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In the Health domain, and specifically in the drug-therapy domain, in order to improve the access to the information of different types of users, several informational resources, semantically annotated, are under development. One of the existing development lines is oriented to reusing the effort spent on the design of the existing resources on the Web and obtaining knowledge-based resources for natural language processing (NLP) tasks. In this line, OntoFIS was designed as a NLP resource aimed at filling the gap of multilingual knowledgebased resources within the domain. The design process used for building OntoFIS merges the best approaches of several ontology design methodologies. However, given the characteristics of the drug-therapy domain, whose needs of knowledge are very precise, the process of formalisation of the domain knowledge led to a set of issues. Thus, this paper discusses the main issues found and the solutions analysed and applied in each case.