We have fostered the formation of taxonomically focused working groups, beginning with three groups (Plants, Arthropods, Vertebrates) and later welcoming the Porifera group for which initial ontology efforts are under way, in addition to an Informatics working group. Each of the RCN PIs leads one of these groups together with an ontologist or logician. An initial focus of each group has been communication. What ontology efforts and resources (e.g., existing glossaries or references) are out there for each of these groups? What ontology development and integration efforts will best further the science in these domains? We are discussing and facilitating the development of common anatomy reference ontologies and phenotype ontology alignments within relatively similar taxonomic groups. By taking advantage of taxonomic “comfort zones” we will be able to identify and proactively address a more comprehensive suite of alignment issues that will arise when attempting to align phenotype ontologies at more inclusive levels (e.g., Metazoa, Eukaryota, etc.).