LSAT: Learning about alternative transcripts in MEDLINE

Bioinformatics

Volumn 22, Issue 7, 2006, Pages 857-865

  Shah, Parantu K ^a,b   Bork, Peer ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACT REPORT; ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; ENTROPY; EUKARYOTE; GENE FUNCTION; GENETIC ANALYSIS; GENETIC VARIABILITY; INFORMATION PROCESSING; INTERNET; MATHEMATICAL COMPUTING; MEDLINE; PRIORITY JOURNAL; PROTEIN DATABASE; QUALITY CONTROL; SEMANTICS; VALIDATION PROCESS;

EUKARYOTA;

EID: 33645344339     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btk044     Document Type: Article

References (32)

1. Black,D.L. (2000) Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell, 103, 367-370.
2. Blaschke,C. and and Valencia,A. (2001) The potential use of SUISEKI as a protein interaction discovery tool. Genome Inform. Ser. Workshop Genome Inform., 12, 123-134.
3. Boeckmann,B. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
4. Boue,S. et al. (2003) Alternative splicing and evolution. Bioessays, 25, 1031-1034.
5. Cohen,J.A. (1960) Coefficient of agreement for nominal scales. Educ. Psychol. Meas., 20, 37-46.
6. Craven,M. and Kumlien,J. (1999) Constructing biological knowledgebases by extracting information from text sources. In Proceedings of the AAAI Conference on Intelligent Systems for Molecular Biology, Heidelberg, Germany, pp. 77-86.
7. Daraselia,N. et al. (2004) Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics, 20, 604-611.
8. Donaldson,I. et al. (2003) PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics, 4, 11.
9. Dumais,S.T., Platt,J., Heckerman,D. and Sahami,M. (1998) Inductive learning algorithms and representations for text categorization. Proceedings of ACM-CIKM98, Bethesda, MD, pp. 148-155.
10. Edwalds-Gilbert,G. et al. (1997) Alternative poly(A) site selection in complex transcription units: Means to an end? Nucleic Acids Res., 25, 2547-2561.
11. Hirschman,L. et al. (2005) Overview of BioCreAtIvE: Critical assessment of information extraction for biology. BMC Bioinformatics, 6 (Suppl. 1), S1.
12. Joachims,T. (2001) Learning to Classify Text Using Support Vector Machines: Methods, Theory and Algorithms. Kluwer Academic Publishers, Boston.
13. Krallinger,M. and Valencia,A. (2005) Text-mining and information-retrieval services for molecular biology. Genome Biol., 6, 224.
14. Lee,C. and Roy,M. (2004) Analysis of alternative splicing with microarrays: Successes and challenges. Genome Biol., 5, 231.
15. Mika,S. and Rost,B. (2004) Protein names precisely peeled off free text. Bioinformatics, 20 (Suppl. 1), 1241-1247.
16. Mitchell,T.M. (1997) Machine Learning. McGraw Hill.
17. Nadon,R. and Shoemaker,J. (2002) Statistical issues with microarrays: processing and analysis. Trends Genet., 18, 265-271.
18. Nigam,K, Lafferty,J. and McCallum,A. (1999) Using maximum entropy for text classification. In IJCAI-99 Workshop on Machine Learning for Information Filtering, Stockholm, Sweden, 61-67.
19. Novichkova,S. et al. (2003) MedScan, a natural language processing engine for MEDLINE abstracts. Bioinformatics, 19, 1699-1706.
20. Pradhan,S., Ward,W., Hacioglu,K., Martin,J. and Jurafsky,D. (2004) Shallow semantic parsing using support vector machines. In Proceedings of NAACL-HLT. Boston, MA.
21. Ray,S. and Craven,M. (2001) Representing sentence structure in hidden Markov models for information extraction. In Proceedings of the 17th International Joint Conference on Artificial Intelligence, Seattle, WA, 1273-1279.
22. Ribeiro-Neto,R.B.-Y.A.B. (1999) Modern Information Retrieval. Addison Wesley, New York.
23. Schmid,H. (1994) Probabilistic part-of-speech tagging using decision trees. In Proceedings of the International Conference on New Methods in Language Processing. Manchester, UK, pp. 4449.
24. Shah,P.K. et al. (2005) Extraction of transcript diversity from scientific literature. PLoS Computat. Biol., 1, e10.
25. Shatkay,H. and Feldman,R. (2003) Mining the biomedical literature in the genomic era: An overview. J. Comput. Biol., 10, 821-855.
26. Tan,C.M. et al. (2002) The use of bigrams to enhance text categorization. J. Inform. Process. Manage., 30, 529-546.
27. Thanaraj,T.A. et al. (2004) ASD: The alternative splicing database. Nucleic Acids Res., 32, D64-D69.
28. Wattarujeekrit,T. et al. (2004) PASBio: Predicate-argument structures for event extraction in molecular biology. BMC Bioinformatics, 5, 155.
29. Yakushiji,A. et al. (2001) Event extraction from biomedical papers using a full parser. Pac. Symp. Biocomput., 408-419.
30. Yeh,A.S. et al. (2003) Evaluation of text data mining for database curation: Lessons learned from the KDD Challenge Cup. Bioinformatics, 19 (Suppl. 1), i331-339.
31. Yiming Yang,X.L. (1999) A re-examination of text categorization methods. In Proceedings of ACM SIGIR Conference on Research and Development in Information Retrieval, Berkley, CA, pp. 42-49.
32. Zavolan,M. et al. (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res., 13, 1290-1300.