A shortest-path graph kernel for estimating gene product semantic similarity.

ABSTRACT:

Background

Existing methods for calculating semantic similarity between gene products using the Gene Ontology (GO) often rely on external resources, which are not part of the ontology. Consequently, changes in these external resources like biased term distribution caused by shifting of hot research topics, will affect the calculation of semantic similarity. One way to avoid this problem is to use semantic methods that are "intrinsic" to the ontology, i.e. independent of external knowledge.

Results

We present a shortest-path graph kernel (spgk) method that relies exclusively on the GO and its structure. In spgk, a gene product is represented by an induced subgraph of the GO, which consists of all the GO terms annotating it. Then a shortest-path graph kernel is used to compute

SUBMITTER: Alvarez MA 

PROVIDER: S-EPMC3161911 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature