A system comprises a toolset to render a protocol, such as an industry clinical treatment guideline, into a process map. The process map includes a workflow having a time-based series of steps determined from the protocol. The system performs recursive matching to match events in electronic medical records (EMRs) to nodes in threads in the protocol map to determine protocol compliance. The EMRs include unstructured data, and specialized query objects may be generated to retrieve relevant data for the process map from the unstructured EMR data.