Cranston Evolution 2013
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The Open Tree of Life project aims to create a complete and freely accessible digital tree of life drawing from published phylogenetic studies and taxonomies. It has synthesized data from over 4,800 phylogenetic trees representing over 2,300 studies and 2.6 million taxonomic names. The synthesis process involves filtering and combining source trees from published studies into a single consensus tree using a graph database, while taxonomies provide taxon coverage. The resulting public tree of life is being refined with user feedback and new data. Future goals include improving the draft tree, developing synthesis methods, and adding user features like comparing trees and on-demand synthesis.
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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
- 13. “Open” Tree of Life
- 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