EXERCISE: More basic classification¶
Go to the taxon-union folder and follow the instructions below. This introduces classification using ‘or’ and ‘not’.
This example extends the previous one introducing ‘or’ (UnionOf) and ‘not’ (complementOf)
Instructions:
- Open taxslim-with-union.owl
- Briefly check the asserted hierarchy - this is a subset of the NCBI taxonomy
- Examine the ‘union’ classes at the top of the class hierarchy. In particular:
- ‘Nematoda or Protostomia’ (note that NCBI classifies nematodes as pseudocoelomata)
- ‘Viridiplantae or Bacteria’
- Select ELK reasoner and start reasoner (ignore the pop-up windows).
- Navigate to the inferred hierarchy. How have the union terms we examined before been placed? * Note that you’ll need to know a little taxonomy here to translate the common names into scientific names (Wikipedia is your friend).
- Create your own grouping classes and classify them. Some examples:
- Mouse or Human
- Mouse or Primate
- Pescetarian dietary component (plant or fish)
- Pescetarian dietary component, more relaxed variant (plant or fish or fungi or mollusc or arthropod)
- Note: don’t manually place these in the hierarchy, let the reasoner do this. How can you quickly tell where this class will be placed using the DL query pane?
- Tip: use the DL query tab to test your class expression first
- Create a non-sensical ‘transgenic hybrid’ class, such as a fly-human - which is both a Drosophila and a human. What happens to this when you classify?
- Try using the explanations feature (the ‘?’). Hint: the explanation is more compact if you choose two sibling taxa - e.g. Deuterostome and Protostome
- Remove the hybrid class before moving on.
- Use the DL query tab to find all mammals that are not humans
- Try creating one or more of the following paraphyletic classes. This will involve the ‘not’ construct
- Nonhuman primate (How can you quickly find the label used for ‘Primates’ if you know that human = ‘Homo sapiens’?)
- Invertebrate
- Invertebrate chordate
- Reptilia, as traditionally defined: (amniote minus aves and mammals)
- A Land mammal
- Classify your classes. What does superclass of the classified class represent? Discuss with your instructors- does this reasoned classification reflect an evolutionary history?!
- See HINTS.txt or talk to an instructor if you get stuck on how to classify things.