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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

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

Taxonomic Concept Transfer Schema (TCS)

 *TCS 1.01 Schema Documentation* can be found at http://tdwg.github.io/tcs/schema/1.01

Darwin Core

 *Darwin Core* terms can be found at http://tdwg.github.io/dwc/terms/

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 / Core Concepts (not classes)

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)