The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes ...a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future.
Public libraries are increasingly addressing issues of diversity and social justice through a variety of avenues, including digital exhibits. This study analyzed digital exhibits offered by large ...public libraries, identifying a total of 27 exhibits that had diversity and/or social justice themes from eight library systems. The exhibits covered a range of topics but tended to focus more on historical oppression or discrimination (81%) rather than on modern inequities (30%). The majority of exhibits (56%) demonstrated collaboration between libraries and the local community, but only 19% provided users with a mechanism for providing feedback. The study developed a framework for evaluating digital exhibits that can serve as a guide for public librarians seeking to curate digital exhibits involving diversity or social justice topics.
The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there ...are no established guidelines for the representation of ancestry information. Here we describe a framework for the accurate and standardized description of sample ancestry, and validate it by application to the NHGRI-EBI GWAS Catalog. We confirm known biases and gaps in diversity, and find that African and Hispanic or Latin American ancestry populations contribute a disproportionately high number of associations. It is our hope that widespread adoption of this framework will lead to improved analysis, interpretation, and integration of human genomics data.
Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental ...stages, diseases and other biological and experimental conditions. The database consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods. The new version of Expression Atlas introduces the concept of 'baseline' expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types. Differential gene expression data benefit from an in-depth curation of experimental intent, resulting in biologically meaningful 'contrasts', i.e. instances of differential pairwise comparisons between two sets of biological replicates. Other novel aspects of Expression Atlas are its strict quality control of raw experimental data, up-to-date RNA-sequencing analysis methods, expression data at the level of gene sets, as well as genes and a more powerful search interface designed to maximize the biological value provided to the user.
Plutocratic Philanthropy Saunders-Hastings, Emma
The Journal of politics,
01/2018, Letnik:
80, Številka:
1
Journal Article
Recenzirano
What kinds of elite influence count as undemocratic? Ongoing debates in American political science have called attention to the ability of the self-interested rich to convert money into influence ...over elected officials. This article argues that democratic criticism of elite influence should also extend to elite philanthropy. It uses the case of philanthropy to argue that elite influence can be undemocratic even when public-spirited in its motivations and even when it bypasses formal political institutions. So far, political theorists writing on philanthropy have focused on insulating formal political institutions from money’s influence or on ensuring tax fairness in incentivizing philanthropy. I argue that this focus is too narrow: democratizing philanthropy requires addressing the policy mechanisms and the public attitudes that privilege the wishes of donors over those of recipient organizations or the broader community.
The privatized state and our own Saunders-Hastings, Emma
Critical review of international social and political philosophy,
02/2023, Letnik:
26, Številka:
2
Journal Article
Recenzirano
Chiara Cordelli's The Privatized State offers a powerful critique of privatization and an inspiring vision of the kind of democratic governance that could secure citizens' equal freedom. This essay ...raises questions about how Cordelli's arguments apply in non-ideal theory. It asks whether her arguments about the illegitimacy of privatization provide us with adequate reasons to reject ongoing processes of privatization. It also queries some of her recommendations for how philanthropy should be practiced by individuals and incentivized by the state.
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) ...recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public sequencing and 42,000 array-based studies comprising over 1.5 million assays in total. The proportion of sequencing-based submissions has grown significantly over the last few years and has doubled in the last 18 months, whilst the rate of microarray submissions is growing slightly. All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold. In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource. Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multi-omics data.
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases ...and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.
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