In this paper we study whether state-of-the-art techniques for multidomain and multilingual entity linking can be ported to the clinical domain. To do so, we compare two known entity linking systems, BabelFly and TagMe, that leverage on Wikipedia and DBpedia, with the standard clinical semantic annotation and disambiguation system, MetaMap, over the SemRep clinical word sense disambiguation gold standard. We show that BabelFly and especially TagMe, while achieving decent precision on clinical annotation, outmatch MetaMap’s F1-score.
Dr. Camilo Thorne is currently postdoctoral researcher at the University of Mannheim (Data and Web Science Group), in Mannheim Germany, working on entity linking, lexical statistics and
probabilistic and weighted logics for the semantic web. He defended his PhD in 2010 at the Free University of Bozen-Bolzano where he worked on controlled languages for the semantic web and on process model extraction. His interests span natural language semantics, information extraction and knowledge representation.