Annotations to data objects are stored in the object instance and may be stored in an annotation file or a reference may be store in a reference file. Once annotated, a cell displaying the data object will provide a notation indicating that the data object has an annotation associated therewith. Retrieval of annotations which are not stored in an annotation file or reference file occurs through a search of the object instances. Retrieval of annotations having a reference in a reference file occurs through use of the reference to access the object instances. Retrieval of annotations in an annotation file occurs through retrieval of the annotation file. Once retrieved, the annotations may be in a final form, such as the nursing progress notes, or may be on a scratch pad to allow the user to electronically transfer annotations from a scratch pad to a permanent record.