In the submission, we refer to a 'Haplotyping Locus.'? Would 'Haplotyping Gene' be a better term? We have reviewed the term and its definition quite extensively so I think this is just an opportunity to check that no-one has second thoughts about it. Particularly as we use 'Locus' in a separate context (see next point).
In the inferred sequence:
The options for 'Locus' are currently 'Heavy, Light-Kappa, Light-Lambda, Alpha, Beta, Gamma, Delta.' Christian suggests that we change to the IMGT terms 'IGH, IGK, IGL, TRA, TRB, TRG, TRD' and this makes sense to me. Do you agree?
When we discussed 'Domain' over the summer, I told you that, digging back through my notes, I had found that this was introduced to distinguish between leader, variable and constant region sequences. We concluded that 'Domain' was the least-worst name for this field. However, while implementing OGRDB I found that I needed to distinguish between V,D and J sequences, and I seem to have re-defined the field so that its options are V,D,J or Constant.
Thinking about this afresh, I propose that we rename 'Domain' to 'Sequence Type' and make its options 'Leader, V, D, J, CH1..CH4'. We could add other types later if desired.? Would this be ok? I can't find a suitable term in the IMGT lexicon. V,D,J,C are described as 'Core Regions' but it's clear from the context that this is a structural description, and has no extension to non-coding sequences.
williamdlees
commented
5 years ago
Arising from Christian's review:
In the inferred sequence:
The options for 'Locus' are currently 'Heavy, Light-Kappa, Light-Lambda, Alpha, Beta, Gamma, Delta.' Christian suggests that we change to the IMGT terms 'IGH, IGK, IGL, TRA, TRB, TRG, TRD' and this makes sense to me. Do you agree?
When we discussed 'Domain' over the summer, I told you that, digging back through my notes, I had found that this was introduced to distinguish between leader, variable and constant region sequences. We concluded that 'Domain' was the least-worst name for this field. However, while implementing OGRDB I found that I needed to distinguish between V,D and J sequences, and I seem to have re-defined the field so that its options are V,D,J or Constant.
Thinking about this afresh, I propose that we rename 'Domain' to 'Sequence Type' and make its options 'Leader, V, D, J, CH1..CH4'. We could add other types later if desired.? Would this be ok? I can't find a suitable term in the IMGT lexicon. V,D,J,C are described as 'Core Regions' but it's clear from the context that this is a structural description, and has no extension to non-coding sequences.