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

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CAMPANULOIDEAE

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CAMPANULOIDEAE

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

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NO NAMES AT ALL Page (2016)

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

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A SEMANTIC CLADE

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

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

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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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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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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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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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WEB ONTOLOGY LANGUAGE

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WEB ONTOLOGY LANGUAGE

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

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

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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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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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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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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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QUESTIONS?

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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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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