Modeling community standards for metadata as templates makes data FAIR.

It is challenging to determine whether datasets are findable, accessible, interoperable, and reusable (FAIR) because the FAIR Guiding Principles refer to highly idiosyncratic criteria regarding the metadata used to annotate datasets. Specifically, the FAIR principles require metadata to be "rich" and to adhere to "domain-relevant" community standards. Scientific communities should be able to define their own machine-actionable templates for metadata that encode these "rich," discipline-specific elements.

A Simple Standard for Sharing Ontological Mappings (SSSOM).

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction).

Design of a FAIR digital data health infrastructure in Africa for COVID-19 reporting and research.

The limited volume of COVID-19 data from Africa raises concerns for global genome research, which requires a diversity of genotypes for accurate disease prediction, including on the provenance of the new SARS-CoV-2 mutations. The Virus Outbreak Data Network (VODAN)-Africa studied the possibility of increasing the production of clinical data, finding concerns about data ownership, and the limited use of health data for quality treatment at point of care. To address this, VODAN Africa developed an architecture to record clinical health data and research data collected on the incidence of COVID-19, producing these as human- and machine-readable data objects in a distributed architecture of locally governed, linked, human- and machine-readable data.

Unleashing the value of Common Data Elements through the CEDAR Workbench.

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Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases.

Metadata-the machine-readable descriptions of the data-are increasingly seen as crucial for describing the vast array of biomedical datasets that are currently being deposited in public repositories. While most public repositories have firm requirements that metadata must accompany submitted datasets, the quality of those metadata is generally very poor. A key problem is that the typical metadata acquisition process is onerous and time consuming, with little interactive guidance or assistance provided to users.

The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories.

The adaptation of high-throughput sequencing to the B cell receptor and T cell receptor has made it possible to characterize the adaptive immune receptor repertoire (AIRR) at unprecedented depth. These AIRR sequencing (AIRR-seq) studies offer tremendous potential to increase the understanding of adaptive immune responses in vaccinology, infectious disease, autoimmunity, and cancer. The increasingly wide application of AIRR-seq is leading to a critical mass of studies being deposited in the public domain, offering the possibility of novel scientific insights through secondary analyses and meta-analyses.

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata.

Background: Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associated repositories, leading to a lack of standardization in the collected metadata. This lack of standardization limits the ability of the source datasets to be broadly discovered, reused, and integrated with other datasets.

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.

In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies.

The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments.

The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed-the CEDAR Workbench-is a suite of Web-based tools and REST APIs that allows users to construct metadata templates, to fill in templates to generate high-quality metadata, and to share and manage these resources. The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies.

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

Background: Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs.

Human ApoE ε4 alters circadian rhythm activity, IL-1β, and GFAP in CRND8 mice.

Disruptions to daily living, inflammation, and astrogliosis are characteristics of Alzheimer's disease. Thus, circadian rhythms, nest construction, IL-1β and TNF-α, and glial fibrillary acidic protein (GFAP) were examined in a mouse model developed to model late-onset Alzheimer's disease-the most common form of the disease. Mice carrying both the mutated human AβPP transgene found in the CRND8 mouse and the human apolipoprotein E ε4 allele (CRND8/E4) were compared with CRND8 mice and wildtype (WT) mice.

The effect of motion on pulse oximetry and its clinical significance.

Pulse oximetry is an important diagnostic and patient monitoring tool. However, motion can induce considerable error into pulse oximetry accuracy, resulting in loss of data, inaccurate readings, and false alarms. We will discuss how motion artifact affects pulse oximetry accuracy, the clinical consequences of motion artifact, and the methods used by various technologies to minimize the impact of the motion noise.