I've been trying to wrap my head around this for a while and I'm running into a roadblock in terms of providing good usability to community members vs. correct information architecture. As an example, let's say I'm running a website about plants, and visitors can add articles about different plants. This is just a crude example to help understand the problem. When a visitor goes to create a new article, they can categorize it as follows:
Plant Part
- Color
-- Produce
For Plant Part, the options are "Fruit" and "Flower". For Color, "Red" and "White". And for Produce "Rosa glauca" and "Red Delicious".
The problem is, both fruits and flowers can have red varieties. So, if I wanted to represent this taxonomy hierarchy in a single vocabulary, I would have to add the term "Red" under both "Fruit" and "Flower". This is not ideal because it duplicates the term and it doesn't allow visitors to view the category for all red plants (regardless of whether they are looking for a fruit or flower).