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Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all(More)
Irony is an important device in human communication , both in everyday spoken conversations as well as in written texts including books, websites, chats, reviews, and Twitter messages among others. Specific cases of irony and sarcasm have been studied in different contexts but, to the best of our knowledge, only recently the first publicly available corpus(More)
MOTIVATION Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures for chemicals like SMILES, InChI, IUPAC or trivial names exist. Only SMILES and InChI names allow a direct structure search, but in(More)
Most relation extraction methods, especially in the domain of biology, rely on machine learning methods to classify a co-occurring pair of entities in a sentence to be related or not. Such an approach requires a training corpus, which involves expert annotation and is tedious, time-consuming, and expensive. We overcome this problem by the use of existing(More)
Opinion mining is often regarded as a classification or segmentation task, involving the prediction of i) subjective expressions, ii) their target and iii) their polarity. Intuitively , these three variables are bidirec-tionally interdependent, but most work has either attempted to predict them in isolation or proposing pipeline-based approaches that cannot(More)
The description of events in biomedical literature often follows discourse patterns. For example, authors may firstly mention the transcription of a gene, and then go on to describe how this transcription is regulated by another gene. Capturing such patterns can be beneficial when we want to extract event mentions from literature. For instance, detecting(More)
BACKGROUND Posttranslational modifications of histones influence the structure of chromatine and in such a way take part in the regulation of gene expression. Certain histone modification patterns, distributed over the genome, are connected to cell as well as tissue differentiation and to the adaption of organisms to their environment. Abnormal changes(More)
Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. The recognition of these named entities relies on appropriate dictionary resources as well as on training and evaluation corpora. In this work we give an overview of publicly available chemical(More)
Retrieving information about highly ambiguous gene/protein homonyms is a challenge , in particular where their non-protein meanings are more frequent than their protein meaning (e. g., SAH or HF). Due to their limited coverage in common bench-marking data sets, the performance of existing gene/protein recognition tools on these problematic cases is hard to(More)