Abstract: A method and system for generating structured semantic annotations from unstructured documents are disclosed. The method may include obtaining a natural language processing model trained to extract unstructured data from an unstructured document and output structured data based on a generic document ontology. The method may further include inputting a plurality of unstructured documents into the natural language processing model to obtain generic structured annotations of the unstructured documents. The method may further include aligning the generic structured annotations to a target ontology specifying a use case to generate target structured annotations for the use case. The target structured annotations may include entities and relations between the entities. The method may further include generating a knowledge representation for the use case based on the target structured annotations and generic structured annotations.