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FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources
[article]
2019
bioRxiv
pre-print
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As more datasets, tools, workflows, APIs, and other digital resources are produced by the research community, it is becoming increasingly difficult to harmonize and organize these efforts for maximal synergistic integrated utilization. The Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge by making these digital resources follow common standards and best practices so that they can become
doi:10.1101/657676
fatcat:zzaotuhtnnafjbn5drzvtmumh4
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... more integrated and organized. Faced with the question of how to make digital resources more FAIR, it has become imperative to measure what it means to be FAIR. The diversity of resources, communities, and stakeholders have different goals and use cases and this makes assessment of FAIRness particularly challenging. To begin resolving this challenge, the FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual, semi- and fully-automated FAIR assessment capabilities. The FAIRshake toolkit contains a database that lists registered digital resources, with their associated metrics, rubrics, and assessments. The FAIRshake toolkit also has a browser extension and a bookmarklet that enables viewing and submitting assessments from any website. The FAIR assessment results are visualized as an insignia that can be viewed on the FAIRshake website, or embedded within hosting websites. Using FAIRshake, a variety of bioinformatics tools, datasets listed on dbGaP, APIs registered in SmartAPI, workflows in Dockstore, and other biomedical digital resources were manually and automatically assessed for FAIRness. In each case, the assessments revealed room for improvement, which prompted enhancements that significantly upgraded FAIRness scores of several digital resources.
FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources
2019
Cell Systems
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As more digital resources are produced by the research community, it is becoming increasingly important to harmonize and organize them for synergistic utilization. The findable, accessible, interoperable, and reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge. The FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual and automated FAIR assessments. FAIR
doi:10.1016/j.cels.2019.09.011
pmid:31677972
pmcid:PMC7316196
fatcat:bnsncnoz5jfbpoukumw3vhgn2m
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... ents are visualized as an insignia that can be embedded within digital-resources-hosting websites. Using FAIRshake, a variety of biomedical digital resources were manually and automatically evaluated for their level of FAIRness.
Genetic effects on gene expression across human tissues
2017
Nature
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B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-755 (2002). 29. Rakitsch, B. & Stegle, O. ...
L. Cyr for drawing the body map in Fig. 1a, and A. Kundaje and O. Ursu for input on Hi-C analysis. Author Contributions All authors reviewed and revised the manuscript. ...
doi:10.1038/nature24277
pmid:29022597
pmcid:PMC5776756
fatcat:uzywfeg7b5gz3m74axwveme4oy
A vast resource of allelic expression data spanning human tissues
2020
Genome Biology
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L Nedzel 1 , Duyen T Nguyen 1 , Ayellet V Segrè 1,8 , Ellen Todres 1 Analysis Working Group (funded by GTEx project grants): François Aguet 1 , Shankara Anand 1 , Kristin G Ardlie 1 , Brunilda Balliu ...
L Nedzel 1 , Duyen T Nguyen 1 , Andrew B Nobel 43 , Meritxell Oliva 10, 44 , YoSon Park 15, 45 , Yongjin Park 37,1 , Princy Parsana 12 , Abhiram S Rao 46 , Ferran Reverter 47 , John M Rouhana 8,1 ...
doi:10.1186/s13059-020-02122-z
pmid:32912332
pmcid:PMC7488534
fatcat:rie3jfks3jbudfnuzxhmj6c7sy
Landscape of X chromosome inactivation across human tissues
2017
Nature
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. b-l, x axis labels are sample identifiers. ...
XCI results in sex-biased expression of at least 60 genes, a known escape gene that shows escape of varying degrees in the three samples (Pearson's χ 2 test for equal proportions, P = 3.80 × 10 −7 ) (l) ...
The expected concentration of the pooled libraries was 10-30 ng μl −1 with a size distribution of 300-700 bp. ...
doi:10.1038/nature24265
pmid:29022598
pmcid:PMC5685192
fatcat:bkdhcafyzba5bfhisp5adbb5oq
The impact of rare variation on gene expression across tissues
2017
Nature
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1 2 o c t o b e r 2 0 1 7 | V o L 5 5 0 | N A t U r e | 2 3 9 Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk 1-4 . ...
L. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 44, 837-845 (1988). ...
We model each conditional probability distribution as follows: β ψ ψ ′ |~= − G G F Bernoulli( ), l ogit ( ) 1 θ |Ẽ F categorical( ) β λ N 0, 1 i θ~C C Beta( , ) with parameters β and ...
doi:10.1038/nature24267
pmid:29022581
pmcid:PMC5877409
fatcat:thl5q4fhgrayzams37kfedk45m
Dynamic landscape and regulation of RNA editing in mammals
2017
Nature
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Mason and L. Pipes for help with non-human primate RNA-seq data, Y. Hu, P. Sahbaie, A. Chang, K. ...
Each pre-amplification reaction consisted of 6 μl 5× KAPA2G Multiplex PCR Mix (Kapa Biosystems), 3 μl cDNA (typically 50-200 ng), and 21 μl pooled primers. ...
Tissues from inbred 129S1/SvImJ 6 months old mice were provided by L. Attardi. ...
doi:10.1038/nature24041
pmid:29022589
pmcid:PMC5723435
fatcat:l5pujkurerfbvoqxvguj6rvs2m
Natural variation of the cardiac transcriptome in humans
[article]
2020
bioRxiv
pre-print
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We also thank Jared Nedzel from Broad Institute for help with the Gtex analyzes. . ...
Genes related to the renal system process regulation were upregulated in individuals A, C, F, I, and L ( Fig 4B) . ...
doi:10.1101/2020.10.06.328591
fatcat:7rqflvbk7vgj7m4r36gbtppdcm
Shared Regulatory Pathways Reveal Novel Genetic Correlations Between Grip Strength and Neuromuscular Disorders
2020
Frontiers in Genetics
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We would like to thank Kane Hadley and Jared Nedzel from Genotype-Tissue Expression (GTEx) consortium for their technical support and the funders of GTEx Projectcommon Fund of the Office of the Director ...
doi:10.3389/fgene.2020.00393
pmid:32391060
pmcid:PMC7194178
fatcat:q5n5ccyshjcgljxe6iw6etpubm