Phyloreferencing: Creating Computable Clade Definitions in the Web Ontology Language (OWL)

Phyloreferencing aims to provide a standard mechanism for defining biological clades with precise and fully machine-processable semantics. We use ontologies and OWL (a formal ontology language developed by the W3C) to enable users to create definitions with precise, unambiguous, and fully computable semantics for any organismal clade. We call such definitions phyloreferences, in analogy to georeferences, which have enabled countless geo-enabled applications. We employ machine reasoners to determine which elements in a phylogeny match a phyloreference. We are developing the OWL ontologies, OWL data models, and tooling infrastructure needed to put our approach into practice, and to validate that it works correctly and scalably. We will also develop web applications that allow users to create, find, and reuse phyloreferences, and to apply them to phylogenies both small and Tree of Life-scale, for the purpose of integrating biodiversity data of interest. To accomplish this, we will be working with other biodiversity e-Science projects (including Open Tree of Life and the Encyclopedia of Life) as well as large organismal research collaborations.

Gaurav Vaidya was the lead developer of this project as a postdoctoral researcher before he started working at RENCI. The University of Florida has subcontracted some of the remaining work to RENCI.

• Duke University
• University of Florida

• National Science Foundation