1. A method of operating 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 data elements; for individual ones of the data elements, maintaining an internal data element set of the other unique identifiers for the other data elements and knowledge elements that are directly associated with that one individual data element; and for the individual ones of the data elements, maintaining an external data element set of the other unique identifiers for the other data elements that have that one individual data element in their own internal data element sets, said method further comprising: receiving a data query indicating the molecular feature data for an individual biological entity and a search scope indicator; processing the molecular feature data and the data elements to identify ones of the data elements having corresponding biological molecular features; if the search scope indicator comprises an internal and external scope, then generating a knowledge sub-graph for the individual biological entity based on both the internal data element sets and the external data element sets of the identified data elements having the corresponding biological molecular features; if the search scope indicator comprises an internal scope, then generating the knowledge sub-graph for the individual biological entity based on the internal data element sets but not the external data element sets of the identified data elements having the corresponding biological molecular features; and if the search scope indicator comprises an external scope, then generating the knowledge sub-graph for the individual biological entity based on the external data element sets but not the internal data element sets of the identified data elements having the corresponding biological molecular features.