Class: Taxon

A set of organisms asserted to represent a natural cohesive biological unit.

__

URI: schema:Taxon

diagram

Slots

Name Cardinality and Range Description Inheritance
id 1
String		 An identifier chosen from the range given to your work package by WP1 direct
metadataPublisherId 1
PersonOrOrganization		 The MBO Persistent IDentifier (mPID) of the person who entered this row of da... direct
metadataDescribedForActionId 1
Action		 The Action which resulted in this metadata record being described direct
name 1
String		 A name/title direct
taxonScientificName 0..1
String		 The full scientific name, with authorship and date information, if known direct
taxonKingdom 0..1
String		 The full scientific name of the kingdom in which the dwc:Taxon is classified direct
taxonPhylum 0..1
String		 The full scientific name of the phylum or division in which the dwc:Taxon is ... direct
taxonOrder 0..1
String		 The full scientific name of the order in which the dwc:Taxon is classified direct
taxonFamily 0..1
String		 The full scientific name of the family in which the dwc:Taxon is classified direct
taxonGenus 0..1
String		 The full scientific name of the genus in which the dwc:Taxon is classified direct
taxonSpecificEpithet 0..1
String		 The name of the first or species epithet of the dwc:scientificName direct
taxonomicStatus 0..1
String		 The status of the use of the dwc:scientificName as a label for a taxon direct
taxonVerbatimTaxonRank 0..1
String		 The taxonomic rank of the most specific name in the dwc:scientificName as it ... direct
taxonIdentifier 0..1
String		 An identifier for this specific taxon direct
taxonLifeScienceIdentifier 0..1
URN		 The life science identifier for this taxon direct

Usages

used by used in type used
Dataset aboutTaxonMboIds range Taxon
Document aboutTaxonMboIds range Taxon

Rules

Rule Applied Preconditions Postconditions Elseconditions
slot_conditions {'taxonScientificName': {'required': True}} {'taxonIdentifier': {'required': True}, 'taxonomicStatus': {'required': True}, 'taxonVerbatimTaxonRank': {'required': True}, 'taxonKingdom': {'required': True}}

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/marco-bolo/csv-input-classes

Mappings

Mapping Type Mapped Value
self schema:Taxon
native mbo:Taxon

LinkML Source

Direct

name: Taxon
extensions:
  csvw_virtual_triples:
    tag: csvw_virtual_triples
    value: "<> schema:additionalProperty <#ScientificName>,\n                    \
      \         <#Kingdom>,\n                             <#Phylum>,\n           \
      \                  <#Order>,\n                             <#Family>,\n    \
      \                         <#Genus>,\n                             <#SpecificEpithet>,\n\
      \                             <#Status>,\n                             <#VerbatimTaxonRank>.\n\
      \n<#ScientificName> a schema:PropertyValue;\n                  schema:propertyID\
      \ dwc:scientificName.\n<#Kingdom> a schema:PropertyValue;\n                \
      \  schema:propertyID dwc:kingdom.\n<#Phylum> a schema:PropertyValue;\n     \
      \             schema:propertyID dwc:phylum.\n<#Order> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:order.\n<#Family> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:family.\n<#Genus> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:genus.\n<#SpecificEpithet> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:specificEpithet.\n<#Status> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:taxonomicStatus.\n<#VerbatimTaxonRank>\
      \ a schema:PropertyValue;\n                  schema:propertyID dwc:verbatimTaxonRank.\n"
description: 'A set of organisms asserted to represent a natural cohesive biological
  unit.

  '
from_schema: https://w3id.org/marco-bolo/csv-input-classes
slots:
- id
- metadataPublisherId
- metadataDescribedForActionId
- name
- taxonScientificName
- taxonKingdom
- taxonPhylum
- taxonOrder
- taxonFamily
- taxonGenus
- taxonSpecificEpithet
- taxonomicStatus
- taxonVerbatimTaxonRank
- taxonIdentifier
- taxonLifeScienceIdentifier
class_uri: schema:Taxon
rules:
- preconditions:
    slot_conditions:
      taxonScientificName:
        name: taxonScientificName
        required: true
  postconditions:
    slot_conditions:
      taxonIdentifier:
        name: taxonIdentifier
        required: true
      taxonomicStatus:
        name: taxonomicStatus
        required: true
      taxonVerbatimTaxonRank:
        name: taxonVerbatimTaxonRank
        required: true
      taxonKingdom:
        name: taxonKingdom
        required: true
  description: If scientific name is provided, identifier, status, and rank are required

Induced

name: Taxon
extensions:
  csvw_virtual_triples:
    tag: csvw_virtual_triples
    value: "<> schema:additionalProperty <#ScientificName>,\n                    \
      \         <#Kingdom>,\n                             <#Phylum>,\n           \
      \                  <#Order>,\n                             <#Family>,\n    \
      \                         <#Genus>,\n                             <#SpecificEpithet>,\n\
      \                             <#Status>,\n                             <#VerbatimTaxonRank>.\n\
      \n<#ScientificName> a schema:PropertyValue;\n                  schema:propertyID\
      \ dwc:scientificName.\n<#Kingdom> a schema:PropertyValue;\n                \
      \  schema:propertyID dwc:kingdom.\n<#Phylum> a schema:PropertyValue;\n     \
      \             schema:propertyID dwc:phylum.\n<#Order> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:order.\n<#Family> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:family.\n<#Genus> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:genus.\n<#SpecificEpithet> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:specificEpithet.\n<#Status> a schema:PropertyValue;\n\
      \                  schema:propertyID dwc:taxonomicStatus.\n<#VerbatimTaxonRank>\
      \ a schema:PropertyValue;\n                  schema:propertyID dwc:verbatimTaxonRank.\n"
description: 'A set of organisms asserted to represent a natural cohesive biological
  unit.

  '
from_schema: https://w3id.org/marco-bolo/csv-input-classes
attributes:
  id:
    name: id
    description: 'An identifier chosen from the range given to your work package by
      WP1.

      '
    title: MBO Permanent Identifier
    comments:
    - "This is the identifier (mPID) for this row of the spreadsheet \nand for whatever\
      \ information is being described in this row. \nIt must start with `mbo_`, only\
      \ use printable ASCII characters\nand should be unique in this column. \n"
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    identifier: true
    alias: id
    owner: Taxon
    domain_of:
    - Action
    - HowTo
    - HowToStep
    - HowToTip
    - Dataset
    - PersonOrOrganization
    - ContactPoint
    - License
    - PropertyValue
    - DataDownload
    - DatasetComment
    - SoftwareSourceCode
    - SoftwareApplication
    - Service
    - EmbargoStatement
    - DefinedTerm
    - Place
    - GeoShape
    - MonetaryGrant
    - Taxon
    - Audience
    - Document
    - Instrument
    - Platform
    range: string
    required: true
    pattern: ^mbo_[a-zA-Z0-9_-]+$
  metadataPublisherId:
    name: metadataPublisherId
    description: 'The MBO Persistent IDentifier (mPID) of the person who entered this
      row of data.

      '
    title: Data Entry Person (mPID - you)
    comments:
    - 'Should be an mPID from the first column of Person.csv

      '
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:creator
    alias: metadataPublisherId
    owner: Taxon
    domain_of:
    - Action
    - HowTo
    - HowToStep
    - HowToTip
    - Dataset
    - Person
    - Organization
    - ContactPoint
    - License
    - PropertyValue
    - DataDownload
    - DatasetComment
    - SoftwareSourceCode
    - SoftwareApplication
    - Service
    - EmbargoStatement
    - DefinedTerm
    - Place
    - GeoShape
    - MonetaryGrant
    - Taxon
    - Audience
    - Document
    - Instrument
    - Platform
    range: PersonOrOrganization
    required: true
    multivalued: false
  metadataDescribedForActionId:
    name: metadataDescribedForActionId
    description: 'The [Action](#action) which resulted in this metadata record being
      described.


      Is likely to be the Action associated with a MARCO-BOLO Task.

      '
    title: Data Entered for Action (mPID)
    comments:
    - "The mPID from the first column of the Action.csv. \nNote that you can reference\
      \ the same mPID in multiple rows.\n\nUses the <https://w3id.org/marco-bolo/isResultOf>\
      \ predicate but ultimately ends up being \nrepresented as a triple in the form\
      \ `<action> schema:result <this-entity>`.\n"
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: mbo:isResultOf
    alias: metadataDescribedForActionId
    owner: Taxon
    domain_of:
    - Action
    - HowTo
    - HowToStep
    - HowToTip
    - Dataset
    - Person
    - Organization
    - ContactPoint
    - License
    - PropertyValue
    - DataDownload
    - DatasetComment
    - SoftwareSourceCode
    - SoftwareApplication
    - EmbargoStatement
    - DefinedTerm
    - Place
    - GeoShape
    - MonetaryGrant
    - Taxon
    - Audience
    - Document
    - Instrument
    - Platform
    range: Action
    required: true
    multivalued: false
  name:
    name: name
    description: A name/title
    title: Name
    comments:
    - "The commonly used name. \nFor example: `MBA` for Marine Biological Association\n"
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: Taxon
    domain_of:
    - Action
    - HowTo
    - HowToStep
    - HowToTip
    - Dataset
    - Organization
    - ContactPoint
    - License
    - PropertyValue
    - DataDownload
    - SoftwareSourceCode
    - SoftwareApplication
    - Service
    - Place
    - GeoShape
    - MonetaryGrant
    - Taxon
    - Audience
    - Document
    - Instrument
    - Platform
    range: string
    required: true
    multivalued: false
  taxonScientificName:
    name: taxonScientificName
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#ScientificName'
    description: "The full scientific name, with authorship and date information,\
      \ if known. \n\nActually represents dwc:scientificName via a schema:PropertyValue\
      \ (schema:additionalProperty/schema:value).\n"
    title: Scientific Name
    comments:
    - "When forming part of a dwc:Identification, \nthis should be the name in lowest\
      \ level taxonomic rank that can be determined. This term should not contain\
      \ \nidentification qualifications (e.g. 'cf.'), which should instead be supplied\
      \ in the dwc:identificationQualifier term.\n"
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonScientificName
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonKingdom:
    name: taxonKingdom
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#Kingdom'
    description: 'The full scientific name of the kingdom in which the dwc:Taxon is
      classified.


      Actually represents dwc:kingdom via a schema:PropertyValue (schema:additionalProperty/schema:value).

      '
    title: Kingdom
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonKingdom
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonPhylum:
    name: taxonPhylum
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#Phylum'
    description: 'The full scientific name of the phylum or division in which the
      dwc:Taxon is classified.


      Actually represents dwc:phylum via a schema:PropertyValue (schema:additionalProperty/schema:value).

      '
    title: Phylum
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonPhylum
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonOrder:
    name: taxonOrder
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#Order'
    description: 'The full scientific name of the order in which the dwc:Taxon is
      classified.


      Actually represents dwc:order via a schema:PropertyValue (schema:additionalProperty/schema:value).

      '
    title: Order
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonOrder
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonFamily:
    name: taxonFamily
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#Family'
    description: 'The full scientific name of the family in which the dwc:Taxon is
      classified.


      Actually represents dwc:family via a schema:PropertyValue (schema:additionalProperty/schema:value).

      '
    title: Family
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonFamily
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonGenus:
    name: taxonGenus
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#Genus'
    description: 'The full scientific name of the genus in which the dwc:Taxon is
      classified.


      Actually represents dwc:genus via a schema:PropertyValue (schema:additionalProperty/schema:value).

      '
    title: Genus
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonGenus
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonSpecificEpithet:
    name: taxonSpecificEpithet
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#SpecificEpithet'
    description: 'The name of the first or species epithet of the dwc:scientificName.


      Actually represents dwc:specificEpithet via a schema:PropertyValue (schema:additionalProperty/schema:value).

      '
    title: Specific Epithet
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonSpecificEpithet
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonomicStatus:
    name: taxonomicStatus
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#Status'
    description: "The status of the use of the dwc:scientificName as a label for a\
      \ taxon. \nRequires taxonomic opinion to define the scope of a dwc:Taxon. \n\
      Rules of priority then are used to define the taxonomic status of the \nnomenclature\
      \ contained in that scope, combined with the experts opinion. \nIt must be linked\
      \ to a specific taxonomic reference that defines the concept.\n\nActually represents\
      \ dwc:taxonomicStatus via a schema:PropertyValue (schema:additionalProperty/schema:value).\n"
    title: Status
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonomicStatus
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonVerbatimTaxonRank:
    name: taxonVerbatimTaxonRank
    extensions:
      csvw_about_url:
        tag: csvw_about_url
        value: '#VerbatimTaxonRank'
    description: 'The taxonomic rank of the most specific name in the dwc:scientificName
      as it appears in the original record.


      Actually represents dwc:verbatimTaxonRank via a schema:PropertyValue (schema:additionalProperty/schema:value).

      '
    title: Verbatim Taxon Rank
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:value
    alias: taxonVerbatimTaxonRank
    owner: Taxon
    domain_of:
    - Taxon
    range: string
    required: false
    multivalued: false
  taxonIdentifier:
    name: taxonIdentifier
    description: 'An identifier for this specific taxon. Preferably as a CURIE (e.g.
      `worms:146419`, `col:CS5HF`) or URI (`https://www.checklistbank.org/dataset/3LR/taxon/CS5HF`)

      '
    title: Identifier
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:identifier
    alias: taxonIdentifier
    owner: Taxon
    domain_of:
    - Taxon
    subproperty_of: identifier
    range: string
    required: false
    multivalued: false
  taxonLifeScienceIdentifier:
    name: taxonLifeScienceIdentifier
    description: 'The life science identifier for this taxon.

      '
    title: Life Science Identifier (PID)
    comments:
    - 'For example: `urn:lsid:marinespecies.org:taxname:578941`

      For more information, see https://www.lsid.info/

      '
    from_schema: https://w3id.org/marco-bolo/csv-input-classes
    rank: 1000
    slot_uri: schema:identifier
    alias: taxonLifeScienceIdentifier
    owner: Taxon
    domain_of:
    - Taxon
    subproperty_of: identifier
    range: URN
    required: false
    multivalued: false
    pattern: ^urn:lsid:[^:\s]+:[^:\s]+:[^:\s]+(:[^:\s]+)?$
class_uri: schema:Taxon
rules:
- preconditions:
    slot_conditions:
      taxonScientificName:
        name: taxonScientificName
        required: true
  postconditions:
    slot_conditions:
      taxonIdentifier:
        name: taxonIdentifier
        required: true
      taxonomicStatus:
        name: taxonomicStatus
        required: true
      taxonVerbatimTaxonRank:
        name: taxonVerbatimTaxonRank
        required: true
      taxonKingdom:
        name: taxonKingdom
        required: true
  description: If scientific name is provided, identifier, status, and rank are required