Semantic standards and human language technologies are key enablers for semantic interoperability across heterogeneous document and data collections in clinical information systems. Data provenance is awarded increasing attention, and it is especially critical where clinical data are automatically extracted from original documents, e.g. by text mining. This paper demonstrates how the output of a commercial clinical text-mining tool can be harmonised with FHIR, the leading clinical information model standard. Character ranges that indicate the origin of an annotation and machine generates confidence values were identified as crucial elements of data provenance in order to enrich text-mining results. We have specified and requested necessary extensions to the FHIR standard and demonstrated how, as a result, important metadata describing processes generating FHIR instances from clinical narratives can be embedded.