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Data format for summary level GWAS data

 

Do we need data exchange format for summary data also? I compiled check list from Engage meta study to start with. Please have a look at it and feel free to add more attributes. The chklist is based on meta-studies and HGVBaseG2P may have different set of attributes for summary data. Object model we made for individual level data in meeting is attached.

 

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#1 HI JUha I can't access the

HI JUha

I can't access the jpg

In answer to your question "Do we need data exchange format for summary data" - I don't know!! Assuming you mean for GWAS and other association data, then at the start of GEN2PHEN I assumed we would need such a thing. Indeed, if people were allowed to share even summary-level data widely, and actually wanted to share any data widely, then I guess we would need an exchange format. But currently, that doesn't seem to be the case.

I guess it would be nice to have;

- a format for exchanging individual level data (ISA-tab and Plink outputs seem fine here)

- a format for exchanging summary level data (which I would think you could quickly throw together from the ENGAGE work and the PaGE model, no?

- a format for the metadata (here's where it gets important to get it right, and where I'd like to see solid work done! ...lots of issues to think about though)

- a minimal content reccommendation (several exist, e.g., Strega, just need to all be integrated and boiled down to a true minimium, & I suspect someones already working on that ...perhaps sniff around a bit)

Cheers
Tony

#2 To follow up on the previous

To follow up on the previous comment: here's a couple of references for the STREGA checklist published earlier in the year:

von Elm et al. Reporting genetic association studies: the STREGA statement. Lancet (2009) vol. 374 (9684) http://pubmed.org/19595330

Little et al. STrengthening the REporting of Genetic Association Studies (STREGA): an extension of the STROBE statement. PLoS Med (2009) vol. 6 (2)
http://dx.doi.org/10.1371/journal.pmed.1000022

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