<div style="font-size: xx-large"> # Phyloreferencing: Advisory Board Meeting </div> 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 - 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 ---- ### Ontology product 2:<br>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 ---  --- ## 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