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Initial attempt to move repo from gcode. USE OBOPHENOTYPE
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NTR - effector memory CD8-positive, alpha-beta T cell - Terminally differentiated #110

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
New term request

label: effector memory CD8-positive, alpha-beta T cell - Terminally 
differentiated
synonym: terminally differentiated effector memory CD8+ cell
synonym:  TEMRA
Definition: A CD8-positive, alpha beta memory T cell with the phenotype 
CCR7-negative, CD127-positive, CD45RA-positive, and CD25-negative. 
[PMID:16237082]
is a: CL:0000909 - CD8-positive, alpha-beta T cell CD8-positive, alpha-beta T 
cell
Relationship:   develops_from CL:0000913 - effector memory CD8-positive, 
alpha-beta T cell

Original issue reported on code.google.com by david.m....@gmail.com on 24 Jan 2014 at 1:35

GoogleCodeExporter commented 9 years ago 
Added draft term as requested.  This has not yet been release, but can be 
reviewed in cl-edit.owl in the trunk.  Assigning to Alex to review before 
release.

Original comment by dosu...@gmail.com on 4 Mar 2014 at 11:45

GoogleCodeExporter commented 9 years ago 
Notes on this term from Alex:
"This is a rather tricky cell type.  Based on the provided reference, 
PMID:16237082 and an earlier review, PMID:15032595, it is clear that this cell 
type, 'effector memory CD8-positive, alpha-beta T cell, terminally 
differentiated' or TEMRA, is found in human but not mouse, and breaks the 
phenotype used commonly to define memory T cells, that of being CD45RO+, as 
PMID:15032595 indicates it is CD45RO-negative and CD45RA+.

I have adjusted the definition and created the appropriate logical definition 
to match. 

Although this cell type is named as a memory T cell, since we define the 
general 'memory T cell' class in CL as being CD45RO+, this cell type does not 
get placed upon reasoning under 'memory T cell' in the hierarchy, unlike all 
other memory T cells in the CL.  We'll need to come up with an alternate, 
probably functional definition of T cell memory to unite all the cell types 
called memory T cells.

Also, I noticed after reasoning that this cell type, 'effector memory 
CD8-positive, alpha-beta T cell, terminally differentiated' is actually quite 
similar to another cell type I added for the HIPC project, 'effector 
CD8-positive, alpha-beta T cell' (CL:001050), and I suspect the two terms 
actually refer to the same cell type.  I will follow up with the HIPC people to 
see if they think this is true.

In any case for now I think this term can be included in a release, although we 
may make changes later based on expert advice and additional literature review."

Original comment by dosu...@gmail.com on 5 Mar 2014 at 7:05