The discoverability of datasets resulting from the diverse range of translational and biomedical projects remains sporadic. It is especially difficult for datasets emerging from pre-competitive projects, often due to the legal constraints of data-sharing agreements, and the different priorities of the private and public sectors. The Translational Data Catalog is a single discovery point for the projects and datasets produced by a number of major research programmes funded by the European Commission. Funded by and rooted in a number of these European private-public partnership projects, the Data Catalog is built on FAIR-enabling community standards, and its mission is to ensure that datasets are findable and accessible by machines. Here we present its creation, content, value and adoption, as well as the next steps for sustainability within the ELIXIR ecosystem.
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http://dx.doi.org/10.1038/s41597-023-02258-0 | DOI Listing |
BMC Oral Health
January 2025
Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
Background: Previous studies have indicated that retinol and vitamin D may be associated with the oncogenesis of tongue cancer. Therefore, we aimed to assess the causal relationships of retinol and vitamin D with the risk of tongue cancer using the two-sample Mendelian randomization (MR) method.
Methods: Single nucleotide polymorphisms (SNPs) related to retinol, vitamin D and tongue cancer were obtained from the up-to-date genome-wide association study (GWAS) catalogue, which was screened for instrumental variables (IVs).
Database (Oxford)
January 2025
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues.
View Article and Find Full Text PDFComput Biol Chem
January 2025
Bioinformatics Lab, Department of Statistics, Begum Rokeya University, Rangpur 5404, Bangladesh. Electronic address:
The advancements in single-cell RNA sequencing (scRNAseq) technology have significantly transformed genomics research, enabling the handling of thousands of cells in each experiment. As of now, 32,068 research studies have been cataloged in the Pubmed database. The primary aim of scRNAseq investigations is to identify cell types, understand the antitumor immune response, and identify new and uncommon cell types.
View Article and Find Full Text PDFNat Commun
January 2025
Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
Genomic variants causing abnormal splicing play important roles in genetic disorders and cancer development. Among them, variants that cause the formation of novel splice-sites (splice-site creating variants, SSCVs) are particularly difficult to identify and often overlooked in genomic studies. Additionally, these SSCVs are frequently considered promising candidates for treatment with splice-switching antisense oligonucleotides (ASOs).
View Article and Find Full Text PDFJ Biomech
December 2024
Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, United States of America.
Medical image-based diagnostic techniques have become increasingly common in the clinic. Estimating fractional flow reserve in coronary stenoses from medical image data is among the most prominent examples. The modeling techniques used in these clinical tools require rigorous experimental validation yet there is currently no standardized, public toolset to help assess model credibility.
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