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Biomedical Hypothesis Generation by Text Mining and Gene Prioritization

[ Vol. 21 , Issue. 8 ]

Author(s):

Ingrid Petric, Balazs Ligeti, Balazs Gyorffy and Sandor Pongor   Pages 847 - 857 ( 11 )

Abstract:


Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database.

Keywords:

Biomedical hypothesis generation, disease gene prediction, gene prioritization, ovarian cancer, text mining.

Affiliation:

Centre for Systems and Information Technologies, University of Nova Gorica, Vipavska 13, SI-5000 Nova Gorica, Slovenia.



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