Abstract
Construction and maintenance of signaling pathway is a time-consuming and labor-intensive task. In addition, integration of various pathways is also ineffective since several markup languages are used to express pathways. To overcome these limitation, automatic pathway construction and extension with a standard format may provide a solution. The proposed approach has constructed a gold standard corpus that describes the signaling pathways, and it has been used to training and evaluating the automatic pathway construction and extension. Moreover, a standard format to express the signaling pathways has been developed and has been used to express the previous major 10 signaling pathways. An effective visualization tool has been also developed for the standardized format as well. The visualization tool can help to construct pathways and extend the current pathways using all articles in PubMed.
Chapter PDF
Similar content being viewed by others
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
References
Ananiadou, S., Kell, D.B., Tsujii, J.: Text mining and its potential applications in systems biology. Trends Biotechnology 24, 571–579 (2006)
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M.: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research 40, D109–D114 (2012) (Database issue)
Joshi-Tope, G., Gillespie, M., Vastrik, I., DEustachio, P., Schmidt, E., Bono, B., Jassal, B., Gopinath, G.R., Wu, G.R., Matthews, L., Lewis, S., Birney, E., Stein, L.: Reactome: a knowledgebase of biological pathways. Nucleic Acids Research 33, D428–D432 (2005) (Database issue)
Karp, P.D., Ouzounis, C.A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V., López-Bigas, N.: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 33(19), 6083–6089 (2005)
Song, S.-K., Choi, Y.-S., Chun, H.-W., Jeong, C.-H., Choi, S.-P., Sung, W.-K.: Multi-words Terminology Recognition Using Web Search. In: Kim, T.-H., Adeli, H., Ma, J., Fang, W.-C., Kang, B.-H., Park, B., Sandnes, F.E., Lee, K.C. (eds.) UNESST 2011. CCIS, vol. 264, pp. 233–238. Springer, Heidelberg (2011)
Chun, H.-W., Jeong, C.-H., Song, S.-K., Choi, Y.-S., Choi, S.-P., Sung, W.-K.: Relation Extraction Based on Composite Kernel Combining Pattern Similarity of Predicate-Argument Structure. In: Kim, T.-h., Adeli, H., Ma, J., Fang, W.-c., Kang, B.-H., Park, B., Sandnes, F.E., Lee, K.C. (eds.) UNESST 2011. CCIS, vol. 264, pp. 269–273. Springer, Heidelberg (2011)
Choi, S.P., Myaeng, S.H.: Simplicity is better: revisiting single kernel PPI extraction. In: Proceedings of the 23rd International Conference on Computational Linguistics, pp. 206–214 (2010)
Chun, H.-W., Jeong, C.-H., Song, S.-K., Choi, Y.-S., Jeong, D.-H., Choi, S.-P., Sung, W.-K.: Smart Searching System for Virtual Science Brain. In: Zhong, N., Callaghan, V., Ghorbani, A.A., Hu, B. (eds.) AMT 2011. LNCS, vol. 6890, pp. 324–332. Springer, Heidelberg (2011)
Miyao, Y., Ohta, T., Masuda, K., Tsuruoka, Y., Yoshida, K., Ninomiya, T., Tsujii, J.: Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. In: Proceedings of COLING-ACL, pp. 1017–1024 (2006)
Tsuruoka, Y., Tsujii, J., Ananiadou, S.: FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics 24(21), 2559–2560 (2008)
Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J., Ananiadou, S.: Kleio: a knowledge-enriched information retrieval system for biology. In: Proceeding of ACM SIGIR, pp. 787–788 (2008)
Miyao, Y., Tsujii, J.: Feature Forest Models for Probabilistic HPSG Parsing. Computational Linguistics 34(1), 35–80 (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Chun, HW. et al. (2013). Pathway Construction and Extension Using Natural Language Processing. In: Yamamoto, S. (eds) Human Interface and the Management of Information. Information and Interaction for Health, Safety, Mobility and Complex Environments. HIMI 2013. Lecture Notes in Computer Science, vol 8017. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39215-3_4
Download citation
DOI: https://doi.org/10.1007/978-3-642-39215-3_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-39214-6
Online ISBN: 978-3-642-39215-3
eBook Packages: Computer ScienceComputer Science (R0)