Extracting and mining protein-protein interaction network from biomedical literature

Xiaohua Hu, Illhoi Yoo, Il Yeol Song, Min Song, Jianchao Han, Mark Lechner

Research output: Chapter in Book/Report/Conference proceedingConference contribution

13 Citations (Scopus)

Abstract

In this paper we present a biomedical literature data mining system SPIE-DM (Scalable and Portable Information Extraction and Data Mining) to extract and mine the protein-protein interaction network from biomedical literature such as MedLine. SPIE-DM consists of two phases: in Phase 1, we develop a Scalable and Portable IE method (SPIE) to extract the protein-protein interaction from the biomedical literature. These extracted protein-protein interactions form a scale-free network graph. In Phase 2, we apply a novel clustering method SFCluster to mine the protein-protein interaction network. The clusters in the network graph represent some potential protein complexes, which are very important for biologist to study the protein functionality. The clustering algorithm considers the characteristics of the scale-free network graphs and is based on the local density of the vertex and its neighborhood functions that can be used to find more meaningful clusters at different density levels. The experiments of SPIE-DM on around 1600 chromatin proteins indicate that our system is very promising for extracting and mining from biomedical literature databases.

Original languageEnglish
Title of host publicationProceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04
Pages244-251
Number of pages8
Publication statusPublished - 2004 Dec 1
EventProceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04 - La Jolla, CA, United States
Duration: 2004 Oct 72004 Oct 8

Other

OtherProceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04
CountryUnited States
CityLa Jolla, CA
Period04/10/704/10/8

Fingerprint

Proteins
Data mining
Complex networks
Clustering algorithms
Experiments

All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Hu, X., Yoo, I., Song, I. Y., Song, M., Han, J., & Lechner, M. (2004). Extracting and mining protein-protein interaction network from biomedical literature. In Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04 (pp. 244-251)
Hu, Xiaohua ; Yoo, Illhoi ; Song, Il Yeol ; Song, Min ; Han, Jianchao ; Lechner, Mark. / Extracting and mining protein-protein interaction network from biomedical literature. Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04. 2004. pp. 244-251
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Hu, X, Yoo, I, Song, IY, Song, M, Han, J & Lechner, M 2004, Extracting and mining protein-protein interaction network from biomedical literature. in Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04. pp. 244-251, Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04, La Jolla, CA, United States, 04/10/7.

Extracting and mining protein-protein interaction network from biomedical literature. / Hu, Xiaohua; Yoo, Illhoi; Song, Il Yeol; Song, Min; Han, Jianchao; Lechner, Mark.

Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04. 2004. p. 244-251.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Hu X, Yoo I, Song IY, Song M, Han J, Lechner M. Extracting and mining protein-protein interaction network from biomedical literature. In Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'04. 2004. p. 244-251