So other than the package name, this class name change is the only outstanding suggestion that I'm aware of. I'm leaning toward not changing it. Unclear how it would clarify anything (biom is an acronym that implies matrix aka table, already). Furthermore, and more importantly, on the R-side the "biom" class right now is a very general class, basically a subclass of "list", with some validity methods that are mainly checking that it looks like the RJSONIO-created list from a biom object, has the biom-format required keys, and that things are self-consistent. Very easy to define additional sub-class(es) that inherit this one, and give them a more specialized name. So (1) I don't see how adding "table" to the end of the class name will help clarify anything, instead adding to the list of words users have to remember; and (2) just from a practical standpoint -- and this is my fault for not clarifying this ahead of time -- there are a lot of things with "biom" in part of their name, so the find/replace, `gsub`, take your pick is actually context specific and will be a pain for me to change at this stage. If there was some functional issue, present or planned, that could be solved by changing this class name I'd be up for it. Without that I probably won't have the motivation, especially when this is a scenario (package name, class name, constructor name all the same) R users are familiar with. 

My two cents. Let me know if I missed something. And thanks for all the tedious reviews @jrrideout I know those are time consuming and it's always useful.