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)
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.
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.identificationcolumn (and a few more if we take leading white space into account)If we prune this list we can add
lysateandoverlapping-peptide-poolas 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.donorcolumn would also do the trick, but I think the difference in important information justifies the addition of an extra template.