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Karen CranstonNational Evolutionary Synthesis Center@kcranstn / @opentreeoflifehttp://www.slideshare.net/kcranstnopentreeofl...
Gordon BurleighKeith CrandallKaren CranstonKarl GudeDavid HibbettMark HolderLaura KatzRick ReeStephen SmithDoug SoltisTiff...
What does it mean to “have” the tree of life?complete & dynamicbrowse, download, queryuse for research questionsimplies di...
Open Tree of LifeTaxonomy +Source trees•filter / weight input trees•combine into synthetic tree•feedback•input new data sets
~ 4% of all publishedphylogenetic treesStoltzfus et al 2012Inputs: Phylogenetic dataArchiving sequence data is a community...
Heroic data collection effortsSurveyed >7000 phylogenetic studies in plants, fungi andanimals, unicellular organismsResult...
Inputs: TaxonomiesLarge fraction of species not represented in phylogeniestaxonomy provides backbone & coverage at tips2,6...
Synthesis processSource trees(Phylografter) Data storage &synthesis(treemachine)OpenTree: visualize,comment, search,downlo...
Source tree managementphylografter.opentreeoflife.org
Synthesizing trees and taxonomiesGraph database for phylogenies (treemachine) andtaxonomy (taxomachine)Allows for extremel...
OpenTree browserdev.opentreeoflife.org/opentree
Public tree of lifepublictreeoflife.com/tree
“Open” Tree of Life
Collaborationsproviding images and text for public treedeveloping methods for subtree extractionsummer student providing l...
August 2013 release
Year 2 & 3 goalsRefine draft tree based on user feedback / new dataResearch into phylogenetic synthesisUser featuresHow doe...
Gordon BurleighKeith CrandallKaren CranstonKarl GudeDavid HibbettMark HolderLaura KatzRick ReeStephen SmithDoug SoltisTiff...
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Cranston Evolution 2013

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Open Tree of Life talk at Evolution symposium

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Cranston Evolution 2013

  1. 1. Karen CranstonNational Evolutionary Synthesis Center@kcranstn / @opentreeoflifehttp://www.slideshare.net/kcranstnopentreeoflife.org
  2. 2. Gordon BurleighKeith CrandallKaren CranstonKarl GudeDavid HibbettMark HolderLaura KatzRick ReeStephen SmithDoug SoltisTiffani Williams
  3. 3. What does it mean to “have” the tree of life?complete & dynamicbrowse, download, queryuse for research questionsimplies digital access
  4. 4. Open Tree of LifeTaxonomy +Source trees•filter / weight input trees•combine into synthetic tree•feedback•input new data sets
  5. 5. ~ 4% of all publishedphylogenetic treesStoltzfus et al 2012Inputs: Phylogenetic dataArchiving sequence data is a community norm
  6. 6. Heroic data collection effortsSurveyed >7000 phylogenetic studies in plants, fungi andanimals, unicellular organismsResult: data for >2300 studies, >4800 treesPoster P133003 tonight!
  7. 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. 8. Synthesis processSource trees(Phylografter) Data storage &synthesis(treemachine)OpenTree: visualize,comment, search,downloadTaxonomies(taxamachine)
  9. 9. Source tree managementphylografter.opentreeoflife.org
  10. 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. 11. OpenTree browserdev.opentreeoflife.org/opentree
  12. 12. Public tree of lifepublictreeoflife.com/tree
  13. 13. “Open” Tree of Life
  14. 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. 15. August 2013 release
  16. 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. 17. Gordon BurleighKeith CrandallKaren CranstonKarl GudeDavid HibbettMark HolderLaura KatzRick ReeStephen SmithDoug SoltisTiffani Williams

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