You say this table is real but all I see are some numbers and a description that doesn’t reflect that layout. My botany degree may be back in the last millennium but your headings imply a taxonomy†. For instance, if Phylum 1 is the descendant of Kingdom 1 and Phylum 2 of Kingdom 2, from what does Phylum 5 descend? Your model doesn’t explain that.
† Genealogy has nothing to do with this. Let’s try to get uor terminology correct or things get even more confusing 
No! It uses taxonomic information, which is an outline in terms of of how a species’ ancestry is derived. My model showed a single species but gave you easy building blocks to make more, which would lead to a more complex outline once finished. Though this is only part of the overall file, it is the easiest way to make per-species note items with all the ancestor info you say you nee. Once done you can move them into a map, or alias them as the ancestor information will be correct and won’t change.
Actually, no. A class is a taxonomic descendant. In terms of storing a note, you don’t have to to store the one within the other. But, to capture the taxonomic information you want, an outline is a good way to capture and set ancestral properties. By all means move the notes once that data is added. Think of the notes as leaves growing at the tip og a branch (of the outline). Once the leaf is grown you can detach them and put them in a pile, e.g. all on the same map.
I’m confused as to how and why you need a prototype for what you refer to as your table. The prototype lets one note (the prototype itself) seed attribute values to any note(s) that use it. The more notes that use a prototype, the more effort you save. If only one note will ever use a prototype, you don’t need a prototype for that purpose. Your ‘table’ consists of many cells though it seems unlikely each cell needs a prototype, not least because all the ‘cell’ in the table are different.
Now I’m truly confounded. How, as per your table, can you have a phylum of rock? Much as I’m trying to to help, the frame of reference and terminology keep changing. I think the underlying problem at this point is you don’t yet have a clear and unambiguous description of what you are trying to do, conflated with inconsistent terminology. Please don’t misread that as me suggesting you don’t know what you want to achieve. Not at all my point. Rather, it is articulating that idea with sufficient clarity so we can give you helpful advice.
So, it might help you if you spent a bit more time making a better descriptive model than the current ‘table’. A bunch of numbered spreadsheet cells don’t explain what’s going on especially when mixed with headings that don’t seem to fit the scenario being described.
I’m not sure there’s anything else I can practically suggest at this point, though if there are some smaller-scoped more practical questions, I’ll be happy to try and answer them. Late here, so I’ll finish now.