A reader message me and sent over two files. One was familiar and my advise has been to transcribe the data; the other was a new format and it was very possible to code an uploader for in less than a day.

The small one, bacteria-count is what can be uploaded.

The analysis one has less taxonomy data than the bacteria count one and starts up with the type of page shown below. Dissecting it to get the data would likely be six full man-weeks of development. My attitude is for clients to hassle the provider to make a more friendly format (i.e. tab or comma delimited text files).

The Sweet Bacteria Count File

This file looks like below and is relatively easy to extract the data for (i.e. less than one developer day).

How to Upload

Go to MicrobiomePrescription : Microbiome Sample Uploads and select the highlighted link.

This will open MicrobiomePrescription : Ganzimmun Diagnostics Uploads, with the usual format.

Some Caveat’s

We have only a hundred bacteria at different levels reported. If you go to the microbiome tree, you will see a lot more! Why, we build all of the missing levels of the bacteria hierarchy from the missing data. The upload has no family, order or class information … so we make a best effort attempt to estimate them.

We also apply percentile based on all samples uploaded (until we get 200 samples for a specific test) … again best efforts. See The taxonomy nightmare before Christmas… for background.