Add high level classification

[katiermullen]

Address #129

The inferred breed hierarchy is classifying correctly except for the South American camelid breeds - Llama breed, Alpaca breed, Vicuna breed and Guanaco breed should be children of South American camelid breed.

[sabrinatoro]

Great job @katiermullen

• please see comments in the high-level classification spreadsheet
• we need to add "vertebrate breeds" as a "has ontology root term" for the ontology (instead of "vertebrata ". We can do this together so you see what I mean
• The cat component was not refreshed, so we cannot see how the classification was updated.
• Some of the high-level classification terms should be under another high-level classification terms (eg. 'Ass breed' and 'horse breed' should be under 'equid breed'
• Note to ourselves: once we havereviewed the cat, we should update all breeds and add the "vertebrate breed" parent

[katiermullen]

@sabrinatoro thank you for your review!

• please see comments in the high-level classification spreadsheet

done! A couple of questions remain for us to address on a call.

• we need to add "vertebrate breeds" as a "has ontology root term" for the ontology (instead of "vertebrata ". We can do this together so you see what I mean

Looking forward to it.

• The cat component was not refreshed, so we cannot see how the classification was updated.

Will update and refresh.

• Some of the high-level classification terms should be under another high-level classification terms (eg. 'Ass breed' and 'horse breed' should be under 'equid breed'

Can I make the SC of the 'Ass breed' and 'Horse breed' be 'Equid breed' VBO:0400033? This way, the high level classification will be apparent in the inferred and asserted views of the ontology. Or is there another way I should address this for Equid, Bird, Poultry breed, etc?

• Note to ourselves: once we have reviewed the cat, we should update all breeds and add the "vertebrate breed" parent

can't wait!

[katiermullen]

@matentzn could you please review this PR with emphasis on the high level classification and update to the ontology root term.

@sabrinatoro has kindly offered to review the other changes that this PR encompasses.

Thank you!!!

[matentzn]

There is too much to review here effectively but too notes:

1. The logical equivalence axiom for "vertebrate breed" is circular and should be removed
2. The human definition of "South American camelid breed" is "Vertebrate breeds including Llama, Guanaco, Vicuña and Alpaca breeds." That is not a good definition, at best a "description". A definition should always roughly follow the "genus+differentiae" model. The word "including" is a real risk for a definition as the enumeration is expected to be exhaustive.
   What other specific questions do you have for me?

[katiermullen]

@matentzn Thank you for your review comments and further explanations today! Much appreciated.

[sabrinatoro]

This is fantastic job, @katiermullen !!!
Thank you!

I will merge and ask Nico to update the monarch VBO OLS instance