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Karen Cranston
National Evolutionary Synthesis Center
@kcranstn / @opentreeoflife
http://www.slideshare.net/kcranstn
opentreeoflife.org
Gordon Burleigh
Keith Crandall
Karen Cranston
Karl Gude
David Hibbett
Mark Holder
Laura Katz
Rick Ree
Stephen Smith
Doug Soltis
Tiffani Williams
What does it mean to “have” the tree of life?
complete & dynamic
browse, download, query
use for research questions
implies digital access
Open Tree of Life
Taxonomy +
Source trees
•filter / weight input trees
•combine into synthetic tree
•feedback
•input new data sets
~ 4% of all published
phylogenetic trees
Stoltzfus et al 2012
Inputs: Phylogenetic data
Archiving sequence data is a community norm
Heroic data collection efforts
Surveyed >7000 phylogenetic studies in plants, fungi and
animals, unicellular organisms
Result: data for >2300 studies, >4800 trees
Poster P133003 tonight!
Inputs: Taxonomies
Large fraction of species not represented in phylogenies
taxonomy provides backbone & coverage at tips
2,644,685 names: NCBI (structure) + GBIF (completeness)
https://github.com/OpenTreeOfLife/opentree/wiki/Open-
Tree-Taxonomy
Synthesis process
Source trees
(Phylografter) Data storage &
synthesis
(treemachine)
OpenTree: visualize,
comment, search,
download
Taxonomies
(taxamachine)
Source tree management
phylografter.opentreeoflife.org
Synthesizing trees and taxonomies
Graph database for phylogenies (treemachine) and
taxonomy (taxomachine)
Allows for extremely efficient storage and retrieval
Rules to extract binary tree from highly conflicting graph
More details? Stephen
Smith 8:30 am Monday!
OpenTree browser
dev.opentreeoflife.org/opentree
Public tree of life
publictreeoflife.com/tree
“Open” Tree of Life
Collaborations
providing images and text for public tree
developing methods for subtree extraction
summer student providing links to ToLWeb
pages
treeviz project from U Indiana MOOC,
GNOME summer intern
partner for data archiving / harvest
August 2013 release
Year 2 & 3 goals
Refine draft tree based on user feedback / new data
Research into phylogenetic synthesis
User features
How does my tree compare with others?
Synthesis on demand
Quantifying / visualizing conflict
Suggestions?
Gordon Burleigh
Keith Crandall
Karen Cranston
Karl Gude
David Hibbett
Mark Holder
Laura Katz
Rick Ree
Stephen Smith
Doug Soltis
Tiffani Williams

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Cranston Evolution 2013

  • 1. Karen Cranston National Evolutionary Synthesis Center @kcranstn / @opentreeoflife http://www.slideshare.net/kcranstn opentreeoflife.org
  • 2. Gordon Burleigh Keith Crandall Karen Cranston Karl Gude David Hibbett Mark Holder Laura Katz Rick Ree Stephen Smith Doug Soltis Tiffani Williams
  • 3. What does it mean to “have” the tree of life? complete & dynamic browse, download, query use for research questions implies digital access
  • 4. Open Tree of Life Taxonomy + Source trees •filter / weight input trees •combine into synthetic tree •feedback •input new data sets
  • 5. ~ 4% of all published phylogenetic trees Stoltzfus et al 2012 Inputs: Phylogenetic data Archiving sequence data is a community norm
  • 6. Heroic data collection efforts Surveyed >7000 phylogenetic studies in plants, fungi and animals, unicellular organisms Result: data for >2300 studies, >4800 trees Poster P133003 tonight!
  • 7. Inputs: Taxonomies Large fraction of species not represented in phylogenies taxonomy provides backbone & coverage at tips 2,644,685 names: NCBI (structure) + GBIF (completeness) https://github.com/OpenTreeOfLife/opentree/wiki/Open- Tree-Taxonomy
  • 8. Synthesis process Source trees (Phylografter) Data storage & synthesis (treemachine) OpenTree: visualize, comment, search, download Taxonomies (taxamachine)
  • 10. Synthesizing trees and taxonomies Graph database for phylogenies (treemachine) and taxonomy (taxomachine) Allows for extremely efficient storage and retrieval Rules to extract binary tree from highly conflicting graph More details? Stephen Smith 8:30 am Monday!
  • 12. Public tree of life publictreeoflife.com/tree
  • 14. Collaborations providing images and text for public tree developing methods for subtree extraction summer student providing links to ToLWeb pages treeviz project from U Indiana MOOC, GNOME summer intern partner for data archiving / harvest
  • 16. Year 2 & 3 goals Refine draft tree based on user feedback / new data Research into phylogenetic synthesis User features How does my tree compare with others? Synthesis on demand Quantifying / visualizing conflict Suggestions?
  • 17. Gordon Burleigh Keith Crandall Karen Cranston Karl Gude David Hibbett Mark Holder Laura Katz Rick Ree Stephen Smith Doug Soltis Tiffani Williams