publication . Article . 2013

Negated bio-events: analysis and identification

Nawaz, R; Thompson, P; Ananiadou, S;
Open Access English
  • Published: 16 Jan 2013 Journal: BMC Bioinformatics, volume 14, pages 14-14 (eissn: 1471-2105, Copyright policy)
  • Publisher: BioMed Central
  • Country: United Kingdom
Abstract Background Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations. Results We have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP’09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP’09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events. Conclusions Recently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The resulting systems will be able to extract bio-events with attached polarities from textual documents, which can serve as the foundation for more elaborate systems that are able to detect mutually contradicting bio-events.
Persistent Identifiers
free text keywords: Research Article, Applied Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Structural Biology, Field (computer science), Biomedical text mining, Event (computing), Selection (linguistics), Feature engineering, Identification (information), Relationship extraction, Computer science, Negation, Information retrieval, lcsh:Computer applications to medicine. Medical informatics, lcsh:R858-859.7, lcsh:Biology (General), lcsh:QH301-705.5
Related Organizations
Any information missing or wrong?Report an Issue