Using literature-based discovery to identify disease candidate genes

International Journal of Medical Informatics

Volumn 74, Issue 2-4, 2005, Pages 289-298

  Hristovski, Dimitar ^a,b   Peterlin, Borut ^c   Mitchell, Joyce A ^b,d   Humphrey, Susanne M ^b  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c UNIVERSITY MEDICAL CENTRE LJUBLJANA   (Slovenia)

^d UNIVERSITY OF MISSOURI   (United States)

Author keywords

Data mining; Discovery support; Diseases; Genes; Knowledge discovery; Medical informatics; MEDLINE

Indexed keywords

BIBLIOGRAPHIC RETRIEVAL SYSTEMS; CHROMOSOMES; DATABASE SYSTEMS; DISEASES; KNOWLEDGE ACQUISITION; SOCIETIES AND INSTITUTIONS;

BIBLIOGRAPHIC DATABASES; CHROMOSOMAL LOCATION; HUMAN GENOME ORGANIZATION (HUGO); MEDLINE DATABASE;

GENES;

ARTICLE; BIOINFORMATICS; CHROMOSOMAL LOCALIZATION; COMPUTER INTERFACE; COMPUTER SYSTEM; DATA BASE; GENE IDENTIFICATION; GENE INTERACTION; GENE LIBRARY; GENETIC ALGORITHM; MEDICAL INFORMATICS; MEDLINE; PRIORITY JOURNAL;

ALGORITHMS; CHROMOSOME MAPPING; DATABASES, FACTUAL; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MEDICAL SUBJECT HEADINGS;

EID: 13444278595     PISSN: 13865056     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijmedinf.2004.04.024     Document Type: Article

References (25)

1. D.R. Swanson Fish oil, Raynaud's syndrome, and undiscovered public knowledge Perspect. Biol. Med. 30 1 1986 7 18
2. M.D. Gordon, and R.K. Lindsay Toward discovery support systems: a replication, re-examination, and extension of Swanson's work on literature-based discovery of a connection between Raynaud's and fish oil J. Am. Soc. Inf. Sci. 47 2 1996 116 128
3. M. Weeber, H. Klein, L.T.W. De Jong-Van Den Berg, and R. Vos Using concepts in literature-based discovery: simulating Swanson's Raynaud-fish oil and migraine-magnesium discoveries J. Am. Soc. Inf. Sci. Technol. 52 7 2001 548 557
4. M. Weeber, R. Vos, H. Klein, L.T.W. De Jong-Van Den Berg, A.R. Aronson, and G. Molema Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomide J. Am. Med. Inform. Assoc. 10 3 2003 252 259
5. P. Srinivasan Text mining: generating hypotheses from MEDLINE J. Am. Soc. Inf. Sci. Technol. 55 5 2004 396 413
6. D. Hristovski, J. Stare, B. Peterlin, and S. Dzeroski Supporting discovery in medicine by association rule mining in MEDLINE and UMLS Medinformation 10 2 2001 1344 1348
7. 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 2001 21 28
8. B.J. Stapley, and G. Benoit Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in MEDLINE abstracts Pac. Symp. Biocomput. 2000 529 540
9. M. Stephens, M. Palakal, S. Mukhopadhyay, R. Raje, and J. Mostafa Detecting gene relations from MEDLINE abstracts Pac. Symp. Biocomput. 2001 483 495
10. T. Sekimizu, H.S. Park, and J. Tsujii Identifying the interaction between genes and gene products based on frequently seen verbs in MEDLINE abstracts Genome Inform Ser. Workshop Genome Inform. vol. 9 1998 62 71
11. T.C. Rindflesch, B. Libbus, D. Hristovski, A.R. Aronson, and H. Kilicoglu Semantic relations asserting the etiology of genetic diseases Proceedings of the AMIA Symposium 2003 554 558
12. C. Perez-Iratxeta, P. Bork, and M.A. Andrade Association of genes to genetically inherited diseases using data mining Nat. Genet. 31 3 2002 316 319
13. J. Freudenberg, and P. Propping A similarity-based method for genome-wide prediction of disease-relevant human genes Bioinformatics 18 Suppl. 2 2002 S110 S115
14. M.A. van Driel, K. Cuelenaere, P.P. Kemmeren, J.A. Leunissen, and H.G. Brunner A new web-based data mining tool for the identification of candidate genes for human genetic disorders Eur. J. Hum. Genet. 11 1 2003 57 63
15. F.S. Turner, D.R. Clutterbuck, and C.A. Semple POCUS: mining genomic sequence annotation to predict disease genes Genome Biol. 4 11 2003 R75
16. Unified Medical Language System (UMLS), January 28, 2003. http://www.nlm.nih.gov/research/umls/.
17. B.L. Humphreys, D.A.B. Lindberg, H.M. Schoolman, and G.O. Barnett The Unified Medical Language System: an informatics research collaboration JAMIA 5 1 1998 1 11
18. K.D. Pruitt, and D.R. Maglott RefSeq and LocusLink: NCBI gene-centered resources Nucl. Acids Res. 29 1 2001 137 140
19. H.M. Wain, R.C. Lovering, E.A. Bruford, M.J. Lush, M.W. Wright, and S. Povey Guidelines for human gene nomenclature Genomics 79 4 2002 464 470
20. R. Agrawal Fast discovery of association rules U. Fayyad Advances in Knowledge Discovery and Data Mining 1996 MIT Press Cambridge, MA
21. O. Bodenreider, J.A. Mitchell, and A.T. McCray Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics Proceedings of the AMIA Symposium 2002 61 65
22. J.A. Mitchell, A.T. McCray, and O. Bodenreider From phenotype to genotype: issues in navigating the available information resources Meth. Inf. Med. 42 2003 557 563
23. J.A. Mitchell, A.R. Aronson, J.G. Mork, L.C. Folk, S.M. Humphrey, and J.M. Ward Gene indexing: characterization and analysis of NLM's GeneRIFs J. AMIA, Suppl. 2003 460 465
24. S.M. Humphrey Automatic indexing of documents from journal descriptors: a preliminary investigation J. Am. Soc. Inf. Sci. 50 8 1999 661 674
25. S.M. Humphrey, T.C. Rindflesch, and A.R. Aronson Automatic indexing by discipline and high-level categories: methodology and potential applications D. Soergel P. Srinivasan B. Kwasnik Proceedings of the 11th ASIST SIG/CR Classification Research Workshop November 12, 2000, Chicago 2000 American Society for Information Science and Technology Silver Spring, MD 103 116