A literature based method for identifying gene-disease connections

Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002

Volumn , Issue , 2002, Pages 109-117

  Adamic, L A ^a   Wilkinson, D ^a   Huberman, B A ^a   Adar, E ^a  

^a HEWLETT PACKARD LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; STATISTICAL METHODS;

BREAST CANCER;

GENES;

ANIMAL; ARTICLE; CLASSIFICATION; DATA BASE; DOCUMENTATION; EVALUATION; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETIC MARKER; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; HUMAN; INFORMATION RETRIEVAL; LINGUISTICS; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PUBLICATION;

ABSTRACTING AND INDEXING; ANIMALS; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC SCREENING; HUMANS; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PERIODICALS; VOCABULARY, CONTROLLED;

EID: 1542664516     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2002.1039334     Document Type: Conference Paper

References (23)

1. M. V. Blasoklonny and A. B. Pardee, "Unearthing the gems," Nature, 416, 373.(2002)
2. C. Friedman, P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky, "GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles," Bioinformatics, 2001 Jun;17 Suppl 1:S74-82.
3. M. Andrade and P. Bork, "Automated extraction of information for molecular biology," FEBS Lett., 476, 12 (2000).
4. S.K. Ng and M. Wong, "Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts," Genome Informatics, 1999 Dec 14-15;10:104-112.
5. M. Krauthammer, A. Rzhetsky, P. Morozov, and C. Friedman, "Using BLAST for identifying gene and protein names in journal articles," Gene. 2000Dec 23;259(1-2):245-52.
6. C. Blaschke, M. Andrade, C. Ouzounis and A. Valencia, "Automated extraction of biological information from scientific text: protein-protein interactions," Intelligent Systems for Molecular Biology, Heidelberg, 60 (1999).
7. J. Thomas, D. Milward, C. Ouzounis, S. Pulman and M. Carroll, "Automated extraction of protein interactions from scientific abstracts," Pac. Symp. Biocomput., 538 (2000).
8. B. Stapley and G. Benoit, "Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts,". Pac. Symp. Biocomput., 526 (2000).
9. K. Humphreys, G. Demetriou and R. Gaizauskas. "Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures,". Pac. Symp. Biocomput., 505 (2000).
10. D. Proux, F. Rechenmann, L. Julliard, V. Pillet, and B. Jacq, "Detecting gene symbols and names in biological texts : a first step toward pertinent information extraction," 9th Workshop on Genome Informatics, 72-80 (1998).
11. T. C. Rindflesch, L. Tanabe, J.N. Weinstein, and L. Hunter, "EDGAR: extraction of drugs, genes and relations from the biomedical literature," Pac. Symp. Biocomput., 217 (2000).
12. J. Pustejovsky, J. Castaño, J. Zhang, B. Cochran, and M. Kotecki, "Robust Relational Parsing over Biomedical Literature: Extracting Inhibit Relations," Pac. Symp. Biocomput., 2002.
13. M. Stephens, M. Palakal, S. Mukhopadhyay, and R. Raje. "Detecting Gene Relations from MEDLINE Abstracts,". Pac. Symp. Biocomput., 2001.
14. M. Andrade and A. Valencia, "Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families,". Bioinformatics 14(7): 600-607, 1998.
15. T.-K. Jenssen, A. Laegreid, J. Komorowski and E. Hovig. "A literature network of human genes for high-throughput analysis of gene expression," Nat Genet. 28(1): 21-28, 2001.
16. H.M Wain,, M. Lush, F. Ducluzeau, and S. Povey, "Genew: The Human Nomenclature Database," Nucleic Acids Research 2002, Jan 1;30(1):169-71.
17. Online Mendelian Inheritance in Man, OMIM. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 2000.
18. K.D. Pruitt, and D.R. Maglott, "RefSeq and LocusLink: NCBI gene-centered resources," Nucleic Acid Research 2001, Jan 1;29(1):137-40.
19. J.L. Huret. AML1 (acute myeloid leukemia 1). Atlas Genet Cytogenet Oncol Haematol. December 1997 .URL : http://www.infobiogen.fr/services/chromcancer/Genes/AML1.html
20. E. Adar, "Simple Abbreviation Definition, Clustering and Disambiguation," unpublished manuscript
21. L. S. Larkey, et. al., "Acrophile: an automated acronym extractor and server," Proceedings of the Fifth ACM Conference on Digital Libraries, June 2-7, 2000, San Antonio, TX.
22. th World Congress on Health and Medical Informatics, September 2-5, 2001, London.
23. S. Yeates, et. al. "Using Compression to Identify Acronyms in Text," Data Compression Conference 2000, March 28-30, 2000, Snowbird, Utah.