Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents

Xiaohua Hu; T. Y. Lin; Il Yeol Song; Xia Lin; Illhoi Yoo; Mark Lechner; Min Song

Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents

Xiaohua Hu, T. Y. Lin, Il Yeol Song, Xia Lin, Illhoi Yoo, Mark Lechner, Min Song

Department of Library and Information Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

15 Citations (Scopus)

Abstract

Automated discovery and extraction of biological knowledge from biomedical web documents has become essential because of the enormous amount of biomedical literature published each year, In this paper we present an ontology-based scalable and portable information extraction system to automatically extract biological knowledge from huge collection of online biomedical web documents. Our method integrates ontology-based semantic tagging, information extraction and data mining together, automatically learns the patterns based on a few user seed tuples, and then extract new tuples from the biomedical web documents based on the discovered patterns. A novel system SPIE (Scalable and Portable Information Extraction) is implemented and tested on the PuBMed to find the chromatin protein-protein interaction and the experimental results indicate our approach is very effective in extracting biological knowledge from huge collection of biomedical web documents.

Original language	English
Title of host publication	Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004
Editors	N. Zhong, H. Tirri, Y. Yao, L. Zhou
Pages	77-83
Number of pages	7
Publication status	Published - 2004
Event	Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004 - Beijing, China Duration: 2004 Sep 20 → 2004 Sep 24

Publication series

Name	Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004

Other

Other	Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004
Country/Territory	China
City	Beijing
Period	04/9/20 → 04/9/24

All Science Journal Classification (ASJC) codes

Engineering(all)

Cite this

Hu, X., Lin, T. Y., Song, I. Y., Lin, X., Yoo, I., Lechner, M., & Song, M. (2004). Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents. In N. Zhong, H. Tirri, Y. Yao, & L. Zhou (Eds.), Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004 (pp. 77-83). (Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004).

Hu, Xiaohua ; Lin, T. Y. ; Song, Il Yeol ; Lin, Xia ; Yoo, Illhoi ; Lechner, Mark ; Song, Min. / Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents. Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004. editor / N. Zhong ; H. Tirri ; Y. Yao ; L. Zhou. 2004. pp. 77-83 (Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004).

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title = "Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents",

abstract = "Automated discovery and extraction of biological knowledge from biomedical web documents has become essential because of the enormous amount of biomedical literature published each year, In this paper we present an ontology-based scalable and portable information extraction system to automatically extract biological knowledge from huge collection of online biomedical web documents. Our method integrates ontology-based semantic tagging, information extraction and data mining together, automatically learns the patterns based on a few user seed tuples, and then extract new tuples from the biomedical web documents based on the discovered patterns. A novel system SPIE (Scalable and Portable Information Extraction) is implemented and tested on the PuBMed to find the chromatin protein-protein interaction and the experimental results indicate our approach is very effective in extracting biological knowledge from huge collection of biomedical web documents.",

author = "Xiaohua Hu and Lin, {T. Y.} and Song, {Il Yeol} and Xia Lin and Illhoi Yoo and Mark Lechner and Min Song",

year = "2004",

language = "English",

isbn = "0769521002",

series = "Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004",

pages = "77--83",

editor = "N. Zhong and H. Tirri and Y. Yao and L. Zhou",

booktitle = "Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004",

note = "Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004 ; Conference date: 20-09-2004 Through 24-09-2004",

}

Hu, X, Lin, TY, Song, IY, Lin, X, Yoo, I, Lechner, M & Song, M 2004, Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents. in N Zhong, H Tirri, Y Yao & L Zhou (eds), Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004. Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004, pp. 77-83, Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004, Beijing, China, 04/9/20.

Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents. / Hu, Xiaohua; Lin, T. Y.; Song, Il Yeol; Lin, Xia; Yoo, Illhoi; Lechner, Mark; Song, Min.

Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004. ed. / N. Zhong; H. Tirri; Y. Yao; L. Zhou. 2004. p. 77-83 (Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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T1 - Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents

AU - Hu, Xiaohua

AU - Lin, T. Y.

AU - Song, Il Yeol

AU - Lin, Xia

AU - Yoo, Illhoi

AU - Lechner, Mark

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N2 - Automated discovery and extraction of biological knowledge from biomedical web documents has become essential because of the enormous amount of biomedical literature published each year, In this paper we present an ontology-based scalable and portable information extraction system to automatically extract biological knowledge from huge collection of online biomedical web documents. Our method integrates ontology-based semantic tagging, information extraction and data mining together, automatically learns the patterns based on a few user seed tuples, and then extract new tuples from the biomedical web documents based on the discovered patterns. A novel system SPIE (Scalable and Portable Information Extraction) is implemented and tested on the PuBMed to find the chromatin protein-protein interaction and the experimental results indicate our approach is very effective in extracting biological knowledge from huge collection of biomedical web documents.

AB - Automated discovery and extraction of biological knowledge from biomedical web documents has become essential because of the enormous amount of biomedical literature published each year, In this paper we present an ontology-based scalable and portable information extraction system to automatically extract biological knowledge from huge collection of online biomedical web documents. Our method integrates ontology-based semantic tagging, information extraction and data mining together, automatically learns the patterns based on a few user seed tuples, and then extract new tuples from the biomedical web documents based on the discovered patterns. A novel system SPIE (Scalable and Portable Information Extraction) is implemented and tested on the PuBMed to find the chromatin protein-protein interaction and the experimental results indicate our approach is very effective in extracting biological knowledge from huge collection of biomedical web documents.

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M3 - Conference contribution

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BT - Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004

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Hu X, Lin TY, Song IY, Lin X, Yoo I, Lechner M et al. Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents. In Zhong N, Tirri H, Yao Y, Zhou L, editors, Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004. 2004. p. 77-83. (Proceedings - IEEE/WIC/ACM International Conference on Web Intelligence, WI 2004).

Ontology-based scalable and portable information extraction system to extract biological knowledge from huge collection of biomedical Web documents

Abstract

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All Science Journal Classification (ASJC) codes

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