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What is a phyloreference?

  • A semantic representation of a clade definition
  • Consists of specifiers: units of taxonomy (species, specimens, ...)
    • We match nodes to specifiers so we can resolve the phyloreference to a node
  • Two types of specifiers:
    • Internal specifiers must be included in the clade
    • External specifiers must be excluded from the clade

Internal specifiers External specifiers Status
Node-based 2+ None Testing
Branch-based 1+ 1+ Only with a single external specifier
Apomorphy-based One taxon and one apomorphy None Not started

Major driving use cases

  1. Querying GBIF using phyloreferences on the Open Tree of Life
  2. Quantify the resolvability of phyloreferences

Querying GBIF using phyloreferences on the Open Tree of Life


Benefits of this approach

  1. Exact definition of the clade being used can be documented and reproduced
  2. Not dependent on the clade being included in a checklist
  3. Some parts of the Tree of Life might not be completely named for a long time, such as microbial groups

Quantify the resolvability of phyloreferences

  • Given enough phyloreferences, we can try to resolve them on the Open Tree of Life and determine:
    • What proportion we can resolve at all
    • Reasons why phyloreferences could not be resolved: missing or unmatchable specifiers, logical inconsistencies, and so on
    • What distinguishes resolvable phyloreferences from unresolvable phyloreferences

Major driving use cases

  1. Compare relationships among phyloreferences between two different phylogenies

Compare relationships among phyloreferences between two different phylogenies


Question

  • Do phyloreferences maintain the same relationships with each other on different phylogenies?
    • Determine relationships between clades on the original phylogeny and the Open Tree of Life
    • Determine the proportion of clade-to-clade relationships that remain identical between these two phylogenies

Major challenges

  • Specifier matching

    • Most phylogenies will have few (or none) of the specifiers for any phyloreference
  • How will users specify a query phyloreference?

    • Initially from an ontology of vetted clade definitions (Ontology of Phyloreferences)
    • Look up by name?
    • Support authoring one on the fly?
      • Record these for possible reuse?
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