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

Volumn , Issue , 2004, Pages 244-251

  Hu, Xiaohua ^a   Yoo, Illhoi ^a   Song, Il Yeol ^a   Song, Min ^a   Han, Jianchao ^b   Lechner, Mark ^c  

^a Drexel University   (United States)

^b CALIFORNIA STATE UNIVERSITY   (United States)

^c DREXEL UNIVERSITY   (United States)

Author keywords

Graph; Protein protein interaction; Text mining

Indexed keywords

GRAPH; PROTEIN-PROTEIN INTERACTION; SCALABLE AND PORTABLE INFORMATION EXTRACTION AND DATA MINING; SPIE-DM; TEXT MINING;

ALGORITHMS; BIOMEDICAL ENGINEERING; DATA MINING; DATABASE SYSTEMS; GENES; GRAPH THEORY;

PROTEINS;

EID: 17044371130     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. I. Xenarios, E. Fernandez, L. Salwinski, X.J. Duan, M.J. Thompson, E.M. Marcotte and D. Eisenberg. "DIP: The database of interacting proteins: 2001 update," Nucleic Acids Reg., vol. 29(1), pp. 239-241.
2. G. Bader and C. Hogue. (2003), "An automated method for finding molecular complexes in large protein interaction networks," BMC Informatics, 4(1):2.
3. L. Hirschman J.C. Park, J. Tsujii, L. Wong and C.H. Wu (2002), "Accomlishments and challenges in literature data mining for biology," Bioinformatics, vol. 18(12), pp. 1553-1561.
4. K. Fukuda, T. Tsunoda, A. Tamura and T. Takagi. (1998), "Toward information extraction: identifying protein names from biological papers," Proceedings of the Pacific Symposium on Biocomputing'98, pp. 707-718.
5. T. Ono, H. Hishigaki, A. Tanigami and T. Takagi. (2001), "Automated extraction of information on protein-protein interactions from the biological literature," Bioinformatics, vol. 17(2), pp. 155-161.
6. th ACM International Conference on Digital Libraries, pp. 85-94.
7. W. Cohen. (1995), "Fast effective rule induction," Proceeding of if International Conference on Machine Learning, pp. 115-123.
8. S. Robertson and K. Sparck Jones. (1976), "Relevance weighting of search terms," Journal of the American Society for Information Science, vol. 27(3), pp. 129-146.
9. E. Riloff. (1996), "Automatically generating extraction patterns from untagged text," Proceedings of the Thirteenth National Conference on Artificial Intelligence (AAAI-96),pp. 1044-1049.
10. S. Soderland. (1999), "Learning information extraction rules for semi-structured and free text," Machine Learning, vol. 34(1-3), pp. 233-272.
11. J. Weizenbaum. (1966), "ELIZA - a computer program for the study of natural language communications between men and machine," Communications of the ACM, vol. 9(1), pp. 36-45.
12. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori and Y. Sakaki. (2001), "A comprehensive two-hybrid analysis to explore the yeast protein interactome," Proc Natl Acad Sci, USA, vol. 98, pp. 4569-4574.
13. R. Albert, H. Jeong and A.L. Barabasi. (2000), "Error and attach tolerance of complex networks," Nature, vol. 406, pp. 378-382.
14. A.L. Barabási and R. Albert. (1999), "Emergence of scaling in random network," Science, vol. 286, pp. 509-512.
15. th International World Wide Web Conference on Computer Networks, pp. 309-320.
16. nd Workshop on Fractals, Power Laws and Other Next Generation Data Mining Tools, August, 24-27.
17. X. Hu X., J. Han and N. Cercone, "Discovering of cyber communities from the WWW," in Proc. of COMPSAC 2003, Dallas, TX, Nov. 3-6, 2003.
18. th ACM SIGMOD-SIFACT-SIGART Symposium on Principles of Databases Systems, pp. 1-10.
19. th ACM SIGKDD International Conference on Knowledge and Data Mining, pp. 81-90.
20. P. Erdos and A. Rényi. (1960), "On the evolution of random graphs," Publ. Math. Inst. Hungar. Acad. Sci., vol. 5, pp. 17-62.
21. H. Matsuda, T. Ishihara and A. Hashimoto. (1999), "Classifying molecular sequences using a linkage graph with their pairwise similarities," Theoretical Computer Science, vol. 210(2), pp. 305-325.
22. R. Urquhart. (1982), "Graph theoretical clustering based on limited neighborhood sets," Pattern Recognition, vol. 15(3), pp. 173-187.
23. J. Rougemont and P. Hingamp. (2003), "DNA microarray data and contextual analysis of correlation graphs," BMC Informatics, vol. 4(1):15.