Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations
Abstract The coronavirus disease 2019 (COVID-19) pandemic has been severely impacting
global society since December 2019. The related findings such as vaccine and drug …
global society since December 2019. The related findings such as vaccine and drug …
Bridging scales in Alzheimer's disease: biological framework for brain simulation with the virtual brain
Despite the acceleration of knowledge and data accumulation in neuroscience over the last
years, the highly prevalent neurodegenerative disease of AD remains a growing problem …
years, the highly prevalent neurodegenerative disease of AD remains a growing problem …
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology
The COVID-19 crisis has elicited a global response by the scientific community that has led
to a burst of publications on the pathophysiology of the virus. However, without coordinated …
to a burst of publications on the pathophysiology of the virus. However, without coordinated …
Automated assembly of molecular mechanisms at scale from text mining and curated databases
The analysis of omic data depends on machine‐readable information about protein
interactions, modifications, and activities as found in protein interaction networks, databases …
interactions, modifications, and activities as found in protein interaction networks, databases …
A survey on event extraction for natural language understanding: Riding the biomedical literature wave
Motivation: The scientific literature embeds an enormous amount of relational knowledge,
encompassing interactions between biomedical entities, like proteins, drugs, and symptoms …
encompassing interactions between biomedical entities, like proteins, drugs, and symptoms …
Expressing high-level scientific claims with formal semantics
The use of semantic technologies is gaining significant traction in science communication
with a wide array of applications in disciplines including the life sciences, computer science …
with a wide array of applications in disciplines including the life sciences, computer science …
Ten simple rules for creating reusable pathway models for computational analysis and visualization
K Hanspers, M Kutmon, SL Coort… - PLoS computational …, 2021 - journals.plos.org
Pathway models are an effective way to capture and share our current understanding of
biological processes. A pathway model is defined here as a set of interactions among …
biological processes. A pathway model is defined here as a set of interactions among …
Leveraging structured biological knowledge for counterfactual inference: a case study of viral pathogenesis
Counterfactual inference is a useful tool for comparing outcomes of interventions on
complex systems. It requires us to represent the system in form of a structural causal model …
complex systems. It requires us to represent the system in form of a structural causal model …
Nanopublication-based semantic publishing and reviewing: a field study with formalization papers
With the rapidly increasing amount of scientific literature, it is getting continuously more
difficult for researchers in different disciplines to keep up-to-date with the recent findings in …
difficult for researchers in different disciplines to keep up-to-date with the recent findings in …
Systems biology approach highlights mechanistic differences between Crohn's disease and ulcerative colitis
PA Ruiz Castro, H Yepiskoposyan, S Gubian… - Scientific Reports, 2021 - nature.com
The molecular mechanisms of IBD have been the subject of intensive exploration. We,
therefore, assembled the available information into a suite of causal biological network …
therefore, assembled the available information into a suite of causal biological network …