Reis et al. (2008)  cites an earlier paper from Albert Ko’s research group, Ko et al. (1999) .
In conventional parlance, as the following diagram shows, the word “reference” can mean either what is found in the text, what is found in the reference list, the act of citation, or the object of the citation itself, as in the sentence “All the references you will need to prepare for the journal club are on Kevin’s desk”.
This situation does not make for unambiguous machine-readable encoding, so to improve the situation we have, in the SPAR (Semantic Publishing and Referencing) Ontologies, introduced a more principled way of referring to these items and actions, as the second diagram illustrates:
This permits us to create RDF describing all aspect of the citation process. Within the body of the text we have an in-text citation containing an in-text reference pointer, while the actual bibliographic reference that the in-text reference pointer denotes is to be found within the article’s reference list. That bibliographic reference references the cited article, while the whole performative act of including the reference in the article constitutes the act of citation.
Are we all clear now?
 Reis RB, Ribeiro GS, Felzemburgh RDM, Santana FS, Mohr S, Melendez AXTO, Queiroz A, Santos AC, Ravines RR, Tassinari WS, Carvalho MS, Reis MG, Ko AI (2008) Impact of Environment and Social Gradient on Leptospira Infection in Urban Slums. PLoS Negl Trop Dis 2(4): e228. doi:10.1371/journal.pntd.0000228
 Ko AI, Reis MG, Ribeiro Dourado CM, Johnson WD Jr, Riley LW and the Salvador Leptospirosis Study Group. (1999) Urban epidemic of severe leptospirosis in Brazil. Lancet 354: 820–825. doi:10.1016/S0140-6736%2899%2980012-9.