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Cranston Evolution 2013

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Open Tree of Life talk at Evolution symposium

Open Tree of Life talk at Evolution symposium

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  • 1. Karen CranstonNational Evolutionary Synthesis Center@kcranstn / @opentreeoflifehttp://www.slideshare.net/kcranstnopentreeoflife.org
  • 2. Gordon BurleighKeith CrandallKaren CranstonKarl GudeDavid HibbettMark HolderLaura KatzRick ReeStephen SmithDoug SoltisTiffani Williams
  • 3. What does it mean to “have” the tree of life?complete & dynamicbrowse, download, queryuse for research questionsimplies digital access
  • 4. Open Tree of LifeTaxonomy +Source trees•filter / weight input trees•combine into synthetic tree•feedback•input new data sets
  • 5. ~ 4% of all publishedphylogenetic treesStoltzfus et al 2012Inputs: Phylogenetic dataArchiving sequence data is a community norm
  • 6. Heroic data collection effortsSurveyed >7000 phylogenetic studies in plants, fungi andanimals, unicellular organismsResult: data for >2300 studies, >4800 treesPoster P133003 tonight!
  • 7. Inputs: TaxonomiesLarge fraction of species not represented in phylogeniestaxonomy provides backbone & coverage at tips2,644,685 names: NCBI (structure) + GBIF (completeness)https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-Taxonomy
  • 8. Synthesis processSource trees(Phylografter) Data storage &synthesis(treemachine)OpenTree: visualize,comment, search,downloadTaxonomies(taxamachine)
  • 9. Source tree managementphylografter.opentreeoflife.org
  • 10. Synthesizing trees and taxonomiesGraph database for phylogenies (treemachine) andtaxonomy (taxomachine)Allows for extremely efficient storage and retrievalRules to extract binary tree from highly conflicting graphMore details? StephenSmith 8:30 am Monday!
  • 11. OpenTree browserdev.opentreeoflife.org/opentree
  • 12. Public tree of lifepublictreeoflife.com/tree
  • 13. “Open” Tree of Life
  • 14. Collaborationsproviding images and text for public treedeveloping methods for subtree extractionsummer student providing links to ToLWebpagestreeviz project from U Indiana MOOC,GNOME summer internpartner for data archiving / harvest
  • 15. August 2013 release
  • 16. Year 2 & 3 goalsRefine draft tree based on user feedback / new dataResearch into phylogenetic synthesisUser featuresHow does my tree compare with others?Synthesis on demandQuantifying / visualizing conflictSuggestions?
  • 17. Gordon BurleighKeith CrandallKaren CranstonKarl GudeDavid HibbettMark HolderLaura KatzRick ReeStephen SmithDoug SoltisTiffani Williams

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