A method and system for annotating and linking electronic documents is described herein. Separate annotation layers or connectors are used to store each annotation or connection associated with a document in order to improve the efficiency and robustness of collaborative annotation. When a user creates an annotation for a document, a new annotation layer is generated, containing information describing the annotation. The annotation layer is separate from the annotated document. The annotation layer may be transmitted to another user without transmission of the document, thereby reducing network traffic and avoiding metadata contamination within the document itself. This facilitates real-time collaborative annotation of electronic documents by multiple users. This also facilitates robust connections between documents or other data sources, which contain information regarding both the source and target documents.