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'element' terms have textual and logical definitions that differ #3375

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allenbaron opened this issue Sep 27, 2024 · 0 comments
Open

'element' terms have textual and logical definitions that differ #3375

allenbaron opened this issue Sep 27, 2024 · 0 comments

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@allenbaron
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There is a small pattern in Uberon where terms ending with element have textual and logical definitions that differ. The textual definitions are inclusive of organs and elements, while the logical axioms limit descendants to organs only.

This table shows all the terms that I am aware of with this pattern:

id label definition equivalentclass
UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. organ and ('part of' some abdomen)
UBERON:0005173 abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. organ and ('part of' some 'abdominal segment of trunk')
UBERON:0005174 dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. organ and ('part of' some dorsum)
UBERON:0005177 trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. organ and ('part of' some trunk)
UBERON:0005178 thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. organ and ('located in' some 'thoracic cavity')
UBERON:0005179 pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. organ and ('part of' some 'pelvic region of trunk')

Background & expectations

I noticed this because, after reading the textual definition of thoracic cavity element (UBERON:0005178), I expected to find bronchus (UBERON:0002185) and pair of lungs (UBERON:0000170), among many other "elements" as descendants of this term and they are not there. I have, possibly mistakenly, interpreted "elements" in Uberon to mean material entities.

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