Defining 'Healthy' samples

[Vito Spadavecchio]

Hello 

Is there a preferred or suggested method for querying samples that are opposite of a diseased state? For example, I can find all of the "acute myeloid leukemia" samples, but would also like to find all of the samples which may have been the controls in these studies, or otherwise "healthy". 

[Matthew Bernstein]

Hi,

Thank you for your question. Unfortunately, there is currently no direct way to make such a query.  The best one can do is to use the absence of a diseased term as evidence that the sample is healthy (which, admittedly, is not perfect). My suggestion would to use both the MetaSRA in conjunction with the SRAdb database (https://bioconductor.org/packages/release/bioc/html/SRAdb.html).  I would do something like the following: query the MetaSRA for all samples of the disease of interest, then for all studies included in the results, query the SRAdb for all remaining samples (i.e. those samples in the resultant studies that are ~not~ labeled with the target disease).

We will keep this use case in mind when deciding on future features to add to the search interface.

Best,

Matt