A method exploiting syntactic patterns and the UMLS semantics for aligning biomedical ontologies: The case of OBO disease ontologies

International Journal of Medical Informatics

Volumn 76, Issue SUPPL. 3, 2007, Pages

  Marquet, Gwenaëlle ^a   Mosser, Jean ^a   Burgun, Anita ^a  

^a UNIVERSITÉ DE RENNES 1   (France)

Author keywords

Alignment; Lexical methods; Medical ontologies; OBO ontologies; Ontology; Patterns; UMLS

Indexed keywords

DISEASES; MAMMALS; ONTOLOGY; SEMANTICS;

LEXICAL METHODS; MEDICAL ONTOLOGIES; OBO ONTOLOGIES;

BIOMEDICAL ENGINEERING;

ARTICLE; CONCEPT FORMATION; INFORMATION RETRIEVAL; LINGUISTICS; MEDICAL DOCUMENTATION; MEDICAL INFORMATICS; MEDICAL INFORMATION SYSTEM; PRIORITY JOURNAL; SEMANTICS; SYSTEMATIZED NOMENCLATURE OF MEDICINE;

EID: 35448967900     PISSN: 13865056     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijmedinf.2007.03.004     Document Type: Article

References (25)

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., et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25 (2000) 25-29
2. M. Klein, Combining and relating ontologies: an analysis of problems and solutions. In: Workshop on Ontologies and Information Sharing (IJCAI'01), Seattle, USA. Uschold AG-PaMGaHSaM, 2001.
3. Lambrix P., and Tan H. SAMBO-a system for aligning and merging biomedical ontologies. J. Web Semantics (2006) 4
4. Bouquet P., Euzenat J., Franconi L., Serafini L., Stamou G., and Tessaris S. Specification of a common framework for characterizing alignment. Knowl. Web Deliv. 2.2.1 (2004)
5. Euzenat J. An API for ontology alignment. Proceedings of the Third International Semantic Web Conference (ISWC'04). Hiroshima, Japan (2004) 683-697
6. Ogren P.V., Cohen K.B., Acquaah-Mensah G.K., Eberlein J., and Hunter L. The compositional structure of gene ontology terms. Pac. Symp. Biocomp. (2004) 214-225
7. Bodenreider O. The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32 (2004) D267-D270
8. Euzenat J., Bach T.L., Barrasa J., Bouquet P., Bo J.D., Dieng-Kuntz R., Ehrig M., Hauswirth M., Jarrar M., Lara R., et al. State of the art on ontology alignment. Knowl. Web Deliv. 2.2.3 (2004)
9. Cohen W.W., Ravikumar P., and Fienberg S.E. A comparison of string metrics for matching names and records. Proceedings of the KDD-2003 Workshop on Data Cleaning, Record Linkage, and Object Consolidation (2003)
10. Noy N.F., and Musen M. PROMPT: algorithm and tool for automated ontology merging and alignment. Proceedings of the 17th National Conference on Artificial Intelligence (AAAI-2000). Austin, TX, USA (2000) 450-455
11. Noy N.F., and Musen M. The PROMPT suite: interactive tools for ontology merging and mapping. Int. J. Hum.: Comput. Stud. 59 (2003) 983-1024
12. Miller G. WordNet: a lexical database for English. ACM (1995) 39-41
13. Mougin F., Burgun A., and Bodenreider O. Using WordNet to improve the mapping of data elements to UMLS for data sources integration. Proceedings of the AMIA Annual Symposium (2006)
14. Aleksovski Z., Ten Kate W., and Van Harmelen F. Exploiting the structure of background knowledge used in ontology matching. Proceedings of the First International Workshop on Ontology Matching (OM-2006) Collocated with the Fifth International Semantic Web Conference (ISWC-2006). Athens, Georgia, USA (2006)
15. Bouquet P., Serafini L., and Zanobini S. Semantic coordination: a new approach and an application. LNCS, the Second International Semantic Web Conference (ISWO'03), vol. 2870 (2003) 130-145
16. Hearst M.A. Automatic acquisiton of hyponyms from large text corpora. Proceedings of the 14th International Conference on Computational Linguistics (COLING) (1992) 539-545
17. Bodenreider O., Burgun A., and Rindflesch T.C. Assessing the consistency of a biomedical terminology through lexical knowledge. Int. J. Med. Inf. 67 (2002) 85-95
18. Ruge G. Automatic detection of thesaurus relations for information retrieval applications. Lect. Notes Comput. Sci. 1337 (1997) 499-506
19. Grabar N., and Zweigenbaum P. Lexically-based terminology structuring: some inherent limits. Proceedings of the Second International Workshop on Computational Terminology (COLING-02) (2002) 1-7
20. Shvaiko P., Giunchiglia F., Da P., and McGuinness S. Web explanations for semantic heterogeneity discovery. Proceedings of the Second European Semantic Web Conference (ESWC 2005). Heraklion, Greece (2005), Springer
21. Burgun A., and Bodenreider O. An ontology of chemical entities helps identifty dependence relations among gene ontology terms. First International Symposium on Semantic Mining in Biomedicine (SMBM-2005) (2005)
22. Schofield P.N., Bard J.B.L., Booth C., Boniver J., Covelli V., Delvenne P., Ellender M., Engstrom W., Goessner W., Gruenberger M., et al. Pathbase: a database of mutant mouse pathology. Nucleic Acids Res. 32 (2004) D512-D515
23. Smith C.L., Goldsmith C.A.W., and Epping J.T. The mammalian phenotype ontolology as a tool for annotating, analysing and comparing phenotypic information. Genome Biol. 6 (2004) R7
24. McCray A.T., Burgun A., and Bodenreider O. Aggregating UMLS semantic types for reducing conceptual complexity. Medinfo. (2001) 216-220
25. Schmid H. Probabilistic part-of-speech tagging using decision trees. International Conference on New Methods in Language Processing. Manchester, UK (1994)