1. A method of scoring items resulting from a query containing specified terms, wherein the items being scored are annotated to a set of terms in one or more ontologies comprising the steps of: determining whether the set of terms in the one or more ontologies to which the items being scored are annotated are semantically related to the terms in the specified query, assigning an observed semantic similarity score to each of the items being scored; for each item being scored, determining the probability of obtaining the observed semantic similarity score in the event a random set of query terms is used instead of the specified query terms, assigning an individual P-value to the item being scored based on the determined probability, and scoring each of the items, using a computer, according to the assigned P-values.