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FredHutch / wiki

SciWiki: Collective KnowledgeBase for Scientific Data and Use
https://sciwiki.fredhutch.org
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Resources and links for sharing data publicly #129

Closed atombaby closed 5 years ago

atombaby commented 5 years ago

Proposed Domain

Bioinformatics

Content Summary

I don't know if this would go in the existing page about data sharing, but there seems to be a dearth of links to repositories and services for hosting data and the mechanisms for storing data in them. For example, figshare is one project set up for that.

Local Content Expert(s)

Don't know...

sgglick commented 5 years ago

No surprised. I may have a partial list someplace....

vortexing commented 5 years ago

@atombaby neither @ptvan nor I really have a good idea of what exact example of this you are envisioning. Both of us feel like some guidance for how to interact with public data sets would be great, but specifically sharing our own is not something we know much about.

rbarfield commented 5 years ago

For dbGAP, I know some people who have uploaded data there recently. I can reach out and ask if they have links to the forms if we want to include those on the page? Public repositories I know of off top head GTEx, Roadmap, 1000 genomes, UK biobank, TCGA.

Are we suggesting just having a little link to some of these sites? I think some of these (such as GTEx) do involve having an IRB or data-use proposal in place which I'm not super familiar with.

Doing a cursory search, I see two R packages DeepBlueR and Biomartr that could may be used for downloading epigenomics data, but I've never used them.

Sorry, know this was maybe a dormant thread.

vortexing commented 5 years ago

Yes, we should put in links and in my experience, it'd be good to know if there are tools out there to help you actually ACCESS and make sense of public data sets or if someone has actual human advice about it.

Another type of this is Bioconductor's AnnotationHub package.
http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html

I dream of this issue being addressed, it is not dead, just languishing.

vortexing commented 5 years ago

For advice on dbGAP submission: https://sciwiki.fredhutch.org/generation/human_shareDeposits/

vortexing commented 5 years ago

for USING public data: https://sciwiki.fredhutch.org/bioinformatics/dm_ingest/

rbarfield commented 5 years ago

Heard back from one person on dbGAP submission, they pointed me to these webpages

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetPdf.cgi?document_name=HowToSubmit.pdf and https://datascience.cancer.gov/data-sharing/submitting-data#expectations

I think the first one in particular looks good, though maybe good idea to add the pdf to the GitHub so don't lose it if link ever dies.

What do you think? Can add it to https://sciwiki.fredhutch.org/generation/human_shareDeposits/

vortexing commented 5 years ago

Added your two links to pull request #286