This paper presents SemLinker, an open source system that discovers named entities, connects them to a reference knowledge base, and clusters them semantically. SemLinker relies on several modules that perform surface form generation, mutual disambiguation, entity clustering, and make use of two annotation engines. SemLinker was evaluated in the English Entity Discovery and Linking track of the Text Analysis Conference on Knowledge Base Population, organized by the US National Institute of Standards and Technology. Along with the SemLinker source code, we release our annotation files containing the discovered named entities, their types, and position across processed documents.