An application of text categorization methods to gene ontology annotation

SIGIR 2005 - Proceedings of the 28th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval

Volumn , Issue , 2005, Pages 138-145

  Seki, Kazuhiro ^a   Mostafa, Javed ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

automatic database curation; genomic IR; text categorization

Indexed keywords

CODE ANNOTATION; CURATION; DATABASE PROJECTS; GENE ONTOLOGY ANNOTATIONS; K NEAREST NEIGHBOR (KNN); PRACTICAL PROBLEMS; TERM WEIGHTING SCHEME; TEXT CATEGORIZATION;

GENES; INFORMATION RETRIEVAL;

TEXT PROCESSING;

EID: 58049111200     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1076034.1076060     Document Type: Conference Paper

References (19)

1. A. Dayanik, D. Fradkin, A. Genkin, P. Kantor, D. D. Lewis, D. Madigan, and V. Menkov. DIMACS at the TREC 2004 genomics track. In Proceedings of the 13th Text REtrieval Conference (TREC 2004), 2004.
2. Franca Debole and Fabrizio Sebastiani. Supervised term weighting for automated text categorization. In Proceedings of SAC-03, 18th ACM Symposium on Applied Computing, pages 784-788, 2003.
3. Sergei Egorov, Anton Yuryev, and Nikolai Daraselia. A simple and practical dictionary-based approach for identification of proteins in MEDLINE abstracts. Journal of the American Medical Informatics Association, 11(3):174-178, 2004.
4. Sumio Fujita. Revisiting again document length hypotheses TREC-2004 genomics track experiments at Patolis. In Proceedings of the 13th Text REtrieval Conference (TREC 2004), 2004.
5. Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, and Ralf Zimmer. Playing biology's name game: Identifying protein names in scientific text. In Proceedings of the Pacific Symposium on Biocomputing (PSB), volume 8, pages 403-414, 2003.
6. William Hersh. Text retrieval conference (TREC) genomics pre-track workshop. In Proceedings of the 2nd ACM/IEEE-CS joint conference on Digital libraries, page 428, 2002.
7. William Hersh. Report on TREC 2003 genomics track first-year results and future plans. SIGIR Forum, 38(1):69-72, 2004.
8. W.R. Hersh, R.T. Bhuptiraju, L. Ross, A.M. Cohen, and D.F. Kraemer. TREC 2004 genomics track overview. In Proceedings of the 13th Text REtrieval Conference (TREC 2004), 2004.
9. Lynette Hirschman, Jong C. Park, Jun-ichi Tsujii, Limsoon Wong, and Cathy H. Wu. Accomplishments and challenges in literature data mining for biology. Bioinformatics, 18(12):1553-1561, 2002.
10. Julie Beth Lovins. Development of a stemming algorithm. Mechanical Translation and Computational Linguistics, 11:22-31, 1968.
11. Claire O'Donovan, Maria Jesus Martin, Alexandre Gattiker, Elisabeth Gasteiger, Amos Bairoch, and Rolf Apweiler. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform, 3(3):275-284, 2002.
12. Kim D. Pruitt and Donna R. Maglott. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Research, 29(1):137-140, 2001.
13. Gerard Salton and Michael J. McGill. Introduction to Modern Information Retrieval. McGraw-Hill, Inc., 1983.
14. Ariel S. Schwartz and Marti A. Hearst. A simple algorithm for identifying abbreviation definitions in biomedical text. In Proceedings of the Pacific Symposium on Biocomputing (PSB), volume 8, pages 451-462, 2003.
15. Burr Settles. Biomedical named entity recognition using conditional random fields and rich feature sets. In Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA), 2004.
16. Burr Settles and Mark Craven. Exploiting zone information, syntactic rules, and informative terms in gene ontology annotation of biomedical documents. In Proceedings of the 13th Text REtrieval Conference (TREC 2004), 2004.
17. Hagit Shatkay and Ronen Feldman. Mining the biomedical literature in the genomic era: An overview. Journal of Computational Biology, 10(6):821-856, 2003.
18. Yiming Yang and Xin Liu. A re-examination of text categorization methods. In Proceedings of the 22nd annual international ACM SIGIR conference on Research and development in information retrieval, pages 42-49, 1999.
19. Yiming Yang and Jan O. Pedersen. A comparative study on feature selection in text categorization. In Proceedings of the 14th International Conference on Machine Learning, pages 412-420, 1997.