Natural language processing of pharmacological texts includes recognition of drug names and extraction of relationships between them. To this purpose, pharmacological annotated corpora are required. These corpora are usually semantically annotated by domain experts. However, other linguistic aspects should be considered to ensure the quality and consistency of the annotation. This paper introduces several linguistic phenomena affecting the annotation of both drug named entities and drug-drug interaction relationships that arose during the annotation process of the DDI corpus. The detailed documentation of these issues and the decisions on them will improve the quality of the annotated corpus and its usefulness for other researchers or users.
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