There is an avalanche of biomedical data generation and a parallel expansion in
computational capabilities to analyze and make sense of these data. Starting with genome …

Reproducible computational research (RCR) is the keystone of the scientific method for in
silico analyses, packaging the transformation of raw data to published results. In addition to …

Semantic embedding of knowledge graphs has been widely studied and used for prediction
and statistical analysis tasks across various domains such as Natural Language Processing …

Motivation The tremendous success of graphical neural networks (GNNs) already had a
major impact on systems biology research. For example, GNNs are currently being used for …

Motivation Protein functions are often described using the Gene Ontology (GO) which is an
ontology consisting of over 50 000 classes and a large set of formal axioms. Predicting the …

Abstract Motivation Protein–protein interactions (PPIs) play a key role in diverse biological
processes but only a small subset of the interactions has been experimentally identified …

The connection between humans and digital technologies has been documented
extensively in the past decades but needs to be evaluated through the current global …

Background Effective response to public health emergencies, such as we are now
experiencing with COVID-19, requires data sharing across multiple disciplines and data …

Ontology alignment plays a critical role in knowledge integration and has been widely
investigated in the past decades. State of the art systems, however, still have considerable …

Abstract The Gene Ontology (GO) is a formal, axiomatic theory with over 100,000 axioms
that describe the molecular functions, biological processes and cellular locations of proteins …