Background A major bottleneck in our understanding of the molecular underpinnings of life
is the assignment of function to proteins. While molecular experiments provide the most …

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global,
community-driven effort to evaluate and improve the computational annotation of protein …

We present the approach of the Turku NLP group to the PharmaCoNER task on Spanish
biomedical named entity recognition. We apply a CRF-based baseline approach and …

Text mining for the life sciences aims to aid database curation, knowledge summarization
and information retrieval through the automated processing of biomedical texts. To provide …

Objective We executed the Social Media Mining for Health (SMM4H) 2017 shared tasks to
enable the community-driven development and large-scale evaluation of automatic text …

Over the past decade, the demand for automated protein function prediction has increased
due to the volume of newly sequenced proteins. In this paper, we address the function …

During the past few years, several novel text mining algorithms have been developed in the
context of the BioNLP Shared Tasks on Event Extraction. These algorithms typically aim at …

A common approach for improving OCR quality is a post-processing step based on models
correcting misdetected characters and tokens. These models are typically trained on aligned …

Technological advancements in the field of genetics have led not only to an abundance of
experimental data, but also caused an exponential increase of the number of published …

Although advanced text mining methods specifically adapted to the biomedical domain are
continuously being developed, their applications on large scale have been scarce. One of …