tcs.yaml

#
# Terms defined in TCS
#

# class: TaxonConcept
- localName: TaxonConcept
  label: Taxon Concept
  definition: >-
    An identifiable taxonomic position that can be aligned to other such 
    positions through TCS Taxon Relationships.
  usage: The `taxonName` and `accordingTo` properties are required.
  notes: >-
    A taxonomic position is an opinion about the definition of a taxonomic 
    group. A Taxon Concept is identifiable, because it combines a label – 
    `taxonName` in TCS – with a source – `accordingTo`. Both these properties 
    are required. When mentioning a taxon concept, the label and the source are 
    combined, separated by 'sec.' (from, 'secundus', meaning 'according 
    to') or 'sensu' (meaning the same). The term `title` has been borrowed from 
    Dublin Core to provide this taxon concept label. Because of the context 
    provided by the source, taxon concepts are in principle also alignable to 
    other Taxon Concepts using the TCS Taxon Relationship statements.


    The TCS Taxon Concept is a data object and is applied more broadly than the 
    term is used in science (e.g. Franz & Peet 2009). On the one hand, things 
    that are not generally considered to be biological taxa, e.g. hybrids and 
    cultivars, can be casted as TCS Taxon Concepts. Also Operational Taxonomic 
    Units (OTUs, cf. Sokal & Sneath 1963) can be exchanged as Taxon Concepts, 
    if there is a reason to do so, e.g. if one wants to align them with other 
    Taxon Concepts later. On the other hand, entries from treatments that are 
    considered to cite concepts from other treatments can be formulated as 
    Taxon Concepts. Every taxon concept from a treatment that is likely to be 
    referenced as the source of taxonomic context, for example a field guide 
    for a determination of a specimen or a national census for an ecological 
    study, can – and it would be very nice if they would – be stated as a Taxon 
    Concept, so they can be aligned with other Taxon Concepts that may provide 
    more or different taxonomic context.


    By contrast, assertions of synonymy or misapplication and entries in lists 
    of nomenclatural types are not Taxon Concepts.
  examples: 
    - TaxonConcept-1
    - TaxonConcept-2
    - TaxonConcept-3
    - TaxonConcept-4
    - TaxonConcept-5
  type: http://www.w3.org/2000/01/rdf-schema#Class
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonConcept
  required: null
  repeatable: null
  github: 1

# property: taxonName
- localName: taxonName
  label: Taxon Name
  definition: A name or label that is given to a taxonomic group.
  usage: >-
    `taxonName` is an IRI term and is required on a TCS Taxon Concept. A Taxon 
    Concept can only have one `taxonName`.
  notes: >-
    The `taxonName` can be anything from a well-formed scientific name to an 
    informal name, vernacular name, indigenous knowledge label, or even a label 
    containing numbers and/or special symbols, such as are often used for OTUs. 
    

    The object of `taxonName` is an object or IRI, so that it can be reused in 
    other Taxon Concepts. TCS has got the Taxon Name class, which can be used 
    for any type of name, but people are free to use alternatives, e.g. 
    `skosxl:Label`, if they want to restrict the use of the Taxon Name class to 
    scientific (or scientific-y) names only.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonConcept
  required: Yes
  repeatable: No
  github: 2

# property: accordingTo
- localName: accordingTo
  label: According To
  definition: >- 
    Reference to the treatment or other source in which a Taxon Concept is 
    established or used. 
  usage: >-
    `accordingTo` is an IRI term and is required on a Taxon Concept. A 
    Taxon Concept can have only one `accordingTo`. 
  notes: >-
    Every Taxon Concept is in some sort of treatment and this treatment 
    provides important context without which we do not know what a taxon name 
    really means and therefore the `accordingTo` property is required for a TCS 
    Taxon Concept. In TCS 2, `accordingTo` has to be a reference to some sort 
    of resource rather than just a person's name. However, TCS is lenient about 
    the nature of this resource and, apart from references to bibliographic 
    resources, references to personal communications and determinations are 
    also acceptable, if there is value in supplying taxon concepts from such 
    communications as Taxon Concepts.


    The value of `accordingTo` has to be an object or IRI. This object can 
    contain as little as a bibliographic reference but it is much more useful 
    to provide it in a format that can be understood by reference managers 
    such as Zotero or Mendeley.
  examples: 
    - TaxonConcept-accordingTo-1
    - TaxonConcept-accordingTo-2
    - TaxonConcept-accordingTo-3
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonConcept
  required: Yes
  repeatable: No
  github: 4

# property: taxonomicRank
- localName: taxonomicRank
  label: Taxonomic Rank
  definition: The rank at which a taxon is classified.
  usage: >-
    `taxonomicRank` is an IRI property; a Taxon Concept can have only one 
    `taxonomicRank`.
  notes: >-
    The rank is an attribute of elements in a classification and `taxonomicRank` 
    can be applied to Taxon Concepts as well Taxon Names, as the rank of a 
    taxon is reflected in its name. This property takes an object or IRI and it 
    is recommended to use a value from an existing controlled vocabulary. 
    While there is no TDWG vocabulary yet, the GBIF Taxonomic Rank Vocabulary 
    (https://rs.gbif.org/vocabulary/gbif/rank.xml) is recommended.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonConcept
  required: No
  repeatable: No
  github: 32

# property: parent
- localName: parent
  label: Parent
  definition: >-
    The direct parent in a classification.
  usage: >-
    `parent` is another Taxon Concept; a Taxon Concept can have only one 
    `parent`.
  notes: >-
    The `parent` is another Taxon Concept. This is the parent as indicated in 
    the `accordingTo` reference, rather than a third-party classification. The 
    `accordingTo` of the parent will generally, but not necessarily, be the 
    same as that of the child. 
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonConcept
  repeatable: No
  required: No
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  github: 8

# property: synonym
- localName: synonym
  label: Synonym
  definition: >-
    Name considered to apply to the same taxon as the accepted name.
  usage: >-
    `synonym` is a Taxon Name; a Taxon Concept can have multiple synonyms.
  notes: >-
    Synonyms are names and synonymy is between names but, if the names have 
    different nomenclatural types, a Taxon Concept is required. Therefore, 
    `synonym` is a property of the Taxon Concept class. `synonym` is used here 
    in the strict meaning that the type of a name falls within a Taxon Concept. 
    The same goes for the accepted name (`taxonName`) and therefore `synonym` 
    has the same relationship to Taxon Concept as `taxonName`. This allows one 
    to dispose of names without having to deal with the Taxon Concepts that were 
    realised along with the publication of these names. If one wants to include 
    these “original concepts” and indicate a relationship between Taxon 
    Concepts, and the more precise relationship is not provided, the 
    `intersects` Taxon Relationship can be used.
  examples: 
    - TaxonConcept-synonym-1
    - TaxonConcept-synonym-2
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonConcept
  required: No
  repeatable: Yes
  github: 65

# property: vernacularName
- localName: vernacularName
  label: Vernacular Name
  definition: >-
    Common or vernacular name for a taxonomic group, when used besides the 
    `taxonName`.
  usage: >-
    `vernacularName` is an IRI term; a Taxon Concept can have more than one 
    `vernacularName`.
  notes: >-
    The `vernacularName` property can be used when a vernacular name is used 
    alongside a scientific name, which is the `taxonName`. If a vernacular name 
    is the only name, the `taxonName` property should be used. The object of the 
    `vernacularName` property can be a Taxon Name, but another label 
    object, such as the GBIF [Vernacular Name](https://rs.gbif.org/extension/gbif/1.0/vernacularname.xml), 
    might be preferrable, especially if there can be multiple vernacular names 
    for a concept.
  examples: 
    - TaxonConcept-vernacularName-1
    - TaxonConcept-vernacularName-2
    - TaxonConcept-vernacularName-3
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonConcept
  required: No
  repeatable: Yes
  github: 10

# class: TaxonRelationship
- localName: TaxonRelationship
  label: Taxon Relationship
  definition: Topological relationship between two Taxon Concepts.
  examples: 
    - TaxonRelationship-1
    - TaxonRelationship-2
    - TaxonRelationship-3
  usage: >-
    `relationshipType`, `subjectTaxonConcept`, `objectTaxonConcept` and 
    `relationshipAccordingTo` are all required.
  notes: >-
    Taxon Relationships are a set of relationships that allow for the 
    alignment of Taxon Concepts – or taxon concept mapping. The main 
    relationship types coincide with topological relationships that are widely 
    used in spatial analysis, analysis of computer networks, artificial 
    intelligence, etc. In particular, they are the relationships that are used 
    in RCC-5 Region Connection Calculus, which allows for reasoning.


    An extra controlled term `intersects` has been added to the Taxon Concept 
    Relationship Type Vocabulary to accommodate Taxon Relationship 
    statements between Taxon Concepts of which we know that they have at least 
    one member in common, but where the more specific topological relationship 
    is not easily inferred.


    Taxon Relationship statements can be made in the treatment of the 
    subject Taxon Concept or by third parties.
  type: http://www.w3.org/2000/01/rdf-schema#Class
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonRelationship
  repeatable: null
  required: null
  github: 43

# property: relationshipType
- localName: relationshipType
  label: Relationship type
  definition: The type of relationship.
  usage: >-
    This property is required; one MUST use a term from the [Taxon Concept 
    Relationship Vocabulary](taxon-relationship-type-vocabulary.md).
  notes: null
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonRelationship
  required: Yes
  repeatable: No
  github: 44

# property: subjectTaxonConcept
- localName: subjectTaxonConcept
  label: Subject Taxon Concept
  definition: Taxon Concept that is the subject in the relationship statement.
  usage: >-
    `subjectTaxonConcept` is a TCS Taxon Concept; a Taxon Relationship 
    statement can have only one `subjectTaxonConcept`.
  notes: >-
    This is the Taxon Concept at the left-hand side of the relationship 
    statement.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonRelationship
  required: Yes
  repeatable: No
  github: 45

# property: objectTaxonConcept
- localName: objectTaxonConcept
  label: Object Taxon Concept
  definition: Taxon Concept that is the object in the relationship statement.
  usage: >-
    `objectTaxonConcept` is a TCS Taxon Concept; a Taxon Relationship 
    statement can have only one `objectTaxonConcept`.
  notes: >-
    This is the Taxon Concept at the right-hand side of the relationship 
    statement.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonRelationship
  required: Yes
  repeatable: No
  github: 46

# property: relationshipAccordingTo
- localName: relationshipAccordingTo
  label: Relationship According To
  definition: >-
    Reference to the source of the taxon relationship statement.
  usage: >-
    `relationshipAccordingTo` is an IRI term and is required; a Taxon 
    Relationship statement can have only one `relationshipAccordingTo`.
  notes: >-
    In the case of Taxon Relationships from traditional synonymy, the 
    `relationshipAccordingTo` is the same as the `accordingTo` of the Taxon 
    Concept that is the `subjectTaxonConcept`.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonRelationship
  required: Yes
  repeatable: No
  github: 47


# class: TaxonName 
- localName: TaxonName
  label: Taxon Name
  definition: A name or label applied to a taxon or taxonomic group. 
  usage: >-
    A TCS Taxon Name only requires a `taxonNameString`.
  notes: >-
    The word 'name' here is taken in its dictionary meaning and not in the 
    sense of a particular nomenclatural code. This means that the Taxon Name 
    class can be used for any type of name, not just names that are validly 
    published under the relevant nomenclatural code.
  examples: 
    - TaxonName-1
    - TaxonName-2
    - TaxonName-3
    - TaxonName-4
  type: http://www.w3.org/2000/01/rdf-schema#Class
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: null
  repeatable: null
  github: 15

# property: taxonNameString
- localName: taxonNameString
  label: Taxon Name String
  definition: >-
    The complete name string without any authority or year components.
  usage: >-
    `taxonNameString` is a literal and is required on a TCS TAxon Name. A Taxon 
    Name can have only one `taxonNameString`.
  notes: >-
    The `taxonNameString` property differs from the `scientificName` property 
    in Darwin Core in that all kinds of names are allowed. Also, in the case of 
    scientific names, contrary to the `dwc:scientificName`, `taxonNameString` 
    does not include the authorship. In botanical names, it does include the 
    rank prefixes for infrageneric and infraspecific epithets as they are 
    considered part of the name.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: Yes
  repeatable: No
  github: 16

# property: namePublishedIn
- localName: namePublishedIn
  label: Name Published In
  definition: >-
    Reference to the publication in which the name was first published.
  usage: >-
    `taxonNameString` is a literal; there can only be one `taxonNameString` on 
    a Taxon Name.
  notes: >-
    In botany, this would be the protologue. This is the IRI counterpart of 
    the Darwin Core `namePublishedIn`.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: No
  repeatable: No
  github: 29

# property: microreference
- localName: microreference
  label: Microreference
  definition: Specifies any minor reference parts, e.g. page number.
  usage: >-
    `microreference` is a string literal; a Taxon Name can have only one 
    `microreference` and only when `namePublishedIn` is used as well.
  notes: >-
    In taxonomic works it is convention to cite the exact location in a work 
    where a new name is published. The `microreference` property lets one do 
    that on the Taxon Name object, so that the `namePublishedIn` reference can 
    be reused.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: No
  repeatable: No
  github: 30

# property: nomenclaturalCode
- localName: nomenclaturalCode
  label: Nomenclatural Code
  definition: >-
    Nomenclatural code that applies to the group of organisms the taxonomic name 
    is for.
  usage: >-
    `nomenclaturalCode` takes an IRI or object; a Taxon Name can have only one 
    `nomenclaturalCode`.
  notes: >-
    This is the IRI equivalent of the Darwin Core `nomenclaturalCode`. In the 
    absence of a TDWG vocabulary, it is recommended to use a value from the GBIF 
    Nomenclatural Codes Vocabulary 
    (https://rs.gbif.org/vocabulary/gbif/nomenclatural_code.xml).
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: No
  repeatable: No
  github: 33

# property: nomenclaturalStatus
- localName: nomenclaturalStatus
  label: Nomenclatural Status
  definition: >-
    Status related to the original publication of the name and its conformance
    to the relevant rules of nomenclature.
  usage: >-
    `nomenclaturalStatus` takes an IRI or object; a Taxon Name can have only one 
    `nomenclaturalStatus`.

  notes: >-
    This is the IRI equivalent of the Darwin Core `nomenclaturalStatus`. In the 
    absence of a TDWG vocabulary, it is recommended to use a value from the GBIF 
    Nomenclatural Status Vocabulary 
    (https://rs.gbif.org/vocabulary/gbif/nomenclatural_status.xml).
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: No
  repeatable: No
  github: 35

# property: basionym
- localName: basionym
  label: Basionym
  definition: Original name on which the present name is based.
  usage: >-
    A `basionym` is another Taxon Name; a Taxon Name can have only one 
    `basionym`.
  notes: >-
    A basionym is the epithet-bringing name.  The `basionym` property is only 
    used for new combinations ('comb. nov.'). If the new name is an avowed 
    substitute ('nom. nov.') the `replacementNameFor` property should be used 
    instead.
  examples: 
    - TaxonName-basionym-1
    - TaxonName-basionym-2
  required: No
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  repeatable: No
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  github: 36

# property: replacementNameFor
- localName: replacementNameFor
  label: Replacement Name For
  definition: >-
    The legitimate or illegitimate, previously published name on which a 
    replacement name (nomen novum) is based.
  usage: >-
    `replacementNameFor` is another Taxon Name; a Taxon Name can have only one 
    `replaccementNameFor`.
  notes: >-
    In the Botanical Code the term 'replaced synonym' is used. A 'replacement 
    name' is a name that is published as a substitute for an earlier published 
    name that is either illegitimate or for which a new combination cannot be 
    created in the place a taxon is transferred to because of an older blocking 
    name.
  examples: 
    - TaxonName-replacementNameFor-1
    - TaxonName-replacementNameFor-2
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: No
  repeatable: No
  github: 37

# property: conservedAgainst
- localName: conservedAgainst
  label: Conserved Against
  definition: Name(s) against which this name is conserved.
  usage: >-
    The `conservedAgainst` property takes another Taxon Name; a Taxon Name can 
    be conserved against more than one other Taxon Names.
  notes: >-
    A scientific name below the rank of family is not conserved against all 
    other names, but only against one or more names that in turn are rejected 
    against the conserved name. A name can be conserved against more than one 
    other name, so this property is repeatable.
  examples:
    - TaxonName-conservedAgainst
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/TaxonName
  required: No
  repeatable: Yes
  github: 39


# class: NomenclaturalType
- localName: NomenclaturalType
  label: Nomenclatural Type
  definition: Element to which a scientific name is permanently attached.
  usage: >-
    A Nomenclatural Type requires a `typifiedName` and either a `typeName` or 
    `typeSpecimen`.
  notes: >-
    A nomenclatural type fixes the usage of a name to the taxonomic group that 
    contains the type. One or more Nomenclatural Types make up the typification 
    of a Taxon Name. In Darwin Core RDF, NomenclaturalType can be used as object 
    with `dwciri:typeStatus`.
  examples: 
    - NomenclaturalType
  type: http://www.w3.org/2000/01/rdf-schema#Class
  organizedInClass: http://rs.tdwg.org/tcs/terms/NomenclaturalType
  repeatable: null
  required: null
  github: 58

# property: typifiedName
- localName: typifiedName
  label: Typified Name
  definition: >-
    The scientific name for which the specimen or other name is the type.
  usage: >-
    `typifiedName` is a Taxon Name and is required; a Nomenclatural Type can 
    typify only one Taxon Name.
  notes: >-
    The `typifiedName` property links the Nomenclatural Type back to the Taxon 
    Name. Also, when coming from the Preserved Specimen, the typified name is 
    the most important piece of information, because there is no point in 
    knowing what kind of type a specimen is without knowing for what name it 
    is the type. Therefore, `typifiedName` is a required property.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/NomenclaturalType
  required: Yes
  repeatable: No
  github: 59

# property: typeOfType
- localName: typeOfType
  label: Type of Type
  definition: >-
    The kind of type this specimen is, e.g. holotype, isotype etc.
  usage: >-
    `typeOfType` is an IRI term and should take its value from a controlled 
    vocabulary. A Nomenclatural Type can have only one
  notes: >-
    This is an IRI property. In the absence of a TDWG controlled vocabulary, 
    it is recommended to use a value from the GBIF Nomenclatural Type Status 
    Vocabulary (https://rs.gbif.org/vocabulary/gbif/type_status.xml).
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  required: No
  repeatable: No
  organizedInClass: http://rs.tdwg.org/tcs/terms/NomenclaturalType
  github: 60

# property: typeName
- localName: typeName
  label: Type Name
  definition: The name that is the type.
  usage: >-
    `typeName` is a Taxon Name. A nomenclatural type can have only one 
    `typeName`.
  notes: >-
    Taxon names at ranks above species level can be typified by the name of a 
    lower taxon. Ultimately, by following the chain of type names, all names 
    resolve to a type species and thus a type specimen. 
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/NomenclaturalType
  required: No
  repeatable: No
  github: 61

# property: typeSpecimen
- localName: typeSpecimen
  label: Type Specimen
  definition: The specimen that is the type.
  usage: >-
    `typeSpecimen` takes an IRI – or object – that refers to a specimen. A 
    Nomenclatural Type can only have one `typeSpecimen`.
  notes: >-
    Names at ranks of family and below are typified by a specimen. This property 
    is mutually exclusive with `typeName`. This is an IRI property. One could 
    use the Darwin Core Preserved Specimen. While a Taxon Name can have more 
    than one type specimens, each of these type specimens requires its own 
    Nomenclatural Type record, so a Nomenclatural Type can have only one 
    `typeSpecimen`.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/NomenclaturalType
  required: No
  repeatable: No
  github: 62

# property: typePublishedIn
- localName: typePublishedIn
  label: Type Published In
  definition: Publication where the type was nominated
  usage: >-
    `typePublishedIn` is an IRI term. A Nomenclatural Type can have at most one 
    `typePublishedIn`. 
  notes: >-
    `typePublishedIn` is relevant for lectotypes, neotypes, epitypes and 
    conserved types. For other kinds of type the publication where the type is 
    designated is the publication where the name was published.
  type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
  organizedInClass: http://rs.tdwg.org/tcs/terms/NomenclaturalType
  required: No
  repeatable: No
  github: 63