The BioScope corpus: Biomedical texts annotated for uncertainty, negation and their scopes

Veronika Vincze, György Szarvas, Richárd Farkas, György Móra, János Csirik

Research output: Contribution to journalArticle

193 Citations (Scopus)


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. Conclusion: 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.

Original languageEnglish
Article numberS9
JournalBMC bioinformatics
Issue numberSUPPL. 11
Publication statusPublished - Nov 19 2008

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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