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

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
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
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
26. Hillis and Wilcox, 2005 http://dx.doi.org/10.1016/j.ympev.2004.10.007
27. http://phyloref.org/curation-tool/
30. Yuan et al 2016 BEAST tree (fig 3) as curated by the Open Tree of Life (https://doi.org/10.1093/sysbio/syw055)
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.