BACKGROUND: The BioNLP Gene Regulation Task has attracted a diverse collection of submissions showcasing state-of-the-art systems. However, a principal challenge remains in obtaining a significant amount of recall. We argue that this is an important ...
BACKGROUND: The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating system...
BACKGROUND: Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we pre...
BACKGROUND: Biomedical event extraction has been a major focus of biomedical natural language processing (BioNLP) research since the first BioNLP shared task was held in 2009. Accordingly, a large number of event extraction systems have been develope...
BACKGROUND: The acquisition of knowledge about relations between bacteria and their locations (habitats and geographical locations) in short texts about bacteria, as defined in the BioNLP-ST 2013 Bacteria Biotope task, depends on the detection of co-...
The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these R...
The access to medical information (journals, blogs, web-pages, dictionaries, and texts) has been increased due to availability of many digital media. In particular, finding an appropriate structure that represents the information contained in texts i...
BMC medical informatics and decision making
Jun 15, 2015
BACKGROUND: In Western languages the period character is highly ambiguous, due to its double role as sentence delimiter and abbreviation marker. This is particularly relevant in clinical free-texts characterized by numerous anomalies in spelling, pun...
Computational intelligence and neuroscience
May 17, 2015
We investigate the dynamics of semantic organization using social media, a collective expression of human thought. We propose a novel, time-dependent semantic similarity measure (TSS), based on the social network Twitter. We show that TSS is consiste...
BACKGROUND: Biomedical knowledge bases (KB's) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at whi...