The Semantic Clade

The Semantic Clade

A presentation on phyloreferencing at Evolution 2016

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Gaurav Vaidya

June 18, 2016
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Transcript

  1. THE SEMANTIC CLADE Gaurav Vaidya (University of Colorado Boulder/University of

    Florida) Hilmar Lapp (Duke University) Nico Cellinese (University of Florida)
  2. None
  3. CAMPANULOIDEAE Are you kidding me? These are the Campanuloideae! Wang

    et al. 2014
  4. CAMPANULOIDEAE

  5. None
  6. CAMPANULOIDEAE

  7. Linnean names point to concepts Antoine Laurent de Jussieu Genera

    Plantarum, 1789
  8. NO NAMES AT ALL Page (2016)

  9. Hinchliff et al. (2016) www.opentreeoflife.org

  10. A SEMANTIC CLADE

  11. A SEMANTIC CLADE Node-based A B C Last common ancestor

    of B and C The clade originating with:
  12. A SEMANTIC CLADE Node-based Branch-based A A B B C

    C Last common ancestor of B and C Last ancestor of B that is not an ancestor of A The clade originating with:
  13. A SEMANTIC CLADE Node-based Branch-based Apomorphy-based A A A B

    B B C C C Last common ancestor of B and C X Last ancestor of B that is not an ancestor of A Last ancestor of B that exhibits apomorphy X The clade originating with:
  14. A SEMANTIC CLADE Node-based Branch-based Apomorphy-based A A A B

    B B C C C X Phyloreference
  15. Both the Encyclopedia of Life (EOL) and the Open Tree

    of Life suggest that Campanuloideae is a misspelling of Campaniloidea (marine gastropods!) GBIF does not currently have Campanuloideae in its backbone taxonomy.
  16. Both the Encyclopedia of Life (EOL) and the Open Tree

    of Life suggest that Campanuloideae is a misspelling of Campaniloidea (marine gastropods!) GBIF does not currently have Campanuloideae in its backbone taxonomy.
  17. Both the Encyclopedia of Life (EOL) and the Open Tree

    of Life suggest that Campanuloideae is a misspelling of Campaniloidea (marine gastropods!) GBIF does not currently have Campanuloideae in its backbone taxonomy. Campanulaceae: Last ancestor of Campanula latifolia that excludes Roussea simplex
  18. Both the Encyclopedia of Life (EOL) and the Open Tree

    of Life suggest that Campanuloideae is a misspelling of Campaniloidea (marine gastropods!) GBIF does not currently have Campanuloideae in its backbone taxonomy. has_Ancestor some (has_Descendant value Campanula_latifolia and excludes_lineage_to value Roussea_simplex)
  19. WEB ONTOLOGY LANGUAGE

  20. WEB ONTOLOGY LANGUAGE

  21. WHAT ARE WE BUILDING? • An online resource (www.phyloref.org) that

    will allow you to:
  22. WHAT ARE WE BUILDING? • An online resource (www.phyloref.org) that

    will allow you to: • Interactively generate phyloreferences.
  23. WHAT ARE WE BUILDING? • An online resource (www.phyloref.org) that

    will allow you to: • Interactively generate phyloreferences. • Upload a tree to find clades based on one or more phyloreferences.
  24. WHAT ARE WE BUILDING? • An online resource (www.phyloref.org) that

    will allow you to: • Interactively generate phyloreferences. • Upload a tree to find clades based on one or more phyloreferences. • Annotate a tree with known phyloreferences.
  25. INTERESTED? • Check out our website: http://phyloref.org/ • Get in

    touch! • Gaurav Vaidya: @mrvaidya, http://mrvaidya.com/ • Hilmar Lapp: @hlapp • Nico Cellinese: @ncellinese
  26. ACKNOWLEDGEMENTS • NSF: “Collaborative Research: ABI Innovation: An Ontology-Based System

    for Querying Life in a Post-Taxonomic Age” (NSF-DBI 1458604)
  27. QUESTIONS?

  28. FIGURES • Screenshots: • http://www.gbif.org/species/359 • http://www.gbif.org/species/search?q=Campanuloidea&dataset_key=d7dddbf4-2cf0-4f39-9b2a- bb099caae36c • http://www.gbif.org/species/8801

    • https://github.com/hlapp/phyloref/blob/master/Campanulaceae.owl#L86 • Protege 5.0.0: http://protege.stanford.edu/ • Page (2016): https://doi.org/10.7287/peerj.preprints.1649v1, page 7 • Hinchliff et al. (2016): http://dx.doi.org/10.1073/pnas.1423041112 • Trees from Nico Cellinese
  29. WIKIMEDIA COMMONS • CC-BY: • https://commons.wikimedia.org/wiki/ File:An_owl_sitting_on_the_stump_of_a_tree_before _a_forest._colou_Wellcome_V0020561.jpg • PD:

    • https://en.wikipedia.org/wiki/File:Haeckel_arbol_bn.png