1. A method for identifying elements of a system, the method implemented by at least one computer processor coupled to at least one data storage device and comprising: providing a system element store comprising machine-readable representations of system models comprising system elements classified as a whole element of a whole-part relationship, an entity element of an entity-relation-entity relationship, a pair of entity elements of an entity-relation-entity relationship, or a relation element of an entity-relation-entity relationship; electronically receiving a graphical user interface input identifying a system model as a selected electronic representation of the system; in response to the graphical user interface input, extracting corresponding system elements of the identified system model from the system element store, and automatically formulating a query from the extracted system elements, wherein the extracted system elements represent a set of system objectives; searching one or more mereological and functional relationship databases using a knowledge search engine, the one or more merelogical and functional relationship databases including one or more general document repositories that are semantically indexed and contain non-hierarchical database structures and additional one or more knowledge bases selected from the group consisting of: one or more locally accessible knowledge bases, one or more knowledge bases containing corporate knowledge, and one or more publicly accessible knowledge bases; using the query to retrieve component elements useful to form the extracted system elements and identify functional interactions between the component elements, wherein the component elements represent parts of entity-relationship-entity relationships represented in the identified system model; and storing and displaying the retrieved component elements and identified functional interactions as search results in association with the extracted system elements, wherein the search results are represented as user-selectable options indicating design alternatives to satisfy the set of system objectives of the system.