The current document is directed to methods and systems for organizing, storing, searching, aggregating, and distributing large quantities of biological information obtained for individual patients. In one described implementation, the knowledge and information is stored, in data-storage facilities within cloud-computing-like systems, as clinical actions, biological elements, and variants that are logically linked together to form network-like data structures. Individual patient data and clinical-knowledge databases, including the network-like clinical-knowledge data structures, are hosted in cloud-computing-like data centers along with a variety of services that receive and process queries from users, medical-service providers, and electronic-health-record-based applications and that return requested information to the requesting entities. Despite the enormous amounts of patient data and clinical knowledge that may be stored in the cloud-computing-like data centers, certain implementations of the currently disclosed systems return responses to medical-information queries in under a second, with other implementations providing even faster query-processing turnaround times.