As far as I'm aware the group with the greatest experience in ontology building - admittedly a young field - is OBO Foundry. The organizers have thought hard about good practice and community process and have practical experience with what does and doesn't work. The group says they're about biomedical ontologies, but there's nothing about their practices that wouldn't work in taxonomy-related domains.
http://www.obofoundry.org/about.shtml http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html
They are concerned with taxonomy, of course, but mostly as it relates to model organisms. Discussions about how to treat taxa have come up recently and I have told them they should look to the community that has fought these wars already...
Personally I'd like to see a lot more cross-fertilization between taxonomy (biodiversity, collections, ...) and biomedical domains. For example, collections issues come up in contexts such as pathology and biological materials (plasmids etc.). Anatomy is probably another point of overlap. I'm not saying you should join, but I urge you to see if there's anything in what they do you might learn from - and vice versa.
Best Jonathan Rees Science Commons