A method assigns importance ranks to documents within repositories or databases, such as any database of documents such as books or other printed material, electronic documentation, and pages within the world-wide web. The method uses a corpus of indexed documents that has been annotated to the terms of one or more ontologies in order to assign a semantic similarity score to queries based on terms taken from the ontologies. A statistical model is used to test the significance of matches between query terms and documents or categories. The method results in an acceleration of over 10,000-fold for realistic queries and ontologies, and makes it practicable to calculate P-values dynamically or to keep database annotations and the related P-value distributions up to date by frequent recalculation.