UFO

UFO calculates semantic similarity, performs enrichment analysis, and generates functional similarity networks from biomedical ontologies within Cytoscape to analyze ontology-annotated entities.

Key Features:

• Semantic Similarity Calculation: Unifies a broad array of semantic similarity measures applicable to ontology terms and annotated biomedical entities.
• Enrichment Analysis: Performs enrichment analysis on sets of biomedical entities using multiple statistical approaches.
• Network Weighing and Generation: Calculates similarities between two sets of entities, weighs imported entity networks, and generates functional similarity networks.
• Visualization Capabilities: Visualizes structural relationships between ontology terms, annotates connections between entities and terms, and illustrates functional similarities among entities.
• Ontology Format Support: Handles ontologies in OBO (Open Biomedical Ontologies) format and diverse biomedical ontology types.

Scientific Applications:

• Phenotype Similarity Assessment: Identifies and applies semantic similarity measures for assessing similarities between human disease phenotypes.
• Biomarker Prediction: Constructs functional similarity networks to support prediction of disease-associated biomarkers.
• Enrichment Analysis on Phenotypes: Performs enrichment analysis on sets of similar phenotypes to reveal overrepresented biological themes.

Methodology:

Integrates multiple semantic similarity calculation methods and enrichment analysis techniques applied to biomedical ontologies (including OBO-format ontologies) within the Cytoscape environment.