NSF EF-1208727: AVAToL: Automated and community-driven synthesis of the tree of life

A comprehensive synthesis of the tree of life, a grand challenge since Darwin, will yield great benefits across all biological sciences. Recent years have seen great progress in the resolution of many significant clades, but synthesis on a large scale is currently inhibited by limits of available data, analytical power, and informatics infrastructure. Perhaps more importantly, it is also limited by a lack of compelling means and incentives for community participation.

The Open Tree of Life project (www.opentreeoflife.org) is a multi-institutional initiative to build a self-sustaining, community-driven, and continually updated tree based on syntheses of published phylogenetic and taxonomic knowledge using existing and novel methods. It will also enable the systematics community at large to annotate, improve, and expand this “first-draft” tree. Finally, through software development, services, and outreach, it will initiate a cultural transformation in the discipline towards pervasive and ingrained practices of data sharing.

Novel aspects (Ree Lab component):

  • Phylografter software: user-friendly, low-barrier-to-entry storage and retrieval of “source trees”, aligned to a common taxonomic framework, for the purpose of phylogenetic synthesis
  • development of graph-based methods for amalgamating source trees, using the Neo4j graph database
  • incentives for systematists to archive phylogenetic knowledge: specifically, development of tools enabling the creation of publication-quality tree figures that transparently store the data in open formats (e.g., JSON, NexML).