The Semantic Clade

A presentation on phyloreferencing at Evolution 2016

Transcript

1. THE SEMANTIC CLADE
   Gaurav Vaidya (University of Colorado Boulder/University of Florida)
   Hilmar Lapp (Duke University)
   Nico Cellinese (University of Florida)
   

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3. CAMPANULOIDEAE
   Are you kidding me?
   These are the Campanuloideae!
   Wang et al. 2014
   

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4. CAMPANULOIDEAE
   

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6. CAMPANULOIDEAE
   

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7. Linnean names point to concepts
   Antoine Laurent de Jussieu
   Genera Plantarum, 1789
   

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8. NO NAMES AT ALL
   Page (2016)
   

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

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10. A SEMANTIC CLADE
    

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11. A SEMANTIC CLADE
    Node-based
    A B C
    Last common ancestor
    of B and C
    The clade originating with:
    

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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:
    

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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:
    

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14. A SEMANTIC CLADE
    Node-based Branch-based Apomorphy-based
    A A A
    B B B
    C C C
    X
    Phyloreference
    

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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.
    

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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.
    

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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
    

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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)
    

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19. WEB ONTOLOGY LANGUAGE
    

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20. WEB ONTOLOGY LANGUAGE
    

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

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

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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.
    

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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.
    

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25. INTERESTED?
    • Check out our website: http://phyloref.org/
    • Get in touch!
    • Gaurav Vaidya: @mrvaidya, http://mrvaidya.com/
    • Hilmar Lapp: @hlapp
    • Nico Cellinese: @ncellinese
    

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26. ACKNOWLEDGEMENTS
    • NSF: “Collaborative Research: ABI Innovation: An
    Ontology-Based System for Querying Life in a
    Post-Taxonomic Age” (NSF-DBI 1458604)
    

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27. QUESTIONS?
    

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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
    

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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
    

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