DataSTAGE should curate all available GWAS scan results available in GWAS catalog (https://www.ebi.ac.uk/gwas/), the NCBI archie (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639349/), and other privately held repositories (eg GIANT and T2D portal , Broad Inst) to enable PheWAS analysis. Biological insight can be gained in looking at the pleiotropic effects of specific variants that can suggest appropriate functional ...more »
Ideas for DataSTAGE from the scientific researcher community
Collecting ideas from the user community
The NHLBI DataSTAGE (Storage, Toolspace, Access and analytics for biG data Empowerment) project aims to create a community of practice that is motivated to collaboratively solve technical challenges to enable NHLBI investigators to find, access, share, store, cross-link, and compute on large-scale data sets. Though the primary goal of the DataSTAGE Consortium is to build a data science platform, at its core this is a people-centric endeavor. For more information, visit www.nhlbidatastage.org.
We want to hear from the scientific researcher community in order to realize DataSTAGE's mission to develop and integrate advanced cyberinfrastructure, leading edge tools, and findability, accessibility, interoperability, and reusability (FAIR) data to support the NHLBI research community. We would like to hear from you on features that would facilitate your research, including, but not limited to, types of tools, types of datasets, new functionality, type of users reached, and training mechanisms. For a high level view of what we already working on, you can review our User Narratives for 2019-2022 starting on page 7 of our Strategic Framework.
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A novice user (grad student) can log into DataSTAGE and access teaching data sets from BioLINCC (link: https://biolincc.nhlbi.nih.gov/teaching/). She can find material (FAQs, videos, etc.) that will explain what kind of data elements exist within the datasets. She can also find pre-scripted Jupyter notebooks that walk her through how to run standard epidemiological analyses.
Detecting GxE interactions often requires amassing large sample sizes, but identifying cohorts with similar phenotype and environmental exposure data is often cumbersome. dbGaP provides some opportunity for identifying such cohorts, but the complete set of phenotype and environmental variables as well as availability of multi-omics data are often not included. STAGE could provide a venue for aligning cohorts with harmonizable ...more »
PIs have responsibility for the data they generate, including information about subject consent. Such data and consent information may change over time, so dataSTAGE should have tools for PIs to ensure that study data and information is accurate and up to date. It may be useful to develop an interface with documentation, training, and support infrastructure similar to the dbGaP submission tools, documented here: https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/ ...more »
Once a set of associated variants is identified from a genomewide scan, an assessment of their potential function is needed to move forward toward biological insight. It would be useful to leverage the GTEx and MODs (Alliance) data to assess: 1) for GTEx: if the intergenic variants have evidence of regulatory function and, if known, what genes are they regulating? 2) for MODS: if a target gene is identified (eg the ...more »
Apologies - this feature request is captured within existing user narratives. I don't see a way to delete the idea, though!