Karen CranstonNational Evolutionary Synthesis Center@kcranstnhttp://www.slideshare.net/kcranstnopentreeoflife.org
What does it mean to “have” the tree of life?complete & dynamicbrowse, download, queryuse for research questionsimplies di...
0"2000"4000"6000"8000"10000"12000"1978"1979"1980"1981"1982"1983"1984"1985"1986"1987"1988"1989"1990"1991"1992"1993"1994"199...
Goals1. Synthesize a complete draft tree of life from existing phylogenies2. Release in year 1 with:a. engaging public int...
Graph databases oftaxonomy + source trees•filter / weight input trees•combine into synthetic trees•feedback•input new data ...
~ 4% of all publishedphylogenetic treesStoltzfus et al 2012Inputs: Phylogenetic dataArchiving sequence data is a community...
assemblyalignmentinferenceexpertisetime$$$thermore, a paraphyletic relationship of phorids and syrphidswould support the h...
Heroic data collection effortsSurveyed >7000 phylogenetic studies in plants, fungi andanimals, unicellular organismsResult...
Inputs: TaxonomyLarge fraction of species not represented in phylogeniestaxonomy provides backbone & coverage at tipsNeed ...
ProcessSource trees(Phylografter) Data storage &synthesis(treemachine)OpenTree:visualization,search, downloadTaxonomies(ta...
Source tree managementphylografter.opentreeoflife.org
Source tree & taxonomy synthesisNovel graph database for phylogenies (treemachine) andtaxonomy (taxomachine)Allows for effi...
OpenTreedev.opentreeoflife/opentree
Public tree of lifepublictreeoflife.com/tree
open data: requiring CC0 license on source treesopen source software: https://github.com/OpenTreeOfLifewiki: http://opentr...
Community engagement~50 visitors per day to blog.opentreeoflife.org@opentreeoflife on Twitter (~900 followers)Tree of Life s...
Collaborationsproviding images and text for public treedeveloping methods for subtree extractionsummer student providing l...
Assessment: PI surveygeneral satisfaction with progress on data collection,synthesis and software developmentmore focus on...
Assessment: Advisory board	Members:David Hillis (UT Austin)Jan Reichelt (Mendeley)Andy Sinauer (Sinauer Associates)Plannin...
On track for year 1 release1. Synthesize a complete draft tree of life from existing phylogenies2. Release in year 1 with:...
Goals for year 2Refine draft tree based on user feedbackEmpirical use cases drive developmentIncentives for users / data co...
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Open Tree of Life @NSF

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Presentation about Open Tree of Life given at NSF, May 2013

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Open Tree of Life @NSF

  1. 1. Karen CranstonNational Evolutionary Synthesis Center@kcranstnhttp://www.slideshare.net/kcranstnopentreeoflife.org
  2. 2. What does it mean to “have” the tree of life?complete & dynamicbrowse, download, queryuse for research questionsimplies digital access
  3. 3. 0"2000"4000"6000"8000"10000"12000"1978"1979"1980"1981"1982"1983"1984"1985"1986"1987"1988"1989"1990"1991"1992"1993"1994"1995"1996"1997"1998"1999"2000"2001"2002"2003"2004"2005"2006"2007"2008"NumberofpaperspublishedYearPhylogenypapers,1978;2008Source:"ISI"Web"of"Science""Rapid"increase"in"applica?ons"of"phylogeny,"beginning"in"early"1990s"graph from David Hillis
  4. 4. Goals1. Synthesize a complete draft tree of life from existing phylogenies2. Release in year 1 with:a. engaging public interfaceb. ability to upload new data, explore conflict, see provenancec. open data: tree, subtrees and source data
  5. 5. Graph databases oftaxonomy + source trees•filter / weight input trees•combine into synthetic trees•feedback•input new data sets
  6. 6. ~ 4% of all publishedphylogenetic treesStoltzfus et al 2012Inputs: Phylogenetic dataArchiving sequence data is a community norm
  7. 7. assemblyalignmentinferenceexpertisetime$$$thermore, a paraphyletic relationship of phorids and syrphidswould support the hypothesis that their shared special mode ofextraembryonic development (dorsal amnion closure) (26)evolved in the stem lineage of Cyclorrhapha and preceded theorigin of the schizophoran amnioserosa.To test this hypothesis, we used a relatively recent phylogenomicmarker: small, noncoding, regulatory micro-RNAs (miRNAs).miRNAs exhibit a striking phylogenetic pattern of conservationacross the metazoan tree of life, suggesting the accumulation andmaintenance of miRNA families throughout organismal evolutionFig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im-proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The numberof origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology ofthe organisms.Wiegmann et al. PNAS Early Edition | 3 of 6Why do we need to database phylogenetic trees?
  8. 8. Heroic data collection effortsSurveyed >7000 phylogenetic studies in plants, fungi andanimals, unicellular organismsResult: repository of data for >2300 studies, >4800 treesRemaining data not available digitallyManuscript accepted to PLoS Biology
  9. 9. Inputs: TaxonomyLarge fraction of species not represented in phylogeniestaxonomy provides backbone & coverage at tipsNeed name resolution services for data cleaning
  10. 10. ProcessSource trees(Phylografter) Data storage &synthesis(treemachine)OpenTree:visualization,search, downloadTaxonomies(taxamachine)
  11. 11. Source tree managementphylografter.opentreeoflife.org
  12. 12. Source tree & taxonomy synthesisNovel graph database for phylogenies (treemachine) andtaxonomy (taxomachine)Allows for efficient storage and retrieval
  13. 13. OpenTreedev.opentreeoflife/opentree
  14. 14. Public tree of lifepublictreeoflife.com/tree
  15. 15. open data: requiring CC0 license on source treesopen source software: https://github.com/OpenTreeOfLifewiki: http://opentree.wikispaces.com/ (52 members)public mailing list (67 members)“Open” Tree of Life
  16. 16. Community engagement~50 visitors per day to blog.opentreeoflife.org@opentreeoflife on Twitter (~900 followers)Tree of Life symposium: Evolution 2013Hackathon in year 2 (joint with Arbor)
  17. 17. Collaborationsproviding images and text for public treedeveloping methods for subtree extractionsummer student providing links to ToLWebpagestreeviz project from U Indiana MOOC,upcoming summer internyear 2-3 plans for data archiving / harvest
  18. 18. Assessment: PI surveygeneral satisfaction with progress on data collection,synthesis and software developmentmore focus on incentives for usersmore integration across labs
  19. 19. Assessment: Advisory board Members:David Hillis (UT Austin)Jan Reichelt (Mendeley)Andy Sinauer (Sinauer Associates)Planning meeting for start of year 2
  20. 20. On track for year 1 release1. Synthesize a complete draft tree of life from existing phylogenies2. Release in year 1 with:a. engaging public interfaceb. ability to upload new data, explore conflict, see provenancec. open data: tree, subtrees and source data
  21. 21. Goals for year 2Refine draft tree based on user feedbackEmpirical use cases drive developmentIncentives for users / data contributorsCollaboration with external projects (AVAToL, ToLWeb,Phylotastic, Dryad)
  22. 22. opentreeoflife.org

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