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FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources [article]

Daniel J. B. Clark, Lily Wang, Alex Jones, Megan L. Wojciechowicz, Denis Torre, Kathleen M. Jagodnik, Sherry L. Jenkins, Peter McQuilton, Zachary Flamholz, Moshe C. Silverstein, Brian M. Schilder, Kimberly Robasky (+22 others)
2019 bioRxiv   pre-print
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
more » ... 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.
doi:10.1101/657676 fatcat:zzaotuhtnnafjbn5drzvtmumh4

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

Daniel J.B. Clarke, Lily Wang, Alex Jones, Megan L. Wojciechowicz, Denis Torre, Kathleen M. Jagodnik, Sherry L. Jenkins, Peter McQuilton, Zachary Flamholz, Moshe C. Silverstein, Brian M. Schilder, Kimberly Robasky (+22 others)
2019 Cell Systems  
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
more » ... 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.
doi:10.1016/j.cels.2019.09.011 pmid:31677972 pmcid:PMC7316196 fatcat:bnsncnoz5jfbpoukumw3vhgn2m

Genetic effects on gene expression across human tissues

François Aguet, Andrew A. Brown, Stephane E. Castel, Joe R. Davis, Yuan He, Brian Jo, Pejman Mohammadi, YoSon Park, Princy Parsana, Ayellet V. Segrè, Benjamin J. Strober, Zachary Zappala (+340 others)
2017 Nature  
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

Stephane E. Castel, GTEx Consortium, François Aguet, Pejman Mohammadi, Kristin G. Ardlie, Tuuli Lappalainen
2020 Genome Biology  
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

Taru Tukiainen, Alexandra-Chloé Villani, Angela Yen, Manuel A. Rivas, Jamie L. Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby, Beryl B. Cummings, Stephane E. Castel (+247 others)
2017 Nature  
. 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

Xin Li, Yungil Kim, Emily K. Tsang, Joe R. Davis, Farhan N. Damani, Colby Chiang, Gaelen T. Hess, Zachary Zappala, Benjamin J. Strober, Alexandra J. Scott, Amy Li, Andrea Ganna (+244 others)
2017 Nature  
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

Meng How Tan, Qin Li, Raghuvaran Shanmugam, Robert Piskol, Jennefer Kohler, Amy N. Young, Kaiwen Ivy Liu, Rui Zhang, Gokul Ramaswami, Kentaro Ariyoshi, Ankita Gupte, Liam P. Keegan (+256 others)
2017 Nature  
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]

Tatiana Domitrovic, Mariana H. Moreira, Rodolfo L. Carneiro, Marcelo Ribeiro-Alves, Fernando Palhano
2020 bioRxiv   pre-print
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

Sreemol Gokuladhas, William Schierding, David Cameron-Smith, Melissa Wake, Emma L. Scotter, Justin O'Sullivan
2020 Frontiers in Genetics  
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