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Summit on Translat Bioinforma. 2009 Mar 1;2009:124-8.

Extraction of Conditional Probabilities of the Relationships Between Drugs, Diseases, and Genes from PubMed Guided by Relationships in PharmGKB.

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  • 1Departments of Computer Science.


Guided by curated associations between genes, treatments (i.e., drugs), and diseases in pharmGKB, we constructed n-way Bayesian networks based on conditional probability tables (cpt's) extracted from co-occurrence statistics over the entire Pubmed corpus, producing a broad-coverage analysis of the relationships between these biological entities. The networks suggest hypotheses regarding drug mechanisms, treatment biomarkers, and/or potential markers of genetic disease. The cpt's enable Trio, an inferential database, to query indirect (inferred) relationships via an SQL-like query language.

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