Methods, systems, and apparatus, including computer programs encoded on computer storage media, for generated aggregated dependencies between software elements in a code base. One of the methods includes receiving a query that defines a dependency between the software elements in a project. Searching a database to identify matching source software elements having the one or more source attributes and target software elements having the one or more target attributes of the query. Identifying pairs of matching source software elements and matching target software elements having the specified relationship, and generating, for each pair of matching source software elements and matching target software elements having the specified relationship, a new dependency in a raw dependency graph, the new dependency being a dependency from a source software element of the pair to the target software element of the pair.