NTR: antigen-presenting cell

[GoogleCodeExporter]

Should we add "antigen presenting cell"?

In MP this is a distinct concept, sibling to leukocyte

...is_a MP:0000685 ! abnormal immune system morphology
....is_a MP:0000716 ! abnormal immune system cell morphology
.....is_a MP:0005460 ! abnormal leukopoiesis
.....is_a MP:0008195 ! abnormal **antigen presenting cell** morphology
.....is_a MP:0008246 ! abnormal **leukocyte** morphology

wikipedia includes fibroblasts, glia...
http://en.wikipedia.org/wiki/Antigen-presenting_cell

I suspect the omission of this class from CL is deliberate. If so, I suggest 
leaving some kind of indication that this is the case. For example:

* Create a class APC, and immediately obsolete it
* Add APC as a synonym for an existing class (e.g. leukocyte) and add a note 
the the syn

The MP should then be changed to reflect the CL. At the moment, APC is a 
singling to leukocyte - but all the children are leukocytes AFAIK:

...is_a MP:0000685 ! abnormal immune system morphology
....is_a MP:0000716 ! abnormal immune system cell morphology
morphology
.....is_a MP:0008195 ! abnormal antigen presenting cell morphology
......is_a MP:0002446 ! abnormal macrophage morphology
......is_a MP:0005461 ! abnormal dendritic cell morphology
......is_a MP:0008171 ! abnormal mature B cell morphology
......is_a MP:0008196 ! abnormal follicular dendritic cell morphology
.....is_a MP:0008246 ! abnormal leukocyte morphology
......is_a MP:0000217 ! abnormal leukocyte cell number
......is_a MP:0005461 ! abnormal dendritic cell morphology
......is_a MP:0008247 ! abnormal mononuclear cell morphology
......is_a MP:0008250 ! abnormal myeloid leukocyte morphology

Original issue reported on code.google.com by cmung...@gmail.com on 7 May 2013 at 12:49

[GoogleCodeExporter]

CL has long had the following term:

[Term]
id: CL:0000145
name: professional antigen presenting cell
namespace: cell
def: "A cell capable of processing and presenting lipid and protein antigens to 
T cells in order to initiate an immune response." [GOC:add, ISBN:0781735149]
comment: Note change of name; nearly all somatic cells can present antigens to 
T cells via MHC Class I complexes leading to effector responses, but 
professional antigen presenting cells constitutively express MHC Class II as 
well as costimulatory molecules, and thus can initiate immune responses via T 
cells.
synonym: "APC" BROAD []
is_a: CL:0000473 ! defensive cell
relationship: RO:0002215 GO:0002504 ! capable_of antigen processing and 
presentation of peptide or polysaccharide antigen via MHC class II

(sorry, it's easier to show the obo stanza than the OWL)

perhaps we can use this cell type for the MP's purposes.

Also, I would note that "follicular dendritic cell" are not professional 
antigen presenting cells, nor are they even leukocytes or bone marrow-dervied, 
despite the name.  They do serve a function in the immune system in promoting B 
cell responses, but they do not present antigens to T cells (at least according 
to current dogma), which is what antigen presentation is all about.

On the other hand, macrophages, B cells, and other dendritic cells 
(conventional, myeloid, plasmacytoid) are all considered professional antigen 
presenting cells.

-- Alex

Original comment by addi...@buffalo.edu on 7 May 2013 at 3:25

[GoogleCodeExporter]

It appears that I derived the MP "antigen presenting cell" terms from 
CL:0000145 originally, but this was several years ago. There is a note in the 
comment of the CL term that the name had been changed, so it's possible that I 
had an earlier name and relationship to other terms, that have since been 
revised.  I can change the term name to "abnormal professional antigen 
presenting cell morphology" (and also for the physiology term)

I have also moved the "follicular dendritic cell" terms so that they are no 
longer children of "abnormal professional antigen presenting cell" terms. 

-- Cindy

Original comment by cynthia....@jax.org on 7 May 2013 at 3:29