Several interesting talks from the Evolution and iEvoBio meetings in Portland last week. Probably most relevant here were several comparative methods talks, and several ontology related talks at iEvoBio. Among the latter, I'll mention Nico Franz's talk on taxonomic ontologies, as well as a lightning talk by Suzi Lewis on a phylogenetically based ontology annotation tool (PAINT). The later is focused on protein orthologs, so it isn't directly relevant to Phylontal, but was nonetheless interesting. Franz's talk was a broad-ranging overview of some important issues in taxonomic ontologies, including the proposal of Schulz et al. (2008).
I presented a poster on Phylontal, as well as a lightning talk on the taxonomic ontology I developed and maintain for Phenoscape. The later was a brief summary and update (NCBI xrefs, common names, and updates to the collections vocabulary). The Phylontal poster is mostly a cleaned up version of the second half of my NESCent talk, but should give an idea of what it is about.
Recently I've been working on adding 'matrix' support to the Phylontal library, to eventually add alignment of character states as well as the possibility of 'unpacking' the homologies underlying a matrix (e.g., using data when you disagree with the homology judgments of the author).
Of course, if people archived their raw data or observations, there would be less need for unpacking matrices.