Methods and systems for extending keyword searching techniques to syntactically and semantically annotated data are provided. Example embodiments provide a Syntactic Query Engine (“SQE”) that parses, indexes, and stores a data set as an enhanced document index with document terms as well as information pertaining to the grammatical roles of the terms and ontological and other semantic information. In one embodiment, the enhanced document index is a form of term-clause index, that indexes terms and syntactic and semantic annotations at the clause level. The enhanced document index permits the use of a traditional keyword search engine to process relationship queries as well as to process standard document level keyword searches. In one embodiment, the SQE comprises a Query Processor, a Data Set Preprocessor, a Keyword Search Engine, a Data Set Indexer, an Enhanced Natural Language Parser (“ENLP”), a data set repository, and, in some embodiments, a user interface or an application programming interface.