Getting moreArlinStoltzfusResearch Biologist, National Institute of Standards and TechnologyA project of the NESCent HIP (...
THE PROBLEMTree-of-Lifeknowledge• Mostly locked in pics• < 5% of trees archived• Hard to discover &accessResearchers, educ...
What big-tree methods generateWhat users needAPG framework tree Fig. 5 from Butler & King, 2004
~ 5% TO 15% NON-STANDARD NAMESFigure from Riek, 2011 Phylotastic tree after name correctionsOvisammonOreamnusamericanusFel...
Species1Species2Species3condition1condition2PhylotasticSpecies3Species1Species2Sources & methods
UpstreamstepsRectifynamesDiscovertreePrune &GraftAdd branchlengthsIntegrateother dataDownstreamanalysis
DataOperationsUser ControllerRectify Names(TNRS) NameBanksFind matching treesSource treesGraft missing taxaPrune extra tax...
Phylotastic Goal: access to expert ToL knowledge that is convenient – much easier than DIY tree computable – logically ...
HIP HACKATHONSHIP Leadership TeamParticipants
Phylotastic.org demos  pruner
ANNOTATING SOURCE TREES using a formal ontologySee Hilmar Lapp’s lightning talk
TNRSOreamnosamericanusOreamnusamericanus:No exact match
DATELIFE.ORGThe other kind of Dating with FossilsAsk Brian O’Meara, Tracy Heath, or Klaus Schliep-- scales trees by refere...
Julie Allen (software bazaar)
Reconciled Tree (red=duplication,green=speciation)
PHYLOTASTIC.ORGQuestions? Ask Arlin or email toarlin@umd.edu
Work in progress
THANKS! www.phylotastic.orgHIP Leadership TeamParticipants
Getting More Phylotastic
Getting More Phylotastic
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Getting More Phylotastic

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lightning talk for iEvoBio2013, June 25, 2013, delivered by Arlin Stoltzfus on behalf of HIP and the hackathon participants. Phylotastic is a distributed delivery system for expert knowledge of species phylogeny (the tree of life).

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Getting More Phylotastic

  1. 1. Getting moreArlinStoltzfusResearch Biologist, National Institute of Standards and TechnologyA project of the NESCent HIP (hackathons,interoperability, phyogenies) working group
  2. 2. THE PROBLEMTree-of-Lifeknowledge• Mostly locked in pics• < 5% of trees archived• Hard to discover &accessResearchers, educators,& resource-providerswho could use a goodspecies tree?
  3. 3. What big-tree methods generateWhat users needAPG framework tree Fig. 5 from Butler & King, 2004
  4. 4. ~ 5% TO 15% NON-STANDARD NAMESFigure from Riek, 2011 Phylotastic tree after name correctionsOvisammonOreamnusamericanusFeliscatusOvisariesOreamnosamericanusFelissilvestris
  5. 5. Species1Species2Species3condition1condition2PhylotasticSpecies3Species1Species2Sources & methods
  6. 6. UpstreamstepsRectifynamesDiscovertreePrune &GraftAdd branchlengthsIntegrateother dataDownstreamanalysis
  7. 7. DataOperationsUser ControllerRectify Names(TNRS) NameBanksFind matching treesSource treesGraft missing taxaPrune extra taxaTranslate formatsGet branch lengthsCalibrationsSpecies1Species2Species3condition1condition2Phylotastic
  8. 8. Phylotastic Goal: access to expert ToL knowledge that is convenient – much easier than DIY tree computable – logically encoded trees (not pics) credible – useable in a scientific paper
  9. 9. HIP HACKATHONSHIP Leadership TeamParticipants
  10. 10. Phylotastic.org demos  pruner
  11. 11. ANNOTATING SOURCE TREES using a formal ontologySee Hilmar Lapp’s lightning talk
  12. 12. TNRSOreamnosamericanusOreamnusamericanus:No exact match
  13. 13. DATELIFE.ORGThe other kind of Dating with FossilsAsk Brian O’Meara, Tracy Heath, or Klaus Schliep-- scales trees by reference to prior calibrationsDating with Fossils
  14. 14. Julie Allen (software bazaar)
  15. 15. Reconciled Tree (red=duplication,green=speciation)
  16. 16. PHYLOTASTIC.ORGQuestions? Ask Arlin or email toarlin@umd.edu
  17. 17. Work in progress
  18. 18. THANKS! www.phylotastic.orgHIP Leadership TeamParticipants
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