1. A method of operating a computer system to maintain a biological data structure having molecular feature data, the method comprising: receiving data elements indicating biological molecular features and receiving knowledge elements that represent biological concepts; individually associating unique identifiers with the elements; for individual ones of the elements, maintaining an internal element set of the other unique identifiers for the other elements that are directly associated with that one individual element; and for the individual ones of the elements, maintaining an external element set of the other unique identifiers for the other elements that have that one individual element in their own internal element sets.