(apologies if you receive this multiple times - we are trying to reach as many interested researchers from the taxonomic/systematic community as possible)
Under the umbrella of the Open Biomedical Ontologies project (OBO; http://obofoundry.org/) we have created a new mailing list, called obo-taxonomy, for the discussion of ontological representation of taxonomies and phylogenies. The OBO Foundry supports the development of orthogonal, interoperable reference ontologies for biological science.
The Phenoscape project (http://phenoscape.org) develops methods and tools for using ontologies to integrate comparative morphological data with mutant phenotypes of genetic model organisms. As such we are very interested in participation from members of the evolutionary biology community to explore how best to integrate taxonomy into an ontological framework. Issues include proper semantics of the relationship between taxonomic groups, and between specimens and species.
Subscribe to the mailing list: https://lists.sourceforge.net/lists/listinfo/obo-taxonomy
Additional info: http://blog.phenoscape.org/2008/05/15/taxonomy-as-ontology-opening- the-debate/
Acknowledgments: The Phenoscape project (http://phenoscape.org/) is funded by NSF-BDI and supported by the National Evolutionary Synthesis Center (NESCent; http://nescent.org).
-hilmar