So. is taxonomy like a tree? wait, wait... because there is another way to describe a tree: The bole is the part of the tree between the ground and the first branch, the crown which is the part of the tree from the first branch to the top, and the top which is the highest part of the tree.
And...a tree is a plant and there are all kinds of trees and here are just a few: Redwood, Ash, Fir, Spruce, Sequoia. There are banana trees, apple trees, orange trees and how exactly is a Sequoia related to and Avocado tree? And even more: A collection of trees can form a forest, grove, garden, or park which by themselves are not just collections of trees but wider concepts. So of course, the development of a taxonomy involves research, and among other things, one can find that for many domains, especially in life sciences, law, government and many others, it is possible to start the process with an existing taxonomy, see for example the taxonomywarehouse.
It is clear that the scope of concepts in the world is endless due to the Human instinct to stereotype and classify, first explored by Aristotle, or at least - this is our first written record of an arrangement to classes, subclasses and so on, as means to understand our world. But if so, lets keep in mind that children must have an inherent understanding of classification, and by extenuation, of taxonomy. It is only a matter of vocabulary then.
Taxonomy is a communication device, a tricky one because it is important to make sure that the person that communicates the taxonomy and the audience for the taxonomy understand each other. So the first thing is to understand - who will be using your taxonomy and how.
When you talk to a child, you want to talk about the tree using words like brunch, twigs, leaves etc. and you don't want to discuss apical dominance, foliage and phloem because this is not the vocabulary of an eight years old. And since we clearly can apply elementary school education to user experience design, I would add that developing a taxonomy is art as much as it is science, and for that you can read more in Bowker and Star's great book 'Sorting Things Out'.
As a communication device, taxonomy's principal use is in navigation systems and facilitating good search results. But because a taxonomy maps to a known mental model shared by the user and the system, it is important that the appropriate taxonomy will be exposed to the user in navigation systems, drop-lists, and other actionable interface objects. Such a system allows the user to self-identify: I'm a kid, I'm a teacher or I'm a parent/guardian, and the system renders relevant taxonomies based on appropriate synonym mapping. The multidimensionality of relations within a taxonomic plane is supported by explicit content tagging as well as folksonomy - a taxonomy set by users, to provides the necessary flexibility.
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