In this paper we describe how the annotation method-ology adopted in our approach allows us to explain the organization of indexed references in scientific research articles. We identify the semantic values of author judg-ments in the text segments containing indexed refer-ences. We use an automated semantic annotation plat-form to annotate our corpora. Exploiting this result, we obtain a representation of the annotation distribution on different scales. Finally, we present two evaluations of the annotation.