURCES; COMPLEX TASKS; DATA SETS; IMPROVE-A; KNOWLEDGE INTEGRATION; MEDICAL DATUM; MEDICAL ONTOLOGIES; MEDICAL TERMS; MESH ONTOLOGY; MULTI MODALS; MULTIMODAL INFORMATION RETRIEVALS; NATURAL LANGUAGE PROCESSING; QUERY EXPANSION; RELEVANCE JUDGMENTS;

COMPUTATIONAL LINGUISTICS; INFORMATION SERVICES; NATURAL LANGUAGE PROCESSING SYSTEMS; ONTOLOGY;

INFORMATION RETRIEVAL;

ARTICLE; COMPUTER; DATA BASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MEDICAL INFORMATICS; MEDICAL INFORMATION SYSTEM; MESH HEADING; NOMENCLATURE; PRIORITY JOURNAL; SEARCH ENGINE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER GRAPHICS; DATABASE MANAGEMENT SYSTEMS; DATABASES, BIBLIOGRAPHIC; DECISION SUPPORT SYSTEMS, CLINICAL; HUMANS; INFORMATICS; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; SOFTWARE; USER-COMPUTER INTERFACE; VOCABULARY, CONTROLLED;

EID: 62849114711     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2009.01.012     Document Type: Article

References (41)

1. Rosset A., Müller H., Martins M., Dfouni N., Vallee J.P., and Ratib O. Casimage project: a digital teaching files authoring environment. Computers in Thoracic Radiology. Journal of Thoracic Imaging. 19 (2004) 103-108
2. Wallis J.W., Miller M.M., Miller T.R., and Vreeland T.H. An Internet-based nuclear medicine teaching file. Journal of Nuclear Medicine 36 (1995) 1520-1527
3. Jones K.N., Kreisle R., Geiss R.W., Holliman J.H., Lill P.H., and Anderson P.G. Group for research in pathology education online resources to facilitate pathology instruction. Archives of Pathology and Laboratory Medicine 126 (2004) 346-350
4. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Research 32 (2004) 267-270
5. S.J. Nelson, M. Schopen, A.G. Savage, J.L. Schulman, N. Arluk, The MeSH translation maintenance system: structure, interface design, and implementation, in: M. Fieschi, et al. (Ed.), Proceedings of the 11th World Congress on Medical Informatics, 2004, pp. 67-69.
6. Aronson A.R. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proceedings of the AMIA Symposium (2001) 17-21
7. Bhogal J., Macfarlane A., and Smith P. A review of ontology based query expansion. Information Processing and Management 43 (2007) 866-886
8. Ide N.C., Loane R.F., and Demner-Fushman D. Essie: a concept-based search engine for structured biomedical text. Journal of the American Medical Informatics Association 14 (2007) 253-263
9. Gruber T.R. Toward principles for the design of ontologies of ontologies used for knowledge sharing. International Journal of Human-Computer Studies 43 (1997) 907-928
10. Miller G.A. WordNet: a lexical database for English. Communications of the ACM 38 (1995) 39-41
11. Rau L.F., Jacobs P.S., and Zernik U. Information extraction and text summarization using linguistic knowledge acquisition. Information Processing and Management 25 (1989) 419-428
12. Martín-Valdivia M.T., Ureña-López L.A., and García-Vega M. The learning vector quantization algorithm applied to automatic text classification tasks. Neural Networks 20 (2007) 748-756
13. Alani H., Sanghee D.E., Weal M.J., Hall W., Lewis P.H., and Shadbolt N.R. Automatic ontology-based knowledge extraction from web documents. Intelligent Systems 18 (2003) 14-21
14. Stevens R., Goble C.A., and Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief Bioinformatics 2000 1 (2000) 398-414
15. Apweiler R., Bairoch A., Wu C.H., et al. UniProt: the universal protein knowledgebase. Nucleic Acids Research 32 (2004) 115-119
16. Bairoch A., Boeckmann B., Ferro S., and Gasteiger E. Swiss-Prot: juggling between evolution and stability. Briefings in Bioinformatics 5 (2004) 39-55
17. S.J. Nelson, D. Johnston, B.L. Humphreys, Relationships in medical subject headings, in: Relationships in the Organization of Knowledge, Kluwer Academic Publishers, New York, 2001, pp. 171-184.
18. Myhre S., Tveit H., Mollestad T., and Laegreid A. Additional Gene Ontology structure for improved biological reasoning. Bioinformatics 22 (2006) 2020-2027
19. Kirsch H., Gaudan S., and Rebholz-Schuhmann D. Distributed modules for text annotation and IE applied to the biomedical domain. International Journal of Medical Informatics 75 (2006) 496-500
20. Chiang J.H., Shin J.W., Liu H.H., and Chin C.L. GeneLibrarian: an effective gene-information summarization and visualization system. Bioinformatics 7 (2006)
21. L. Carr, W. Hall, S. Bechhofer, C. Goble, Conceptual linking: ontology-based open hypermedia, in: Proceedings of the 10th International Conference on World Wide Web, Hong Kong, Hong Kong, May 01-05, 2001, WWW '01, ACM, New York, NY, 2001, pp. 334-342.
22. E. Voorhees, Query expansion using lexical-semantic relations, in: Proceedings of the 17th Annual International ACM SIGIR Conference, 1994, pp. 61-69.
23. M. De-Buenaga-Rodríguez, J.M. Gómez-Hidalgo, B. Díaz-Agudo, Using WordNet to complement training information in text categorization, in: Proceedings of RANLP-97. Second International Conference on Recent Advances in Natural Language Processing, Tzigov Chark, Bulgary, 1997.
24. J. Gonzalo, F. Verdejo, I. Chugur, J. Cigarrán, Indexing with WordNet synsets can improve text retrieval, in: Proceedings of Coling-ACL 98 Workshop on Usage of WordNet for NLP, 1998, pp. 38-44.
25. R. Navigli, P. Velardi, An analysis of ontology-based query expansion strategies, in: Proceedings of Workshop on Adaptive Text Extraction and Mining (ATEM 2003), in the 14th European Conference on Machine Learning (ECML 2003), pp. 42-49.
26. D. Vallet, M. Fernández, P. Castells, An ontology-based information retrieval model, In: Proceeding of Workshop on Adaptative Text Extraction and Mining (ATEM 2003), in the 14th European Conference on Machine Learning (ECML 2003).
27. W. Hersh, S. Price, L. Donohoe, Assessing thesaurus-based query expansion using the UMLS metathesaurus, in: Proceedings of the AMIA Symposium, 2000, pp. 344-348.
28. K. Nilsson, H. Hjelm, H. Oxhammar, SUiS-Cross-language ontology-driven information retrieval in a restricted domain, in: Proceedings of the 15th Nodalida Conference, 2005, pp. 139-145.
29. Yu A.C. Methods in biomedical ontology. Journal of Biomedical Informatics 39 (2006) 252-266
30. C. Peters (Ed.), Cross-Language Information Retrieval and Evaluation Workshop of Cross-Language Evaluation Forum, CLEF 2000, Lisbon, Portugal, September 21-22, 2000, revised papers, Lecture Notes in Computer Science, vol. 2069, 2001, Springer, Berlin, 2001, 387pp.
31. H. Müller, T. Deselaers, T. Lehmann, P. Clough, W. Hersh, Overview of the ImageCLEFmed 2006 medical retrieval and annotation tasks, in: Evaluation of Multilingual and Multi-modal Information Retrieval. Workshop of the Cross-Language Evaluation Forum 2006, Springer Lecture Notes in Computer Science, 2007.
32. M.A. García-Cumbreras, L.A. Ureña-López, F. Martínez-Santiago, J.M. Perea-Ortega, BRUJA System, The University of Jaén at the Spanish Task of QA@CLEF 2006, in: Working Notes of the 2006 CLEF Workshop, 2007.
33. Porter M. An algorithm for suffix stripping. Program 14 (1980) 130-137
34. A. Savage, Changes in MeSH data structure, NLM Technical Bulletin (2000) (313) e2.
35. J.P. Chevallet, J.H. Lim, S. Radhouani, Using ontology dimensions and negative expansion to solve precise queries, in: CLEF Medical Task, Working Notes of the 2005 CLEF Workshop, 2005.
36. D.M. Squire, H. Muller, W. Muller, S. Marchand-Maillet, T. Pun, Design and evaluation of a content-based image retrieval system, in: Design and Management of Multi-media Information Systems: Opportunities and Challenges, 2001, pp. 125-151.
37. C. Buckley, E.M. Voorhees, Evaluating evaluation measure stability, in: Proceedings of the 23rd Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, 2000, pp. 33-40.
38. C. Lacoste, J.P. Chevallet, J.H. Lim, X. Wei, D. Raccoceanu, D.L.T. Hoang, R. Teodorescu, N. Vuillenemot, IPAL knowledge-based medical image retrieval in ImageCLEFmed 2006, in: CLEF Medical Task, Working Notes of the 2006 CLEF Workshop, 2006.
39. M.E. Ruiz, S.B. Southwick, UB at CLEF 2005: medical image retrieval task, in: CLEF Medical Task, Working Notes of the 2005 CLEF Workshop, 2005.
40. M.E. Ruiz, UB at ImageCLEFmed 2006, in: CLEF 2006. Lecture Notes in Computer Science, vol. 4730, Springer, Heidelberg, 2007, pp. 702-705.
41. P. Cheng, B. Chien, H. Ke, W. Yang, NCTU_DBLAB@ImageCLEFmed 2005: medical image retrieval task, in: CLEF Medical Task, Working Notes of the 2005 CLEF Workshop, 2005.