First you need to download the ncbi dump files first.

Go to ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

When you unzip the file, you will see the available data.

Load up the c# project at https://github.com/Lassesen/Microbiome2/tree/master/UploadTaxHier

Modify the DB Configuration string to point to your database. Run the application with the location of the dmp files above.

After the upload, we see the number of records that we have

That’s it! If you want to do periodic updates, I will leave that to the reader to do (and add a pull request). Remember this is open source!