Non-linear correlation of content and metadata information extracted from biomedical article datasets

Journal of Biomedical Informatics

Volumn 41, Issue 1, 2008, Pages 202-216

  Theodosiou, Theodosios ^a   Angelis, Lefteris ^a   Vakali, Athena ^a  

^a ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

Author keywords

Biomedical literature; Data reduction; Gene Ontology; MeSH; Non linear canonical correlation; PubMed; Visualization

Indexed keywords

BIOMEDICAL ENGINEERING; DATA REDUCTION; GENE EXPRESSION; INFORMATION SYSTEMS; LEARNING SYSTEMS; METADATA; MULTIVARIABLE SYSTEMS; ONTOLOGY;

BIOMEDICAL LITERATURE; MEDICAL SUBJECT HEADING; NON-LINEAR CANONICAL CORRELATION; PUBMED;

INFORMATION ANALYSIS;

ARTICLE; BIBLIOGRAPHIC DATABASE; CORRELATION ANALYSIS; DATA BASE; DATA EXTRACTION; GENE ONTOLOGY; INFORMATION; INFORMATION RETRIEVAL; KNOWLEDGE; MACHINE LEARNING; MEDICAL LITERATURE; MEDICAL RESEARCH; MESH HEADING; METADATA INFORMATION; MULTIVARIATE ANALYSIS; NONLINEAR CANONICAL CORRELATION ANALYSIS; PRIORITY JOURNAL;

DATABASE MANAGEMENT SYSTEMS; DATABASES, BIBLIOGRAPHIC; DOCUMENTATION; GREECE; INFORMATION STORAGE AND RETRIEVAL; META-ANALYSIS AS TOPIC; NATURAL LANGUAGE PROCESSING; NONLINEAR DYNAMICS; PERIODICALS AS TOPIC; STATISTICS AS TOPIC; VOCABULARY, CONTROLLED;

EID: 37849024158     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2007.06.004     Document Type: Article

References (28)

1. Rubin D.L., Thorn C.F., Klein T.E., and Altman R.B. A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. J Am Med Inform Assoc 12 2 (2005) 121-129
2. PubMed. National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institute of Health (NIH). http://www.pubmed.com.
3. Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium., Nat Genet 2000;25(1):25-9. URL: http://dx.doi.org/10.1038/75556.
4. Consortium G.O. Creating the gene ontology resource: design and implementation. Genome Res 11 8 (2001) 1425-1433
5. In: Bean C.A., and Green R. (Eds). Relationships in the organization of knowledge (2001), Kluwer Academic Publishers, NY
6. Chang A.A., Heskett K.M., and Davidson T.M. Searching the literature using medical subject headings versus text word with PubMed. Laryngoscope 116 2 (2006) 336-340
7. Ruch P. Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics 22 6 (2006) 658-664
8. Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res 2002;12 (1):203-14. URL: http://dx.doi.org/10.1101/gr.199701.
9. Theodosiou T., Angelis L., Vakali A., and Thomopoulos G.N. Gene functional annotation by statistical analysis of biomedical articles. Int J Med Inform 67 8 (2007) 601-613
10. Lee M., Wang W., and Yu H. Exploring supervised and unsupervised methods to detect topics in Biomedical text. BMC Bioinform 7 1 (2006) 140
11. Izumitani T, Taira H, Kazawa H, Maeda E. Assigning gene ontology categories (Go) to yeast genes using text-based supervised learning methods. In: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (CSB 2004); 2004, p. 503-4.
12. Yasunori Y., and Toshihisa T. Biomedical knowledge navigation by literature clustering. J Biomed Inform 40 2 (2007) 114-130
13. Salton G. Automatic text analysis. Science 168 (1970) 335-343
14. Shatkay H, Feldman R. Mining the biomedical literature in the genomic era: an overview. J Comput Biol 2003;10(6):821-55. URL: http://dx.doi.org/10.1089/106652703322756104.
15. Manning C.D., and Schutze H. Foundations of statistical natural language processing (1999), The MIT Press, Cambridge, MA
16. Michailidis G., and De Leeuw J. The Gifi system for descriptive multivariate analysis. Statistical Science 13 (1998) 307-336
17. van der Burg E., De Leeuw J., and Verdegaal R. Non-linear canonical correlation analysis. Leiden: Int Rep (1984) RR12-RR84 Department of data theory
18. Jurafsky D., and Martin J.H. Speech and natural language processing (2000), Prentice Hall, Engelwood Cliffs, NJ ISBN: 0-13-095069-6
19. Paice C. Another stemmer. SIGIR Forum 24 3 (1990) 56-61
20. Iliopoulos I., Enright A.J., and Ouzounis C.A. Textquest: document clustering of Medline abstracts for concept discovery in molecular biology. Pac Symp Biocomput (2001) 384-395
21. Zobel J., and Moffat A. Exploring the similarity space. SIGIR Forum 32 1 (1998) 18-34
22. Meulman JJ, Heiser WJ, SPSS Categories User's Manual v. 14.0, SPSS Inc.
23. Lattin J., Carroll D., and Green R. Analyzing multivariate data (2003), Curt Hinrichs
24. Hair J.F., Anderson R.E., Tatham R.L., and Black W.C. Mutlivariate data analysis. 5th ed. (1998), Prentice Hall, Englewood Cliffs, NJ ISBN: 0-13-930587-4
25. Shah Parantu K., Carolina P.-I., Peer B., and Andrade Miguel A. Information extraction from full text scientific articles: where are the keywords?. BMC Bioinform 4 (2003) 20
26. Hong P., Li Z., Vidhu C., Zhuo Z., Houi L.S., Teen C.F., et al. Association miner: a system for exploring transcription factor associations through text-mining. Nucleic Acids Res 32 Web server issue (2004) W230-W234
27. Weiss N.A. Introductory statistics. 6th ed. (2002), Addison-Wesley, Reading, MA ISBN 0-201-71059-5
28. Martin-Sanchez F., Iakovidis I., Nørager S., Maojo V., De Groen P., Van der Lei J., et al. Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care. J Biomed Inform 37 1 (2004) 30-42