The effects of shared information on semantic calculations in the gene ontology.

ABSTRACT: The structured vocabulary that describes gene function, the gene ontology (GO), serves as a powerful tool in biological research. One application of GO in computational biology calculates semantic similarity between two concepts to make inferences about the functional similarity of genes. A class of term similarity algorithms explicitly calculates the shared information (SI) between concepts then substitutes this calculation into traditional term similarity measures such as Resnik, Lin, and Jiang-Conrath. Alternative SI approaches, when combined with ontology choice and term similarity type, lead to many gene-to-gene similarity measures. No thorough investigation has been made into the behavior, complexity, and performance of semantic methods derived from distinct SI approaches. We apply b

SUBMITTER: Bible PW 

PROVIDER: S-EPMC5299144 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature