OntologyTraverser: an R package for GO analysis

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Gene Ontology (GO) annotations are crucial for analyzing large-scale genomic experiments.
• Existing tools for GO analysis may lack integration or accessibility.
• There is a need for user-friendly and robust GO analysis software.

Purpose of the Study:

• To introduce OntologyTraverser, a novel R package and web tool for Gene Ontology analysis.
• To provide an advanced solution for analyzing gene lists derived from genome-scale experiments.
• To enhance the accessibility and usability of GO analysis for researchers.

Main Methods:

• Developed an R package for Gene Ontology (GO) analysis of gene lists.
• Utilized Java to instantiate the GO structure.
• Employed the SJava system for seamless integration of R and Java.
• Deployed the system as a publicly available web tool.

Main Results:

• OntologyTraverser is available as an installable R package.
• The system integrates R and Java for efficient GO structure management.
• A publicly accessible web tool version of OntologyTraverser is provided.
• This represents a significant advancement over previous GO analysis tools.

Conclusions:

• OntologyTraverser offers a powerful and accessible platform for GO analysis.
• The integration of R and Java enhances the efficiency of genomic data analysis.
• The availability of both an R package and a web tool caters to diverse user needs.