Methods, computer systems, and computer storage media are provided for providing real-time analysis and annotation of clinical documents in a distributed system. A clinical transformation session is opened at a clinical transformation server maintaining sessions for one or more editors and agents operating on a clinical document. Sequences of operations on the clinical document are stored at a memory accessible by the server. At least a portion of the clinical document is analyzed in real-time to provide annotations and other document modifications to each of the one or more editors having a session at the server. Parallel annotations or modifications are resolved and a synchronized view of the clinical document is maintained based on operational transformation.