Thank you very much for taking the time to write such a thoughtful and exhaustive reply: I found it most inspiring, especially because it seems to refer to the application of an approach similar to one that has been on my mind lately; here it is.
I have been considering using keywords for my notes (added through $Tags). This would allow me to find all the notes labeled with a given keyword and evaluate whether those notes should be linked to one another, either directly or through other notes.
The problem is that I of course don’t know precisely which keywords are or will be relevant for my growing set of notes. For example, I may think that the keyboard “cell polarity” is and will be sufficient, but over time I may need to differentiate between “cell polarity establishment” and “cell polarity maintenance”. In this case, I know I could find all those notes labeled with the keyword “cell polarity”, but once I had identified for which of those notes I would like to replace the keyword “cell polarity” with the keyword “cell polarity establishment”, would I be able to do that replacement automatically in TB, without doing that one note at a time? I am not asking precisely how to do that at this stage, but only whether you thought one could automate that replacement in TB. If that were the case, I would consider it worth it the investment of time required to apply keywords to all the notes I already have and the ones I will create without worrying about finding the “perfect keyword” from the very beginning.
I suspect that should be possible with TB, but sometimes my suspicions are wrong; for example, I thought that simply by adding $Tags as a KA to a Prototype, all the notes that had been created with that Prototype would automatically inherit $Tags as a KA, but that did not seem to be the case…
Thank you for your consideration.