Phyloreferencing: Advisory Board Meeting

April 23, 2018

Deliverables, Roadmap, Current Status

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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

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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

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Ontology product 1: Phyloreferencing Ontology

• Properties, classes, etc needed to express phyloreferences in OWL
  • In active development: https://github.com/phyloref/phyloref-ontology
  • Imports terms from several other community ontologies (CDAO, RO, IAO, etc)
  • Anticipated to precipitate maintenance effort for CDAO
• Development driven by the Phyloref Specification

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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

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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

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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

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Roadmap

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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

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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

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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)

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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

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Questions & Feedback