We present the concept and current state of implementation of phyloreferences, an informatics tool for integrating taxon-linked data by the use of clade definitions with fully computable semantics based on ancestral relationships. Phyloreferences can be represented in the Web Ontology Language (OWL) as a set of logical constraints using concepts defined in the Comparative Data Analysis Ontology (CDAO) as well as those from a new ontology we are developing. CDAO can also be used to represent an entire phylogeny. Any reasoner capable of classification using the OWL2 Direct Semantics (OWL-DL) profile may then be used to generate a list of nodes and branches included by the phyloreference in that particular phylogeny. This methodology may be applied to any phyloreference and any phylogeny that can be represented in OWL, providing a great deal of flexibility in their definition and use. To continuously validate the correctness and expressive power of our approach, we are building a test suite for a collection of phyloreferences that correspond to phylogenetic clade definitions actually used in the wild. We welcome contributions to this collection, including in the form of taxonomic names whose ambiguity makes existing data integration difficult. In this talk, we will describe our methodology and the current roadmap for implementation. Ultimately we aim for phyloreferences to become a community standard, and we therefore show how the community can participate early on.
