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 anchor...

The system we have developed is called POSOLE, or the POSet Ontology Laboratory Environment. POSOLE consists of a set of modules supporting ontology representation, categorization of nodes in the ontology, and analysis. The analysis modules provide support for analysis of the ontological structure, the structure of input queries to the categorization module with respect to that structure, and t...

Due to the increasing web, there are many challenges to establish a general framework for data mining and retrieving structured data from the Web. Creating an ontology is a step towards solving this problem. The ontology raises the main entity and the concept of any data in data mining. In this paper, we tried to propose a method for applying the "meaning" of the search system, But the problem ...

Community annotation of biological entities with concepts from multiple bioontologies has created large and growing repositories of ontology-based annotation data with embedded implicit relationships among orthogonal ontologies. Development of efficient data mining methods and metrics to mine and assess the quality of the mined relationships has not kept pace with the growth of annotation data....

Communities on the Web capture, represent, and evolve their knowledge using ontologies, either explicitly or implicitly. The Gene Ontology project is a typical and advanced case study of a community-driven ontology creation and evolution. We use this case study to derive and illustrate factors that limit dynamic knowledge sharing in community environments. Specifically, we analyze ontology evol...