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Goals

  1. __ Agreement on a plan for a replacement of the Taxonomic Concept Transfer Schema (TCS) that:

  • _ 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.

== Introduction

Purpose.
workshop abstract …​

Open Data needs open standards, open standards open development, and open development open minds, and TDWG.

Standards are owned by the community.

=== History

=== Issues

  • ___ Taxonomic Concept is too esoteric: people can’t really put their finger on it

=== Previous work

  • _ Bisby

  • __ APNI

  • __ Berlin Model

  • __ IPNI

  • ___ ITIS, CoL

  • __ Flora of Australia

  • _ LinneanCore (SDD)

  • ___ DwC, ABCD

  • __ TCS, TDWG ontology

  • __ ALA-NSL (2008)

  • __ txn:deVriese

  • __ GBIF Checklist

  • _ DwC RDF

  • _ Nomen

  • _ WFO _

  • OpenBiodiv

  • _ BCO _

  • _ ColPlus

  • TaxRef

  • _ + _

=== Shortcomings of TCS and Darwin Core.

Application schema > TCS

Classification in Darwin core

Classes + properties + annotations → RDF

Simple vocabulary

Monographic rather than incremental

Inappropriate use of the taxonomic concept concept

“Taxon Concept”

Syntax ?

Do we need something else?

Positions from floor

Standalone replacement?

Basic vocabulary to support

Darwin Core extension → NFB ← TCS

GBIF checklist guide

Start with!

Darwin Core

  • __ leave “convenience” terms and internal links

  • __ remove external links (id terms)

  • _ Add new terms

  • _ One level ?

  • _ Controlled vocabularies

  • _ Recommend classes

API specification for

  • __ Name

  • __ Instance

  • _ Taxon

  • _ Arrangement

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

(Core competencies / Functional Requirements / Use cases)

  • __ Generic metadata model

  • Vocabulary

  • _ Full code support

  • Code maintenance

  • 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 …​

== Terminology / 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) according to some rules of nomenclature.

A taxonomic name instance is a usage of a taxonomic name establishing taxonomic context: a concept, a synonym, an assertion, a relationship; tax. nov., comb.nov. … misapplication.

Relationship instances

  • __ Synonyms (homotypic or heterotypic): target instance is a primary instance

  • ___ Misapplication: target instance is a secondary instance

  • ___ Relationship where the target instance is a primary instance, but the instance is not a synonym instance (happens when part of the type material (syntypes or paratypes) belongs to a different taxon than the type (lecto- or holotype); rather than calling this ‘pro parte synonym’, which is semantically incorrect, it is better to coin a new term – parasynonym? – or call it a misapplication

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.

Corollaries

  • _ Change of parent, e.g. species transferred to a different genus, genus transferred to a different family (leads to homotypic or nomenclatural synonyms)

→ same taxon, same ID

  • __ Change of rank, e.g. species is demoted to subspecies or variety, subspecies or variety is promoted to species

→ different name, so different taxon, new ID

  • _ Change of circumscription

  • __ Splitting, e.g. splitting a genus into two or more

  • ___ Merging, e.g. lumping two or more species into one (leading to heterotypic or taxonomic synonyms)

→ different taxa, new IDs (also for the taxon that keeps the old name)

A taxonomic arrangement or named tree is a collection of taxa. A classification, checklist, Flora or Fauna.

Note: In a Names standard ‘scientific name’ is a type of taxonomic name rather than a property of a Taxon.

== A Domain Model?

Or list?

Normative or guide.

Taxon vs Name Usage

=== NSL Example[todo]

Bibliographic: Where name is found and how it is used in that place. Every instance.

Just about names and taxa: Authors, References elsewhere → external resources

  • __ 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)

  • __ The system of Name Ranks

  • _ Type of Reference

==

Taxonomic Concept Transfer Schema (TCS)

  • ___ TaxonName

  • _ @id _

  • _ @isAnamorphic

  • __ @nomenclaturalCode

  • __ Simple (full name as string)

  • Rank [TaxonomicRank]

  • _ @code

  • ___ CanonicalName [CanonicalName]

  • Simple

  • __

  • ___ Uninomial

  • _ Genus

  • __

  • ___ InfragenericEpithet

  • _ SpecificEpithet

  • InfraspecificEpithet

  • _ CultivarNameGroup

  • ___ CanonicalAuthorship

  • Simple

  • __

  • _ Authorship [NameCitation]

  • Simple

  • __ Year

  • _ Authors

  • ___ AgentName

  • _ @role

  • _ BasionymAuthorship [NameCitation]

  • CombinationAuthorship [NameCitation]

  • _ PublishedIn [ReferenceType]

  • __ @ref

  • __ Year

  • __ MicroReference

  • __ Typification

  • Simple

  • __

  • __ TypeVouchers

  • _ TypeVoucher

  • _ @typeOfType

  • _ VoucherRefeence [ReferenceType]

  • LectoTypePublication [ReferenceType]

  • _ LectoTypeMicroReference

  • __ TypeName

  • ___ NameReference [ReferenceType]

  • LectoTypePublication [ReferenceType]

  • _ LectoTypeMicroReference

  • __ SpellingCorrectionOf [NomenclaturalNoteType]

  • __ RuleConsidered

  • __ Note

  • _ RelatedName

  • _ PublishedIn

  • __ MicroReference

  • __ Basionym [NomenclaturalNoteType]

  • _ BasedOn [NomenclaturalNoteType]

  • ConservedAgainst [NomenclaturalNoteType]

  • __ LaterHomonymOf [NomenclaturalNoteType]toTaxonConcept

  • __ Sanctioned [NomenclaturalNoteType]

  • __ ReplacementNameFor [NomenclaturalNoteType]

  • _ PublicationStatus [NomenclaturalNoteType]

  • __ ProviderLink

  • __ ProviderSpecificData [PlaceholderType]

  • __ TaxonConcept

  • _ @id _

  • _ @type

  • __ @primary

  • _ @form

  • Name [ReferenceType]

  • Rank [TaxonomicRank]

  • ___ AccordingTo [AccordingToType]

  • __ TaxonRelationships

  • _ TaxonRelationship

  • _ @type

  • __ ToTaxonConcept

  • __ @ref

  • _ @type

  • _ SpecimenCircumscription

  • __ CircumscribedBy \{ReferenceType]

  • __ CharacterCircumscription [PlaceholderType[

  • __ ProviderLink

  • __ ProviderSpecificdata [PlaceholderType]

  • TaxonRelationshipAssertion

  • __ @type [RelationshipType]

  • _ @id _

  • ___ AccordingTo [AccordingToType]

  • Simple

  • ___ AccordingToDetailed

  • _ AuthorTeam [NameCitation]

  • _ According [ReferenceType]

  • __ MicroReference

  • FromTaxonConcept

  • __ TaxonConcept

  • __ ToTaxonConcept

  • __ TaxonConcept

  • __ Specimen

  • _ Publication