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
   

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2. Overview
   • The limitations of names and the value of clade
   definitions
   • Curating clade definitions in the Web Ontology
   Language (OWL)
   

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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
   

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

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

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6. Linnean names point to concepts
   Antoine Laurent de Jussieu
   Genera Plantarum, 1789
   …and 200+
   …and 400+
   

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7. Our life perspective
   

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8. Genealogical relationships among taxa
   Life organized in nested hierarchies
   

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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
   

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11. • We can unclutter concepts, and thereby
    nomenclature
    

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

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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
    

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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
    

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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)
    

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

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20. Life as a street map
    How to navigate life as a machine
    

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21. Mapping data to phylogenetic
    knowledge space
    

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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.
    

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

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

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26. Hillis and Wilcox, 2005
    http://dx.doi.org/10.1016/j.ympev.2004.10.007
    

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

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30. Yuan et al 2016 BEAST tree (fig 3) as curated by the Open Tree of Life
    (https://doi.org/10.1093/sysbio/syw055)
    

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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
    

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35. http://www.github.com/phyloref
    

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

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37. Acknowledgements
    • Funded by the US National Science Foundation
    through collaborative grants DBI-1458484
    and DBI-1458604.
    

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