A task-based approach for Gene Ontology evaluation.

ABSTRACT:

Background

The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact they have on gene set enrichment analysis, along with an example implementation. This task-based approach yields quantitative assessments grounded in experimental data and anchored tightly to the primary use of the annotations.

Results

Applied to specific areas of biological interest, our framework allowed us to understand the progress of annotation and structural ontology changes from 2004 to 2012. Our framework was also able to determine that the quality of annotations and structure in the area under test have been improving in their ability to recall underl

SUBMITTER: Clarke EL 

PROVIDER: S-EPMC3633003 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature