Using biomedical databases as knowledge sources for large-scale text mining

In this paper we discuss how terminological knowledge extracted from biomedical databases can be used effectively in large-scale processing of the biomedical literature. We briefly present an integrated information extraction and text mining environment which is capable of reliably identifying and disambiguating several categories of relevant domain entities, which can then constitute relevant indexing entries in order to allow efficient retrieval of relevant documents and passages. Additionally the system generates ranked lists of candidate interactions among the detected entities, which can be useful for several purposes, from assisted literature curation to question answering systems