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Some datasets do not have donor information #41

Closed bherr2 closed 3 weeks ago

bherr2 commented 4 weeks ago

@mruffalo when using the kidney data products in h5ad format, I'm noticing empty values for age, sex, bmi, etc for some datasets. It seems to be from derived datasets? Is this data redundant? If not, can you fill in those blank values by looking up the donor data for them? It would be best if it were in the data product.

mruffalo commented 3 weeks ago

Thanks @bherr2 -- @pennycuda can you verify this for the data products that are loaded?

bherr2 commented 3 weeks ago

You can test with this notebook (you'll also need to run the downloading notebooks to get the h5ad files), but I specifically test if age, sex, or race is not filled in and call out to the entity api to fill it in (see ~add_hubmap_donor_info)

pennycuda commented 3 weeks ago

Hi Bruce, I've determined this to be an inconsistency in the search API that I was using to grab patient data. Thanks for providing that very useful notebook! I think the entity API will be very helpful in fixing this.

pennycuda commented 3 weeks ago

@bherr2 hi again! With the code you provided, I was able to pull all additional donor information from the Entity API. I am rerunning all data products now and they should be up within a week or so. Again, thank you for bringing this to our attention, and thank you for that notebook!

bherr2 commented 3 weeks ago

Great! Happy to help :-)