BioSharing (http://www.biosharing.org) is a curated, web-based, searchable portal of over 1,300 records describing content standards, databases and data policies in the life sciences, broadly encompassing the biological, natural and biomedical sciences. Among many features, the records can be searched and filtered, or grouped via the ‘Collection’ feature according to field of interest. An example is the Collection curated with the NIH BD2K bioCADDIE project, for various purposes. First, to select and track content standards that have been reviewed during the creation of the metadata model underpinning the Data Discovery Index. Second, as the work progresses and the prototype Index harvests dataset descriptors from different databases, the Collection will be extended to include the descriptions of these databases, including which (if any) standards they implement. This is key to support one of the bioCADDIE project use cases: to allow the searching and filtering of datasets that are compliant to a given community standard. Despite a growing set of standard guidelines and formats for describing their experiments, the barriers to authoring the experimental metadata necessary for sharing and interpreting datasets are tremendously high. Understanding how to comply with these standards takes time and effort and researchers view this as a burden that may benefit other scientists, but not themselves. To tackle this, with and for the NIH BD2K CEDAR project, we will explore methods to serve machine-readable versions of these standards that can inform the creation of metadata templates, rendering standards invisible to the researchers and driving them to strive for easier authoring of the experimental metadata. Lastly, as part of the ELIXIR-UK Node BioSharing is being developed to be the ELIXIR Standards Registry and will be progressively cross-linked to other registries, such as the ELIXIR Tools and Services Registry and the ELIXIR Training e-Support System (TeSS).

CATH Domain Classification List (latest release) - protein structural domains classified into CATH hierarchy.

In this study, we demonstrate the benefit of applying combined strategies to analyze lncRNA action based on bioinformatics and experimental information. This strategy was developed to identify the molecular function of negative regulator of interferon response (NRIR), a type I interferon-stimulated gene (ISG), that we have previously demonstrated to be involved in the upregulation of a subset of ISGs in LPS-stimulated human monocytes. In this study, we provide experimental evidence that NRIR is localized in cellular nuclei, enriched on the chromatin fraction, and upregulates ISGs acting at the transcriptional level. In silico analysis of secondary structures identified distinct NRIR structural domains, comprising putative DNA- and protein-binding regions. In parallel, the presence of a putative DNA-binding domain in NRIR and the five putative NRIR-binding sites in the promoter of NRIR-target genes support the function of NRIR as a transcriptional regulator of its target genes. By use of integrated experimental/bioinformatics approaches, comprising database and literature mining together with in silico analysis of putative NRIR-binding proteins, we identified a list of eight transcription factors (TFs) shared by the majority of NRIR-target genes and simultaneously able to bind TF binding sites enriched in the NRIR-target gene promoters. Among these TFs, the predicted NRIR:STAT interactions were experimentally validated by RIP assay.