title: The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes.
abstract: BACKGROUND
  Detecting uncertain and negative assertions is essential in most BioMedical Text Mining tasks where, in general, the aim is to derive factual knowledge from textual data. This article reports on a corpus annotation project that has produced a freely available resource for research on handling negation and uncertainty in biomedical texts (we call this corpus the BioScope corpus).
  
  
  RESULTS
  The corpus consists of three parts, namely medical free texts, biological full papers and biological scientific abstracts. The dataset contains annotations at the token level for negative and speculative keywords and at the sentence level for their linguistic scope. The annotation process was carried out by two independent linguist annotators and a chief linguist--also responsible for setting up the annotation guidelines --who resolved cases where the annotators disagreed. The resulting corpus consists of more than 20.000 sentences that were considered for annotation and over 10% of them actually contain one (or more) linguistic annotation suggesting negation or uncertainty.
  
  
  CONCLUSIONS
  Statistics are reported on corpus size, ambiguity levels and the consistency of annotations. The corpus is accessible for academic purposes and is free of charge. Apart from the intended goal of serving as a common resource for the training, testing and comparing of biomedical Natural Language Processing systems, the corpus is also a good resource for the linguistic analysis of scientific and clinical texts.
authors.affiliation: University of Szeged, Department of Informatics, Human Language Technology Group, Arpád tér 2, Szeged, Hungary. vinczev@inf.u-szeged.hu
authors.forename: Veronika
authors.initials: V
authors.lastname: Vincze
authors.forename: György
authors.initials: G
authors.lastname: Szarvas
authors.forename: Richárd
authors.initials: R
authors.lastname: Farkas
authors.forename: György
authors.initials: G
authors.lastname: Móra
authors.forename: János
authors.initials: J
authors.lastname: Csirik
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods*; D001185:Artificial Intelligence; D003628:Database Management Systems; D016206:Databases, Bibliographic; D016247:Information Storage and Retrieval / Q000379:methods*; D009323:Natural Language Processing; D018875:Vocabulary, Controlled