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cmungall / cell-ontology-DO-NOT-USE

Initial attempt to move repo from gcode. USE OBOPHENOTYPE
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intraepithelial cells #164

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
These are defined as being part_of the epithelium which is wrong.

They should be located_in the epithelium and part_of the larger structure

e.g.

id: CL:0000797
name: alpha-beta intraepithelial T cell
def: "A mature alpha-beta T cell of the columnar epithelium of the 
gastrointestinal tract. Intraepithelial T cells often have distinct 
developmental pathways and activation requirements." [GOC:add, GOC:tfm, 
ISBN:0781735149]
is_a: CL:0000791  ! mature alpha-beta T cell
is_a: CL:0002496  ! intraepithelial lymphocyte
relationship: RO:0002215 GO:0002385 ! mucosal immune response
relationship: part_of UBERON:0001277 ! intestinal epithelium
intersection_of: CL:0000791  ! mature alpha-beta T cell
intersection_of: RO:0002215 GO:0002385 ! mucosal immune response
intersection_of: part_of UBERON:0001277 ! intestinal epithelium

Should be located_in UBERON:0001277 ! intestinal epithelium (not part_of)

But can also be part_of intestine

(orthogonal aside: the logical axioms are locationally more specific 
[intestine] than the text def [gastrointestinal tract] which is implicitly more 
specific than the label[epithelium])

Original issue reported on code.google.com by cmung...@gmail.com on 6 Jan 2015 at 5:42