How does VarElect score gene-phenotype associations?

Genes receive a relevance score depending (in part) on the weight of each query term that appears in relation to a given gene.  The weight of a term is determined by the frequency it appears in association with a gene (term frequency) compared to all genes (inverse document frequency).  If a term appears more often in the annotations associated with a given gene, and less often in all genes, the weight of that term for the given gene increases.

Boosting factors are applied to important fields (e.g disorders are boosted by 2).  In addition, scores of all field hits are added together.