One thing that has been in the back of my mind for a long time now is that we need to have a way to allow users to hide the “taxonomic level indicators” (e.g., the leading
k__ in Greengenes taxonomy files) from their taxonomy strings in visualizations, especially ones that end up in publications. That’s really hard to build into a visualization though, since a visualization never knows if or what level indicators are present.
I was thinking it might make sense to define some new formats that were database-specific, and these could have transformers that strip that information on import. For example, we could have a
Greengenes-13-8-Taxonomy which could be used to import a taxonomy file in the Greengenes 13_8 format, and a corresponding transformer would strip the
p__, …, from the taxonomy labels on import. We could also have a Silva-specific format which would handle stripping of the Silva level indicators.
Thoughts on this approach?