In this paper we propose an integrated knowledge management system in which terminology-based knowledge acquisition, knowledge integration, and XML-based knowledge retrieval are combined using tag information and ontology management tools. The main objective of the system is to facilitate knowledge acquisition through query answering against XML-based documents in the domain of molecular biology. Our system integrates automatic term recognition, term variation management, context-based automatic term clustering, ontology-based inference, andintelligent tag information retrieval. Tag-based retrieval is implemented through interval operations, which prove to be a powerful means for textual mining and knowledge acquisition. The aim is to provide efficient access to heterogeneous biological textual data and databases, enabling users to integrate a wide range of textual and non-textual resources effortlessly.