Linguistic scope-based and biological event-based speculation and negation annotations in the Genia Event and BioScope corpora

Background: The treatment of negation and hedging in natural language processing has received much interest recently, especially in the biomedical domain. However, open access corpora annotated for negation and/or speculation are hardly available for training and testing applications, and even if they are, they sometimes follow different design principles. In this paper, the annotation principles of the two largest corpora containing annotation for negation and speculation – BioScope and Genia Event – are compared. BioScope marks linguistic cues and their scopes for negation and speculation while in Genia biological events are marked for uncertainty and/or negation. Results: Differences among the annotations of the two corpora are thematically categorized and the frequency of each category is estimated. We found that the largest amount of differences is due to the issue that scopes – which cover text spans – deal with the key events and each argument (including events within events) of these events is under the scope as well. In contrast, Genia deals with the modality of events within events independently. Conclusions: We think that the useful information for the biologist can be acquired from the key events, thus if we aim to detect ”new knowledge”, an automatic scope-detector trained on BioScope can contribute to biomedical information extraction. However, for detecting the negation and speculation status of events (within events) syntax-based rules investigating the dependency path between the modality cue and the event cue may be employed.