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This paper addresses the introduction of Semantic Web and Linked Data technology in Social Science and Humanities research. On the basis of a sample of existing research projects, we examine the impact that the technology has on the research methodology. Three main points of impact were observed. The first is the epistemological foundations of the research, including a focus on individual entities in the research area (or "atomization"), the reification of research objects, and the favouring of analytical skills from researchers. Secondly, in the data analysis phase, research relies more heavily on technical skills during data discovery and processing, and the technology induces growing confusion between data and metadata. Thirdly, we show how the types of models that are built often imply a new encoding of already existing information. [ABSTRACT FROM AUTHOR]