BEERE

BEERE evaluates and ranks lists of genes, proteins, and other biomedical entities by assessing the credibility of associations using literature and database evidence to support entity prioritization and exploration.

Key Features:

• Credibility assessment: Evaluates associative and semantic relationships among input biomedical entities using references from scientific literature and established databases.
• Entity ranking: Computes ranking scores and statistical significance measures for each input entity to determine relative importance.
• Hypothesis generation: Constructs a global entity relationship network to reveal connections that can suggest new gene functions or genotype-phenotype associations.
• Outputs: Produces matched original entities with known relationships, expanded entity lists, ranking scores with significance, and graphical network representations annotated with data provenance linking to external sources.

Scientific Applications:

• Relationship validation: Verifies and quantifies credibility of reported associations among genes, proteins, and other biomedical terms.
• Prioritization: Ranks genes or proteins for downstream experimental validation or study based on computed scores and significance.
• Hypothesis generation: Suggests candidate gene functions and genotype-phenotype associations through network-derived connections.
• Network analysis: Enables exploration of global entity relationship networks to interpret complex biological data.

Methodology:

Evaluates relationships using literature and database references, computes entity ranking scores with statistical significance, constructs a global entity relationship network, and generates matched and expanded entity lists with provenance annotations.