Aannotations on RNA polymers are invalid according to the webservices

[ClairePA]

The following HELM strings are all displayed correctly in the webeditor, but considered invalid by the webservices.

RNA1{R(A"mutation")P.R(N)P.R(G)P}$$$$V2.0 RNA1{R(A)P.R"mutation"(N)P.R(G)P}$$$$V2.0 RNA1{R(A)P.R(N)P"mutation".R(G)P}$$$$V2.0

I can't see why any of these should be invalid.

[MarkusWeisser]

In RNA polymers, annotation is currently only supported for the monomer group (sugar-base-linker) not for each individual element of the group in the HELM2toolkit. Therefore, the last example is considered valid, example 1 and 2 not.

[ClairePA]

Hmm, perhaps we should talk about this in a meeting. Example 3 looks like the annotation is on the P and not the group as there is no specific indication that it is a group in the HELM. It feels odd for this to be valid and the others not. Tianhong - do you have any thoughts?

[ClairePA]

The team agreed that it should be possible to annotate all monomers. Therefore the following examples should be considered valid.

RNA1{R(A"mutation")P.R(N)P.R(G)P}$$$$V2.0 RNA1{R(A)P.R"mutation"(N)P.R(G)P}$$$$V2.0

[MarkusWeisser]

So, it is not a bug but a new feature.

[ClairePA]

An anomaly arising from a later clarification of ambiguous rules. ;-)