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These odd relationships are being inferred by reasoner and actually coming from PATO. For example, in the TO, stem diameter and length (and width) have asserted relation "is_a stem morphology trait". The relation "stem diameter subclass of stem length" is inferred since in PATO "diameter subclass of length" and length subclass of size. I added the asserted relation "and "part of stem size" to all three to help resolve the tree. Also, will request fixed in PATO.
http://browser.planteome.org/amigo/term/TO:0020083
Please correct ASAP the placement of stem length and width. They show up wrong in this diagram
http://browser.planteome.org/visualize?inline=false&term_data=TO%3A0020083&format=png&mode=amigo&term_data_type=string
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