A method and apparatus for capturing annotations about database material in a way that allows queries with conditions or predicates on both the database material and the annotations. Database material may be text, computer programs, graphics, audio, spreadsheets, or any other material which may be stored and indexed. Database material may be in one or multiple sources, and annotations may be stored together with the original material or in a separate store. Annotations can be used to capture information such as additional facts about the database material, the opinions and judgments of experts about the database material, and/or links to other related material. Annotations may be captured in a structured form to enhance queryability and semantic interpretation.