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obophenotype / mouse-anatomy-ontology

Ontologies for mouse anatomy and development
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is the tongue a visceral organ? #14

Open cmungall opened 9 years ago

cmungall commented 9 years ago

The partonomy seems odd:

 / EMAPA:16245 ! visceral organ system
  po EMAPA:16246 ! alimentary system
   po EMAPA:16247 ! gut
    po EMAPA:16548 ! foregut
     po EMAPA:16706 ! pharynx
      po EMAPA:17185 ! tongue ***

I realize 'viscus' and 'visceral organ' is a pretty vague term, sometimes specifically referring to organs in the main body cavity, sometimes loosely meaning any 'internal organ', by which, I suppose, the tongue could be classified... but still seems unusual

tfhayamizu commented 9 years ago

Several issues brought up here:

(1) "visceral organ system" -- a legacy of the original mouse developmental anatomy ontology -- never been precisely clear what was intended here. Have circumvented this ambiguity somewhat by making the children direct subclasses of "organ system," but retained the "visceral organ system" term as a partonomic parent. The term does have annotations in GXD, mostly I think when authors referred to expression in "viscera." In most cases, the system term (rather than "viscus") more appropriately reflects the actual tissue sample being referred to.

(2) definition of "viscus": an internal organ of the body; especially : one (as the heart, liver, or intestine) located in the great cavity of the trunk proper -- key here being "especially" -- Does this mean ONLY?

(3) Also, does every structure that is a hierarchical part of a visceral organ SYSTEM actually have to be a "viscus"?

(4) Conversely, does every structure that is a hierarchical part of a system actually have to be a functional part of that system?

(5) Finally, is the "tongue" misplaced here? Developmentally, perhaps should not be part of "pharynx", but would be difficult to argue that it should not be part of the alimentary system.