Abstract
In this paper we investigate the problem of enriching an existing biological concept ontology into a fuzzy relational ontology structure using generic biological relations and their strengths mined from tagged biological text documents. Though biological relations in a text are defined between a pair of entities, the entities are usually tagged by their concept names in a tagged corpus. Since the tags themselves are related taxonomically, as given in the ontology, the mined relations have to be properly characterized before entering them into the ontology. We have proposed a mechanism to generalize each relation to be defined at the most appropriate level of specificity, before it can be added to the ontology. Since the mined relations have varying degrees of associations with various biological concepts, an appropriate fuzzy membership generation mechanism is proposed to fuzzify the strengths of the relations. Extensive experimentation has been conducted over the entire GENIA corpus and the results of enhancing the GENIA ontology are presented in the paper.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Abulaish, M., Dey, L.: An Ontology-Based Pattern Mining System for Extracting Information from Biological Texts. In: Ślęzak, D., Yao, J., Peters, J.F., Ziarko, W.P., Hu, X. (eds.) RSFDGrC 2005. LNCS (LNAI), vol. 3642, pp. 420–429. Springer, Heidelberg (2005)
Ciaramita, M., Gangemi, A., Ratsch, E., Saric, J., Rojas, I.: Unsupervised Learning of Semantic Relations between Concepts of a Molecular Biology Ontology. In: Proceedings of the 19th Int. Joint Conf. on Artificial Intelligence, pp. 659–664 (2005)
Kim, J.-D., Ohta, T., Tateisi, Y., Tsujii, J.: GENIA Corpus – A Semantically Annotated Corpus for Bio-Textmining. Bioinformatics 19(suppl. 1), i180–i182 (2003)
Ono, T., Hishigaki, H., Tanigami, A., Takagi, T.: Automated Extraction of Information on Protein-Protein Interactions from the Biological Literature. Bioinformatics 17(2), 155–161 (2001)
Rinaldi, F., Scheider, G., Andronis, C., Persidis, A., Konstani, O.: Mining Relations in the GENIA Corpus. In: Proceedings of the 2nd European Workshop on Data Mining and Text Mining for Bioinformatics, Pisa, Italy (2004)
Sekimizu, T., Park, H.S., Tsujii, J.: Identifying the Interaction between Genes and Genes Products Based on Frequently Seen Verbs in Medline Abstract. Genome Informatics 9, 62–71 (1998)
Thomas, J., Milward, D., Ouzounis, C., Pulman, S., Carroll, M.: Automatic Extraction of Protein Interactions from Scientific Abstracts. In: Pacific Symposium on Biocomputing, pp. 538–549 (2000)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Dey, L., Abulaish, M. (2006). Enhancing a Biological Concept Ontology to Fuzzy Relational Ontology with Relations Mined from Text. In: Greco, S., et al. Rough Sets and Current Trends in Computing. RSCTC 2006. Lecture Notes in Computer Science(), vol 4259. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11908029_55
Download citation
DOI: https://doi.org/10.1007/11908029_55
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-47693-1
Online ISBN: 978-3-540-49842-1
eBook Packages: Computer ScienceComputer Science (R0)