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Names for Biodiversity Workshop

Introduction

Recent work on names is fragmented into individual and isolated project efforts. There are now more terms than concepts, more definitions than terms. Many, more-or-less, similar vocabularies, alternative frameworks and non-interoperable, application systems.

This may well be the natural process of evolution but we do need to make time now to discuss synthesis and a more collaborative approach to development of a workable standard for names. Can we work together to fill the gaps, and to resolve the competing requirements of aggregation and science, data and knowledge, product and research, Code-compliance and interoperability.

Purpose

To raise awareness of the importance of names to biodiversity informatics and to re-invigorate a more collaborative phase of standards development with names within the TDWG umbrella.

This workshop will aim for consensus around the idea that we can work together within TDWG to evolve a pragmatic replacement for the existing names standards, and a map to get us there.

Goals

  1. Reconvene the Taxonomic Names and Concepts Interest Group
    • Membership
    • GitHub, tdwg/tnc
    • Standards maintenance.
  2. Agreement on a plan for a replacement of the Taxonomic Concept Transfer Schema (TCS) that:
    • is compliant with the TDWG Standards Documentation Standard and Vocabulary Maintenance Standard.
    • provides for the needs of the various types of users and use cases of Taxonomic Names in the biodiversity informatics space
    • as much as possible synthesises and takes benefit of the work that has been done in the TDWG community so far.

Uses / Stakeholders

  • Simple checklists, aggregators: GBIF, ALA, CoL; agitators: @rdmpage
  • Species Information Systems
  • Floras, Faunas etc.
  • Systems that capture historical (as well as current) name usages: NSL, APNI, AFD
  • Systems that try to capture phylogenetic relationships

Current standards

Issues

Expectation reversal, but

  • Taxa change
    • AFD = taxonomic (opinion) product, not a Nomenclator, not a taxon store.
      • @rdmpage: WTAF
  • Taxonomic Names are stable.
  • Inappropriate use of taxon.

No "Names" standard.

  • Darwin Core RDF Guide recommends separate vocabulary.
  • Ad hoc Darwin Core extensions.
  • Inappropriate use of the taxonomic concept

TCS

  • XML too esoteric:
    • Okay at the enterprise level - Not being used, or ... - used anyway.
  • Application schema
    • Interchange of literature based concept definitions
  • Difficult to distill, harder to extend.
  • Syntax (XML) → path to RDF … JSON.
  • Over engineered for normal usage:)
  • Relationship object

    • Path to RDF, JSON-LD

            How does tcs:TaxonConcept relate to dwc:Taxon?

      How does tcs:TaxonConcept relate to NameUsage and nsl:Instance?

Darwin Core ambiguous

  • Overloaded definitions
    • Many interpretations.
  • Overloaded usage.
    • Classification terms.
  • Ranks.
  • Path to RDF …

Many different application profiles

  • Simple vocabulary required.
  • A Domain Model?

Agreement on definitions

  • Classes
  • Code compliance

???

Previous Work !

  • Bisby
  • APNI
  • Berlin Model
  • IPNI
  • ITIS, CoL
  • Flora of Australia
  • Tropicos
  • LinneanCore (SDD)
  • DwC, ABCD
  • TCS
  • TDWG ontology
  • ALA-NSL (2008)
  • txn:deVriese
  • GBIF Checklist
  • DwC RDF
  • Nomen
  • WFO
  • OpenBiodiv
  • BCO
  • ColPlus
  • TaxRef
  • +++

Strategy / Way Forward?

A new standard or update/replace/extend existing standards?

Restart with ideas in Linnean Core (J.Cooper)

  • A Basic vocabulary for the interchange and use of Taxonomic Names and "names".
  • Darwin Core extensions NFB < TCS.
  • Controlled vocabularies!
  • Recommend classes.
  • Guidelines.

Darwin Core

  • leave "convenience" terms and internal links.
  • remove external links (id terms) ?
  • Add new terms?
  • Darwin Core RDF Guide

A Domain Model or List?

  • Normative or Guide?
  • API specification for:
    • Name
    • Instance (name occurrence) according
    • Usage ( potential/taxonomic concept)
    • Taxon
    • Taxonomic Tree ?
    • Arrangement

What are we looking for in a Name standard/vocabulary?

  • (Core competencies / Functional Requirements / Use cases)
  • Generic metadata model
    • Vocabularies
  • Full Code support
    • ICN, ICZN, ...
    • Code maintenance
      • Domain owners?
  • Interoperability
    • Every name
    • Every instance (name usage)
    • Every relationship
    • Every point of view
    • Every version
    • Every syntax
    • Every application profile
    • Common interchange format
    • Support for publication
    • Extensible
  • Obey the the TDWG laws for standards and vocabularies
  • Independent of serialization
  • Concise vocabulary
  • RDF support
    • Application Profiles
    • Simple enough for …. Anything

Terminology

Some core concepts

A name is a "name", a designation, a label, a string used as a name: in any context.

A taxonomic name is a name used in a taxonomic context; often a scientific name formulated (or attempted to be) according to some rules of nomenclature.

A reference is a citable work: a publication, a resource, ...

A taxonomic name instance is the occurrence of a name in a reference. A fact. One usage of a taxonomic name establishing context: establishment of a name, a concept, a synonym, an assertion, a relationship; tax. nov., comb.nov., … , a misapplication, or assertion; a common name.

A taxonomic concept is a taxonomic name instance establishing or circumscribing a taxonomic entity - often linking synonymic inclusions and adding annotations, description…

A taxonomic tree is a hierarchical arrangement of taxonomic concepts

A taxon is a reusable branch or leaf of a taxonomic tree.

NSL Example [todo]

Bibliographic pattern: Where a name is found and how it is used in that place.

  • Every taxonomic name instance. -Just about names and taxa:

    • Authors, References detail elsewhere - external resources

      Model

      • Name
        • Name Strings
        • Code
        • Type of name (scientific, vernacular, informal, cultivar…)
        • Rank !
        • Status !
        • Authorship
        • Primary reference ( incl. basionym) !
      • Reference
        • Type of reference !
        • Part of Reference !
        • dc:title, dc:creator, dc:created:...
          • CitedAs
        • External resource !
      • Instance
        • Type of instance !
        • Name !
        • Reference !
        • Page citation
        • Citing instance !
        • Cited instance !
        • Taxon
        • Instance !
          • Parent taxon !
          • Included taxa !
          • Taxon !
            • Taxon !
              • ...
        • Annotations
        • Profile
        • Taxonomic arrangement
        • Root
          • Taxon !
      • Vocabularies
        • Code of Nomenclature
        • Status of a Name
        • Code !
        • Status
        • Description
        • Type of Name
        • Type of Instance (usage/relationship)
        • The system of Name Ranks
        • Type of Reference
        • Type of external Resource
        • Type of taxon
          • Type of arrangement

Changes to Darwin Core?

Appropriateness

  • RDF Guide
  • "Convenience terms"

Extension of Darwin Core

  • New/missing terms
  • "Names" guide
  • RDF Guide
  • GBIF Checklist?

Cull Darwin core (TaxonConceptID)