A roadmap for the functional annotation of protein families: a community perspective.

Over the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages.

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources.

Data-driven classification of the certainty of scholarly assertions.

The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems.

The principles of tomorrow's university.

In the 21st Century, research is increasingly data- and computation-driven. Researchers, funders, and the larger community today emphasize the traits of openness and reproducibility. In March 2017, 13 mostly early-career research leaders who are building their careers around these traits came together with ten university leaders (presidents, vice presidents, and vice provosts), representatives from four funding agencies, and eleven organizers and other stakeholders in an NIH- and NSF-funded one-day, invitation-only workshop titled "Imagining Tomorrow's University.

Elsevier's approach to the bioCADDIE 2016 Dataset Retrieval Challenge.

https://data.mendeley.com/datasets/zd9dxpyybg/1.

Automated detection of discourse segment and experimental types from the text of cancer pathway results sections.

Automated machine-reading biocuration systems typically use sentence-by-sentence information extraction to construct meaning representations for use by curators. This does not directly reflect the typical discourse structure used by scientists to construct an argument from the experimental data available within a article, and is therefore less likely to correspond to representations typically used in biomedical informatics systems (let alone to the mental models that scientists have). In this study, we develop Natural Language Processing methods to locate, extract, and classify the individual passages of text from articles' Results sections that refer to experimental data.

Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness.

Out-of-date or incomplete drug product labeling information may increase the risk of otherwise preventable adverse drug events. In recognition of these concerns, the United States Federal Drug Administration (FDA) requires drug product labels to include specific information. Unfortunately, several studies have found that drug product labeling fails to keep current with the scientific literature.

The Future of Research Communication.

This report documents the program and the outcomes of Dagstuhl Perspectives Workshop 11331 "The Future of Research Communication". The purpose of the workshop was to bring together researchers from these different disciplines, whose core research goal is changing the formats, standards, and means by which we communicate science.