Knowledge discovery by automated identification and ranking of implicit relationships

Bioinformatics

Volumn 20, Issue 3, 2004, Pages 389-398

  Wren, Jonathan D ^a   Bekeredjian, Raffi ^b,c   Stewart, Jelena A ^b,c   Shohet, Ralph V ^b,c   Garner, Harold R ^b  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETONE; BROMIDE; CASEIN; CHLORPROMAZINE; CISPLATIN; CONCANAVALIN A; ENDOTOXIN; ESTERASE; GALACTOSE; GLOBULIN; ISOLEUCINE; ISOPRENALINE; MACROGOL; METHANOL; METHOTREXATE; MORPHINE; NEOMYCIN; PHYTOHEMAGGLUTININ; POLYSACCHARIDE; PROGESTERONE; TETRACYCLINE;

ALGORITHM; ARTICLE; AUTOMATION; BIOINFORMATICS; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; DISEASE COURSE; HEART VENTRICLE HYPERTROPHY; MATHEMATICAL COMPUTING; MEDLINE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

RODENTIA;

EID: 1342330525     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg421     Document Type: Article

References (36)

1. Barber,M.D. (2001) Cancer cachexia and its treatment with fish-oil-enriched nutritional supplementation. Nutrition, 17, 751-755.
2. Bardoni,B., Mandel,J.L. and Fisch,G.S. (2000) FMR1 gene and fragile X syndrome. Am. J. Med. Genet., 97, 153-163.
3. Blaschke,C., Andrade,M.A., Ouzounis,C. and Valencia,A. (1999) Automatic extraction of biological information from scientific text: protein-protein interactions. ISMB, 7, 60-67.
4. Caudle,R.M. and Mannes,A.J. (2000) Dynorphin: friend or foe? Pain, 87, 235-239.
5. Colucci,W.S. (1982) Alpha-adrenergic receptor blockade with prazosin. Consideration of hypertension, heart failure, and potential new applications. Ann. Int. Med., 97, 67-77.
6. DiGiacomo,R.A., Kremer,J.M. and Shab,D.M. (1989) Fish-oil dietary supplementation in patients with Raynaud's phenomenon: a double-blind, controlled, prospective study. Am. J. Med., 86, 158-164.
7. Ding,J., Berleant,D., Nettleton,D. and Wurtele,E. (2002) Mining Medline: abstracts, sentences or phrases? Pac. Symp. Biocomput., Kauau, Hawaii, 7, 326-337.
8. Green,J.M. (2000) The B7/CD28/CTLA4 T-cell activation pathway. Implications for inflammatory lung disease. Am. J. Respir Cell Mol. Biol., 22, 261-264.
9. Hamosh,A., Scott,A.F., Amberger,J., Valle,D. and McKusick,V.A. (2000) Online Mendelian Inheritance in Man (OMIM). Hum. Mutat., 15, 57-61.
10. Hasselgren,P.O. and Fischer,J.E. (2001) Muscle cachexia: current concepts of intracellular mechanisms and molecular regulation. Ann. Surg., 233, 9-17.
11. Hristovski,D., Stare,J., Peterlin,B. and Dzeroski,S. (2001) Supporting discovery in medicine by association rule mining in Medline and UMLS. Medinfo, 10, 1344-1348.
12. Jenssen,T.K., Laegreid,A., Komorowski,J. and Hovig,E. (2001)A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28, 21-28.
13. Jin,P. and Warren,S.T. (2000) Understanding the molecular basis of fragile X syndrome. Hum. Mol. Genet., 9, 901-908.
14. Klir,G. and Yuan,B. (1995) Fuzzy Sets and Fuzzy Logic: Theory and Applications. Prentice Hall.
15. Kooy,R.F., Willemsen,R. and Oostra,B.A. (2000) Fragile X syndrome at the turn of the century. Mol. Med. Today, 6, 193-198.
16. Lowe,H.J. and Barnett,G.O. (1994) Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches. JAMA, 271, 1103-1108.
17. Maglott,D.R., Katz,K.S., Sicotte,H. and Pruitt,K.D. (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res., 28, 126-128.
18. Marshak,D.R., Watterson,D.M. and Van Eldik,L.J. (1981) Calcium-dependent interaction of S 100b, troponin C, and calmodulin with an immobilized phenothiazine. Proc. Natl Acad. Sci., USA, 78, 6793-6797.
19. McCoy,K.D. and Le Gros,G. (1999) The role of CTLA-4 in the regulation of T cell immune responses. Immunol. Cell Biol., 77, 1-10.
20. Molkentin,J.D., Lu,J.R., Antos,C.L., Markham,B., Richardson,J., Robbins,J., Grant,S.R. and Olson,E.N. (1998) A calcineurin-dependent transcriptional pathway for cardiac hypertrophy. Cell, 93, 215-228.
21. Morgan,J.P. and Van Maanen,E.F. (1980) The role of differential blockade of alpha-adrenergic agonists in chlorpromazine-induced hypotension. Arch. Int. Pharmacodyn. Ther, 247, 135-144.
22. Perez-Iratxeta,C., Bork,P. and Andrade,M.A. (2002) Association of genes to genetically inherited diseases using data mining. Nat. Genet., 31, 316-319.
23. Povey,S., Lovering,R., Bruford,E., Wright,M., Lush,M. and Wain,H. (2001) The HUGO Gene Nomenclature Committee (HGNC). Hum. Genet., 109, 678-680.
24. Rindflesch,T.C., Tanabe,L., Weinstein,J.N. and Hunter,L. (2000) EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac. Symp. Biocomput., 517-528.
25. Shen,W.W. (1999) A history of antipsychotic drug development. Comp. Psychiatry 40, 407-414.
26. Smalheiser,N.R. and Swanson,D.R. (1998) Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Comp. Meth. Prog. Biomed., 57, 149-153.
27. Stapley,B.J. and Benoit,G. (2000) Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac. Symp. Biocomput., 5, 529-540.
28. Steimann,F. (1997) Fuzzy set theory in medicine. Artif. Intell. Med., 11, 1-7.
29. Steiner,H. and Gerfen,C.R. (1998) Role of dynorphin and enkephalin in the regulation of striatal output pathways and behavior. Exp. Brain Res., 123, 60-76.
30. Swanson,D.R. (1986) Fish oil, Raynaud's syndrome, and undiscovered public knowledge. Perspect. Biol. Med., 30, 7-18.
31. Tisdale,M.J. (2001) Cancer anorexia and cachexia. Nutrition, 17, 438-442.
32. Tomer,Y. (2001) Unraveling the genetic susceptibility to autoimmune thyroid diseases: CTLA-4 takes the stage. Thyroid, 11, 167-169.
33. Weeber,M., Klein,H., Aronson,A.R., Mork,J.G., de Jong-van den Berg,L.T. and Vos,R. (2000) Text-based discovery in biomedicine: the architecture of the DAD-system. Proceedings of AMIA Annual Fall Symposium, Los Angeles, CA, 903-907.
34. Weeber,M., Vos,R., Klein,H., De Jong-Van Den Berg,L.T., Aronson,A.R. and Molema,G. (2003) 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, 252-259.
35. Wren,J.D. and Garner,H.R. (2002) Heuristics for identification of acronym-definition patterns within text: towards an automated construction of comprehensive acronym-definition dictionaries. Meth. Inform. Med., 41, 426-434.
36. Yandell,M.D. and Majoros,W.H. (2002) Genomics and natural language processing. Nat. Rev. Genet., 3, 601-610.