The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes
By V. Vincze, György Szarvas, Richárd Farkas, György Móra, J. Csirik. BMC Bioinformatics, 2008
437 citations recorded by the source corpus.
BackgroundDetecting 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).ResultsThe 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.ConclusionStatistics 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.
Subfields: Artificial Intelligence, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/64db120a86e0fb91d3be5a8e27dae7b38e1c43a7
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In Artificial Intelligence
- Maite Taboada
- Matt Gardner
- Ana Marasovic
- Abhilasha Ravichander
- Sophia Ananiadou
- Paul Thompson
- Syed A. Iqbal
- John McNaught
In Molecular Biology
- Maite Taboada
- Sophia Ananiadou
- Paul Thompson
- Syed A. Iqbal
- John McNaught
- Abhilasha Ravichander
- Ana Marasovic
- Matt Gardner
Citations in the corpus
- Construction of an annotated corpus to support biomedical information extraction (2009, background): “, [47-51]) have reported on attempts to annotate information such as certainty, evidence or negation within biomedical texts.”
- The CoNLL-2010 Shared Task: Learning to Detect Hedges and their Scope in Natural Language Text (2010, methodology): “The biological training dataset consisted of the biological part of the BioScope corpus (Vincze et al., 2008), hence it included abstracts from the GENIA corpus, 5 full articles from the functional genomics literature (related to the fruit fly) and 4 articles from the open access BMC Bioinformatics…”
- CONDAQA: A Contrastive Reading Comprehension Dataset for Reasoning about Negation (2022, background): “(2020) overview datasets with negation as the main phenomenon and mention the following: BioScope (Vincze et al., 2008), ProbBank Focus (Blanco and Moldovan, 2011), ConanDoyle-neg (Morante and Daelemans, 2012), SFU ReviewEN (Konstantinova et al.”
- Sentiment Analysis: An Overview from Linguistics (2016, positive): “The BioScope corpus (Vincze et al. 2008) is a collection of abstracts, papers, and clinical reports annotated with cues that signal negation and speculation, as well as the scope of those cues.”