Generating gene summaries from biomedical literature: A study of semi-structured summarization

Information Processing and Management

Volumn 43, Issue 6, 2007, Pages 1777-1791

  Ling, Xu ^a   Jiang, Jing ^a   He, Xin ^a   Mei, Qiaozhu ^a   Zhai, Chengxiang ^a   Schatz, Bruce ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

Genomics; Probabilistic language model; Summarization

Indexed keywords

AUTOMATION; GENES; GENETIC ENGINEERING; INFORMATION RETRIEVAL; KNOWLEDGE ACQUISITION; SEMANTICS;

BIOLOGISTS; BIOMEDICAL LITERATURE; PROBABILISTIC LANGUAGE MODEL; SCIENTIFIC DISCOVERIES; TEXT SUMMARIZATION;

BIOMEDICAL ENGINEERING;

EID: 34547941970     PISSN: 03064573     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ipm.2007.01.018     Document Type: Article

References (21)

1. Drysdale R.A., Crosby M.A., and Consortium T.F. Flybase: genes and gene models. Nucleic Acids Research 33 (2005) 390-395
2. Goldstein, J., Kantrowitz, M., Mittal, V., & Carbonell, J. (1999). Summarizing text documents: sentence selection and evaluation metrics. In SIGIR '99: Proceedings of the 22nd annual international ACM SIGIR conference on research and development in information retrieval (pp. 121-128).
3. Hearst, M. A., & Pedersen, J. O. (1996). Reexamining the cluster hypothesis: scatter/gather on retrieval results. In Proceedings of SIGIR 1996 (pp. 76-84).
4. Hersh, W., & Bhupatiraju, R. T. (2003). Trec genomics track overview. In Proceeding of text retrieval conference (TREC) (pp. 14-23).
5. Hirschman L., Colosimo M., Morgan A., and Yeh A. Overview of biocreative task 1b: normalized gene lists. BMC Bioinformatics 6 (2005) S11
6. Hirschman L., Park J.C., Tsujii J., Wong L., and Wu C.H. Accomplishments and challenges in literature data mining for biology. Bioinformatics 18 (2002) 1553-1561
7. Iliopoulos, I., Enright, A., & Ouzounis, C. (2001). Textquest: document clustering of medline abstracts for concept discovery in molecular biology. In Proceedings of PSB 2001 (pp. 384-395).
8. Kraaij, W., Spitters, M., & van der Heijden, M. (2001). Combining a mixture language model and naive bayes for multi-document summarisation. In Proceedings of the DUC2001 workshop, New Orleans.
9. Kummamuru, K., Lotlikar, R., Roy, S., Singal, K., & Krishnapuram, R. (2004). A hierarchical monothetic document clustering algorithm for summarization and browsing search results. In Proceedings of WWW 2004 (pp. 658-665).
10. Kupiec, J., Pedersen, J., & Chen, F. (1995). A trainable document summarizer. In Proceedings of the 18th annual international ACM SIGIR conference on research and development in information retrieval (pp. 68-73).
11. Ling, X., Jiang, J., He, X., Mei, Q., Zhai, C., & Schatz, B. (2006). Automatically generating gene summaries from biomedical literature. In Proceedings of pacific symposium of biocomputing (PSB) 2006 (pp. 41-50).
12. Lin, C., & Hovy, E. (2003). Automatic evaluation of summaries using n-gram co-occurrence statistics. In Proceedings of the 2003 conference of the north american chapter of the association for computational linguistics on human language technology (pp. 71-78).
13. Lin, C. (2004). Rouge: a package for automatic evaluation of summaries. In Proceedings of the workshop on text summarization branches out (WAS 2004) (pp. 74-81).
14. Luhn H.P. The automatic creation of literature abstracts. IBM Journal of Research and Development 2 2 (1958) 159-165
15. Mei, Q., & Zhai, C. (2006). A mixture model for contextual text mining. In Proceedings of the 2006 ACM SIGKDD international conference on knowledge discovery and data mining (KDD'06) (pp. 649-655).
16. Radev, D. R., Teufel, S., Saggion, H., Lam, W., Blitzer, J., Qi, H., et al. (2003). Evaluation challenges in large-scale document summarization: the mead project. In Proceedings of the 41st annual meeting on association for computational linguistics (pp. 375-382).
17. Shatkay H., and Feldman R. Mining the biomedical literature in the genomic era: an overview. Journal of Cell Biology 10 (2003) 821-856
18. Sun, J., Shen, D., Zeng, H., Yang, Q., Lu, Y., & Cheni, Z. (2005). Web-page summarization using clickthrough data. In Proceedings of the 28th annual international ACM SIGIR conference on research and development in information retrieval (SIGIR'05) (pp. 194-201).
19. Zamir, O., & Etzioni, O. (1999). Grouper: a dynamic clustering interface to web search results. In Proceeding of WWW 1999.
20. Zeng, H., He, Q., Chen, Z., Ma, W., & Ma, J. (2004). Learning to cluster web search results. In Proceeding of SIGIR 2004.
21. Zhai, C., Velivelli, A., & Yuk, B. (2004). A cross-collection mixture model for comparative text mining. In Proceedings of the 2004 ACM SIGKDD international conference on knowledge discovery and data mining (KDD'04) (pp. 743-748).