Open Tree of Life @Evolution 2012
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This document summarizes the goals of the Open Tree of Life project, which aims to assemble a complete draft tree of life by synthesizing existing phylogenetic trees. The project will publish this draft tree online with tools to allow community annotation, addition of new data, and download of the whole tree or subtrees. The project is in its early stages and seeks community input and participation to help curate data and further develop the online platform.
Open Tree of Life @Evolution 2012
- 1. A community-assembled, continually updated evolutionary history of all life Karen A. Cranston National Evolutionary Synthesis Center Duke University
- 2. opentreeoflife.org Karen Cranston (NESCent) Laura Katz (Smith) Gordon Burleigh (Florida) Rick Ree (FMNH) Keith Crandall (GWU) Stephen Smith (Michigan) Karl Gude (MSU) Doug Soltis (Florida) David Hibbett (Clark) Tiffani Williams (TAMU) Mark Holder (Kansas) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life
- 3. Phylogeny'papers,'1978;2008' 12000" 10000" Number'of'papers'published' 8000" Rapid"increase"in"applica?ons"of" phylogeny,"beginning"in"early"1990s" 6000" 4000" 2000" 0" 1978" 979" 980"1981" 982" 983" 984"1985" 986"1987" 988" 989" 990"1991" 992" 993" 994"1995" 996"1997" 998" 999" 000"2001" 002" 003" 004"2005" 006"2007" 008" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 Year' Source:"ISI"Web"of"Science"" graph from David Hillis
- 4. Where can I browse, search and download a complete tree of life? You can’t. (Yet)
- 6. DATA AVAILABILITY Community norm to archive sequence data ~4% of all published phylogenetic trees
- 7. Year one goals 1. Synthesize a complete draft tree of life from existing phylogenetic trees 2. Publish this draft tree with: a. ability to add annotations and upload new data sets b. highlighted areas of conflict and links to source data c. utilities to download whole tree and subtrees
- 8. + taxonomies of living and extinct species + digital phylogenetic data: Assembling the Tree of Life (and other) projects recent high-profile phylogenies ribosomal RNA trees for Bacteria and Archaea TreeBASE and Dryad trees Graph database holding thousands of input trees with millions of nodes
- 9. Dipsicales graph taxonomy data (578 taxa) + Soltis et al APG III phylogeny (30 taxa)
- 10. Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa
- 11. Graph database holding thousands of input trees with • filter / weight input trees millions of nodes • build synthetic trees • compare to alternate trees • input new data sets
- 12. AUTOMATIC UPDATING update trees with new sequence data detect and synthesize newly published trees
- 13. SMART GENERATION OF FIGURES FOR PUBLICATION • Semantic annotation layers • Collaborative editing EVOLUTION • Integrated submission of data and annotations to archives Weigmann et al. PNAS, 2011 ig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =
- 14. ? • Increasing availability of digital data associated with phylogeny publications • Makingsynthetic tree open to community annotation and data submission • Simple access to search and download the tree of life
- 15. ? • Open Science • project wiki: opentree.wikispaces.com • mailing list (opentreeoflife@googlegroups.com) • development board (trello.org/opentree)
- 17. • provide complete phylogenetic framework • link to biodiversity and systematics content
- 18. • provide complete phylogenetic framework • link to biodiversity and systematics content • API for downloading subtrees to analysis tools
- 19. • provide complete phylogenetic framework • link to biodiversity and systematics content • API for downloading subtrees to analysis tools • source / storage of underlying data
- 20. opentreeoflife.org • We’ve only just started (June 1) • Looking for input, feedback and participation: • join the mailing list • add publications to the Mendeley group • vote / comment on plans on the Trello boards • participate in virtual data curation sprint in August