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