Addition of TCRs from stimulation with undetermined epitope

[ustervbo]

Our laboratory mostly use overlapping peptide pools and occasionally test for allo-reaction in transplantation settings. Others use lysates of whole pathogens.

I think it could be relatively easy to add TCRs from experiments that do not make use of well defined epitope sequences if we expand on the idea of a controlled vocabulary as in the antigen_epitope_species_gene.dict.

Currently we have the following entries in the method.identification column (and a few more if we take leading white space into account)

antigen loaded targets      
antigen-expressing cells    
antigen-expressing-targets
antigen-loaded-targed
antigen-loaded-target
antigen-loaded-targets      
beads
cd8null-tetramer-sort
cla
cloning-by-limiting-dilution
CTL clone
CTL culture                
cultivated-t-cells
cultured-T-cells
dextramer-sort
IFNg capture assay
limited-dilution-cloning
limiting-diffusion-cloning  
limiting-dilution-cloning
MHC-peptide-beads
multimer-sort
pelimer-sort
pentamer-sort
peptide-restimulation       
streptamer-sort
tetramer-magnetic-selection
Tetramer-sort
tetramer-sort

If we prune this list we can add lysate and overlapping-peptide-pool as allowed entries.

I that addition of allo-reactive TCRs require an additional template because the epitope specific columns are irrelevant and will just be in the way, but the donor MHC becomes extremely important.

Adding a mhc.donor column would also do the trick, but I think the difference in important information justifies the addition of an extra template.