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"pancreas" (UBERON:0001264) not part of "digestive system" (UBERON:0001007) or "endocrine system" (UBERON:0000949)? #3208

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hdetering opened this issue Feb 9, 2024 · 2 comments · Fixed by #3227
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@hdetering
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hdetering commented Feb 9, 2024

Uberon term
"pancreas" (UBERON:0001264)

Suggested revision and reasons
should be part of
"digestive system" (UBERON:0001007)
and
"endocrine system" (UBERON:0000949)

It seems to be classified in the expected manner in
Danio dangila (NCBITaxon:7954)
Xenopus (NCBITaxon:8353)

@rays22
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rays22 commented Feb 20, 2024

I think most people would regard the pancreas, or at least the exocrine pancreas, as an anatomical entity that is part of the digestive system.
According to the Terminologia Anatomica international standard for human anatomical terminology, the human pancreas is indeed part of the digestive system (systema digestorum).
However, I would be careful with defining the entire pancreas as part of the digestive system in UBERON, because that would lead to the inference that any part of the UBERON:0001264 pancreas is part of the digestive system. Arguably, some cell types of the pancreas (e.g. CL:0008024 pancreatic endocrine cells) are not part of the digestive system.
I will focus on the "digestive system" related part of your issue, because UBERON:0000016 endocrine pancreas has already been asserted as being part of the UBERON:0000949 endocrine system. I think it might cause problems in some use cases if the cell types of the endocrine pancreas were categorise as being part of the digestive system.

Please note that both the UBERON:0000016 endocrine pancreas and the UBERON:0000017 exocrine pancreas are part of UBERON:0001264 pancreas.

  1. Although the UBERON:2001371 pancreatic system class has no textual definition, it is logically defined as part of both the UBERON:0000949 endocrine system and the UBERON:0001007 digestive system. Is UBERON:0001264 pancreas meant to be equivalent (shadow class) to UBERON:2001371 pancreatic system, or is the UBERON:0001264 pancreas meant to be a part of the UBERON:2001371 pancreatic system?
    The later interpretation (and thereby asserting that "UBERON:0001264 pancreas part of some UBERON:2001371 pancreatic system") would potentially solve this issue.
  2. There are also separate terms for UBERON:0000016 endocrine pancreas and UBERON:0000017 exocrine pancreas. The UBERON:0000016 endocrine pancreas has already been asserted to be part of the UBERON:0000949 endocrine system. However, the UBERON:0000017 exocrine pancreas has not been defined in UBERON as part of the UBERON:0001007 digestive system.
    Analogously with the endocrine pancreas, we could assert that UBERON:0000017 exocrine pancreas is part of the UBERON:0001007 digestive system.

I favour solution 2., i.e. asserting that

exocrine pancreas part of some digestive system

.

@rays22
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rays22 commented Feb 20, 2024

I favour solution 2., i.e. asserting that

exocrine pancreas part of some digestive system

See PR #3227 .

rays22 added a commit that referenced this issue Feb 21, 2024
* Assert the exocrine pancreas to be part of the digestive system

* UBERON:0001007 'exocrine pancreas'

Fix #3208

* Restore uberon-edit.obo from master branch

* Reimplement assertion that pancreas is part of the digestive system
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