Missouri Botanical Garden Open Conference Systems, TDWG 2013 ANNUAL CONFERENCE

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Assembling a draft overall tree of life from phylogenetic trees and taxonomic databases
Jonathan A Rees

Building: Grand Hotel Mediterraneo
Room: America del Nord (Theatre I)
Date: 2013-10-31 09:15 AM – 09:25 AM
Last modified: 2013-10-05

Abstract


The Open Tree of Life project is assembling a large number of phylogenetic trees into a single draft tree of life.  Because the draft tree is open for reuse and links back to the input trees and studies from which it draws, it has the potential to become a useful general resource for 'consumers' of phylogenetic trees.  I will report on progress to date and talk about some of the challenges we have encountered as we have made progress toward this goal, in particular:
  • The response rate to requests for machine-readable phylogenetic trees has been much lower than had been hoped.
  • Tree curation is more labor-intensive than we expected.  Operational taxonomic units need to be mapped onto a canonical taxon list so that they can be unified between trees; this is not always easy, for a variety of reasons.  In addition, ingroup designation and rooting, which are required for assembly purposes, are rarely articulated and not always easy to figure out.
  • Taxonomy has assumed more importance than we initially anticipated.  We need a good taxon list for tree unification, and taxonomic relationships for internal node labeling and for filling in gaps in the set of phylogenetic trees.  The information we needed wasn't available from any single taxonomic source, so we had to put in place a taxonomy assembly process in addition to phylogeny assembly.
We have a web application that allows one to query and browse the assembled tree.  Current efforts are focused on expanding the set of trees that go into the assembly, enhancing our curation tools to enable crowdsourcing, and opening up the corpus of curated trees to recruit reuse and improvement from a broader developer community.