Ideas for DataSTAGE from the scientific researcher community

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.

In this community, you can submit ideas, vote on existing ideas, or add comments.

To submit an idea, please click the Submit New Idea button at the top of the navigation sidebar. You will also have the option to add tags to the idea. To vote on an idea, simply click the up or down arrows to the right of the idea title/description. And to add a comment, click in the box below the idea.

If you would like to see all ideas created with a specific tag, you can click on the word or phrase via the tagcloud in the navigation sidebar area under "What we're discussing". To return to this page, click the All Ideas link.

Ideas for DataSTAGE from the scientific researcher community

PheWAS Analysis

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 »

Voting

4 votes
4 up votes
0 down votes
Ideate
(@kaltmanj)

Ideas for DataSTAGE from the scientific researcher community

Accessing and learning from BioLINCC teaching data sets

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.

Voting

3 votes
3 up votes
0 down votes
Ideate

Ideas for DataSTAGE from the scientific researcher community

Identifying opportunities to harmonize data and enable GxE

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 »

Voting

2 votes
2 up votes
0 down votes
Ideate

Ideas for DataSTAGE from the scientific researcher community

Capabilities for data submission and management

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 »

Voting

2 votes
2 up votes
0 down votes
Ideate

Ideas for DataSTAGE from the scientific researcher community

From genomic association to functional exploration

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 »

Voting

1 vote
1 up votes
0 down votes
Ideate