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Phyloreferencing: Advisory Board Meeting

April 23, 2018

Deliverables, Roadmap, Current Status

Major deliverables

  1. A specification for phyloreference construction and resolution
  2. An Ontology of Phyloreferences
  3. Proof-of-concept application for finding, resolving, and validating phyloreferences on a given tree
  4. Web application demonstrating large-scale biodiversity data integration using phyloreferencing

Phyloreference specification

  • Primary goals of this document:
    • Describe computational properties a phyloreference MUST, SHOULD, and MAY have.
    • Defines a data model and its semantics for phyloreferences.
    • Recommends ontology design patterns (to achieve these properties in OWL).
    • Defines expectations for specifier matching.
  • Currently in draft, in active development: https://github.com/phyloref/specification

Ontology product 1: Phyloreferencing Ontology

  • Properties, classes, etc needed to express phyloreferences in OWL
  • Development driven by the Phyloref Specification

Ontology product 2:
Ontology of Phyloreferences

  • Published and peer-reviewed clade definitions expressed as phyloreferences in OWL
    • Vetted for following good practices (e.g., promoting concept stability)
    • Deemed useful by biologists
  • Entries authored and validated through the Phyloreference Curation Tool
    • Uses the Phyloreferencing Ontology
    • Ensures compliance with specification

Ontology of Phyloreferences: Development plan

  • Major initial milestone is publication of all clade definitions from Phylonym volume
    • ~300 clades defined, named, and published according to the PhyloCode
    • Curation off of RegNum
    • Paper of the ontology to be published in close proximity to appearance of Phylonym volume
  • Currently in planning stage
    • Required tooling, feasibility re: timelines
    • Coordinating with Phylonym team

Authoring and using phyloreferences

  • Phyloreference Curation Tool
    • Authoring phyloreferences
    • Finding, resolving, and validating phyloreferences small-scale
    • Status: in active development, initial release impending
  • Large-scale biodiversity data integration app
    • Use case development initiated
    • Primary target for engagement with clade-oriented research groups

Interaction diagram

Roadmap

Milestones for Year 2

  • Initial releases of major products:
    • Curation tool 1.0
    • Specification 1.0
    • Phyloreferencing ontology 1.0
    • Ontology of Phyloreferences 1.0
    • Small-scale PoC app

Milestones for Year 2 (cont'd)

  • Pre-release phase milestones:
    • Actionable use cases for large-scale PoC app
  • Community milestones:
    • Engagement with clade-oriented research groups

Milestones for Year 3

  • Major software products:
    • Phyloreference authoring tool
    • Sophisticated specifier matching
    • Large-scale biodiversity data integration app
  • Community milestones:
    • Deep collaboration with select clade-oriented research group(s)

Major challenges

  • Near to mid term: choosing a product that drives development and demonstrates utility

    • Ontology of Phyloreferences

  • Mid to long term:

    • Algorithms for specifier replacement
    • Use case and tech development for large-scale data integration app
    • Engagement with community and research groups

Questions & Feedback

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Hilmar Lapp
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