xenopus-anatomy / xao

XAO represents the anatomy and development of the African frogs Xenopus laevis and X. tropicalis.
http://www.xenbase.org/
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multiple locations for delta cell #32

Closed cmungall closed 6 years ago

cmungall commented 7 years ago
id: XAO:0005166
name: delta cell
relationship: BFO:0000050 XAO:0000129 ! intestine
relationship: BFO:0000050 XAO:0000128 ! stomach
relationship: BFO:0000050 XAO:0000159 ! islets of Langerhans
relationship: BFO:0000050 XAO:0000136 ! pancreas
def: "Somatostatin-producing cell that is found in the stomach, intestine and the pancreatic islets." []
xref: CL:0000173
synonym: "delta-cell" EXACT []
synonym: "pancreatic D cell" RELATED []
synonym: "D cell" RELATED []
synonym: "D-cell" RELATED []
synonym: "delta cells" RELATED []
synonym: "delta-cells" RELATED []

The relationship to pancreas is redundant with the islets relationship; let's ignore that for now

If you say

X part_of A
X part_of B
X part_of C

Then think of the venn diagram with the spatial extent of A, B and C. X is in the intersection of all 3. I don't think this is what you mean.

In uberon, stomach is spatially disjoint with intestine so XAO will cause inconsistencies when merged. See: https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern

there is no spatial disjointness between pancreas and intestine but even so you don't mean that every instance of a delta cell is found in the spatial overlap of these.

Another way to think about this: the true path rule in GO

The correct way to do this is to make 3 subtypes as in CL

      is_a CL:0000066 ! epithelial cell
       is_a CL:0000150 ! glandular epithelial cell
        is_a CL:0000164 ! enteroendocrine cell
         is_a CL:0000502 ! type D enteroendocrine cell *** [SYNONYM: "D cell" (exact)]
          is_a CL:0000173 ! pancreatic D cell
          is_a CL:0002265 ! type D cell of colon
          is_a CL:0002266 ! type D cell of small intestine
          is_a CL:0002267 ! type D cell of stomach

I think you should also xref the generic CL class if your delta cell is generic