All the Clades in the World: Building a Semantically-Rich and Testable Ontology of Phylogenetic Clade Definitions

All the Clades in the World: Building a Semantically-Rich and Testable Ontology of Phylogenetic Clade Definitions

Presentation on the Phyloreferencing project (http://phyloref.org) delivered to the SPNHC+TDWG 2018 meeting in Dunedin, New Zealand. The abstract for this talk is available at http://dx.doi.org/10.3897/biss.2.25776

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Gaurav Vaidya

August 29, 2018
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Transcript

  1. All The Clades In The World Building a Semantically-Rich and

    Testable Ontology of Phylogenetic Clade Definitions Gaurav Vaidya, Hilmar Lapp, Nico Cellinese www.phyloref.org
  2. Overview • The limitations of names and the value of

    clade definitions • Curating clade definitions in the Web Ontology Language (OWL)
  3. What’s in a name? • Names and Concepts do not

    reconcile that easily • Names are text strings • Context is lacking or subjective • Meaning is not computable
  4. Linnean names point to concepts Antoine Laurent de Jussieu Genera

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

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

    Plantarum, 1789 …and 200+ …and 400+
  7. Our life perspective

  8. Genealogical relationships among taxa Life organized in nested hierarchies

  9. A clade, also known as monophyletic group, represents a branch

    on the tree of life. It is a group of organisms that consists of a common ancestor and all its descendants. What is a clade? Node = ancestor Descendants
  10. None
  11. • We can unclutter concepts, and thereby nomenclature

  12. Tree-thinking Common descent àevolution at the center of taxonomy B

    C D Branches Synapomorphies A Clades = taxa Discovery
  13. Tree-thinking Common descent àevolution at the center of taxonomy Discovery

    Communication How?? 0 14 7 Density 0.07 0.22 0.72 Diversification rate
  14. Tree-thinking Berberidopsidaceae Opiliones Zingiberaceae Hamamelidaceae Sarcolaenaceae Lingulidae Hymenoptera Mammalia Apocynaceae

    Galliformes Rubiaceae Anarthriaceae Lineidae Crocodylidae Stylosiphonia Andrenidae Cracidae Gavialis Globba Glottidia Micrella Streptotham nus Rhodoleia Phalangiidae Tachyglossa Lyginia Mediusella Chamaeclitandra
  15. Tree-thinking Berberidopsidaceae Opiliones Zingiberaceae Hamamelidaceae Sarcolaenaceae Lingulidae Hymenoptera Mammalia Apocynaceae

    Galliformes Rubiaceae Anarthriaceae Lineidae Crocodylidae Stylosiphonia Andrenidae Cracidae Gavialis Globba Glottidia Micrella Streptotham nus Rhodoleia Phalangiidae Tachyglossa Lyginia Mediusella Chamaeclitandra These names are not generated in an evolutionary-based framework (Groups defined by character similarity vs. common descent)
  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. Are you kidding me? These are the Campanuloideae! Wang et

    al. 2014
  18. None
  19. None
  20. Life as a street map How to navigate life as

    a machine
  21. Mapping data to phylogenetic knowledge space

  22. Phylogenetic Definitions Statements formally expressing the patterns we discover (analogous

    to map coordinates) Node-Based (minimum clade) Branch-Based (maximum clade) Apomorphy-Based A B C A B C A B C X The clade originating with the last common ancestor of B and C. The clade originating with the first ancestor of B that is not an ancestor of A. The clade originating with the first ancestor of C to evolve X.
  23. http://purl.obolibrary.org/obo/UBERON_0001702

  24. http://purl.obolibrary.org/obo/UBERON_0001702

  25. None
  26. Hillis and Wilcox, 2005 http://dx.doi.org/10.1016/j.ympev.2004.10.007

  27. http://phyloref.org/curation-tool/

  28. None
  29. None
  30. Yuan et al 2016 BEAST tree (fig 3) as curated

    by the Open Tree of Life (https://doi.org/10.1093/sysbio/syw055)
  31. None
  32. None
  33. None
  34. Phyloreferences • Portable to any phylogeny that has all the

    specifiers • Resolvable on any phylogeny represented in RDF by using an OWL 2 DL reasoner • Extensible to other kinds of definitions if need be • Working on better ways to match specifiers
  35. http://www.github.com/phyloref

  36. http://phyloref.org/blog/ http://twitter.com/phyloref

  37. Acknowledgements • Funded by the US National Science Foundation through

    collaborative grants DBI-1458484 and DBI-1458604.