What you’re looking for is the species key. Rather than downloading all 6 million names in the backbone taxonomy, I recommend using the species API. For example, if you want to know the species key for Pistia stratiotes, you would call:
This query does simple matching for the scientific name specified. If you want to make sure that only species returned, you can add
rank=species. In the JSON response, the species key is returned right at the beginning, e.g.,
For 9,000 names, you probably wouldn’t want to do this one by one. There are plenty of tools around to help you, and I believe even Excel (on Windows at least) can read JSON from REST APIs. I’m not able to test this myself, but a few Google searches should help you.
If all else fails, you could share your list of species and someone—myself or the kind folks behind email@example.com—will gladly help.