The shift to author intent means shifting our conceptualization of the text towards discourse: that is, a move from viewing the text as a collection of verbs and nouns, to a view of the contextualized pragmatic language used for science. [...] We call this conceptual approach ‘Hypotheses, Evidence and Relationships’ (HypER). We argue that this representation adds essential knowledge to fact extraction, by taking into account how scientific hypotheses are argued, supported by experimental findings, and how they are interconnected. We are thus arguing for the need to add the dimension of pragmatics [Schoop, 2006] to existing semantic representations. [...] To paraphrase [Hovy, 1993]: ‘As an initial assumption, we take it that scientific discourse is goal-oriented: scientists communicate for a reason.’ [...] However, discourse goals are rarely analyzed for biological texts, which is our topic of study. So what intent do biologists have? We argue that primary research articles should be treated, primarily, as persuasive texts.. [...] The author’s main goal is to persuade the reader of the validity of her claims. There are two aspects to this: the value for the author(s) and the value for the reader(s). The author puts a claim forward as having a certain value, but readers are not constrained to accept it that. The persuasiveness of the discourse lies in the authors’ attempt to persuade their readers to accept the epistemic values they put on claims. The predominant goal of scientific authors is to convince their peers of their claims, and share the epistemic values they have assigned to statements. To do this, they use rhetoric, typical to the narrative form, and supported by references and (experimental) data [Latour et al., 1997].