The ScienceWISE system is a collaborative ontology editor and paper annotation tool designed to help researchers in their discovery. In this paper, we describe the system currently deployed at sciencewise.info and the exposition of its data as Linked Data. During the “RDFization” process, we faced issues to encode the knowledge base in SKOS and find resources to link to on the LOD. We discuss these issues and the remaining open challenges to implement some target features.