EVORAO

Class: Taxon (Taxon)

Conceptual entity that groups one or more populations of an organism or organisms, as seen by taxonomists, to form a unit.

URI: EVORAO:Taxon

 classDiagram
    class Taxon
    click Taxon href "../Taxon"
      Term <|-- Taxon
        click Term href "../Term"
      
      Taxon : alternateName
        
          
    
    
    Taxon --> "*" AlternateName : alternateName
    click AlternateName href "../AlternateName"

        
      Taxon : dateIssued
        
      Taxon : dateModified
        
      Taxon : description
        
      Taxon : externalEquivalentTaxon
        
          
    
    
    Taxon --> "*" Taxon : externalEquivalentTaxon
    click Taxon href "../Taxon"

        
      Taxon : identifier
        
      Taxon : inVocabulary
        
          
    
    
    Taxon --> "0..1 _recommended_" Vocabulary : inVocabulary
    click Vocabulary href "../Vocabulary"

        
      Taxon : iri
        
      Taxon : keyword
        
      Taxon : lineage
        
      Taxon : parentTaxon
        
          
    
    
    Taxon --> "0..1 _recommended_" Taxon : parentTaxon
    click Taxon href "../Taxon"

        
      Taxon : previouslyKnownAs
        
          
    
    
    Taxon --> "*" Taxon : previouslyKnownAs
    click Taxon href "../Taxon"

        
      Taxon : publisher
        
          
    
    
    Taxon --> "0..1" PersonOrOrganization : publisher
    click PersonOrOrganization href "../PersonOrOrganization"

        
      Taxon : rank
        
          
    
    
    Taxon --> "0..1 _recommended_" TaxonomicRank : rank
    click TaxonomicRank href "../TaxonomicRank"

        
      Taxon : taxonomicId
        
      Taxon : taxonomicNodeId
        
      Taxon : taxonomy
        
          
    
    
    Taxon --> "* _recommended_" Taxonomy : taxonomy
    click Taxonomy href "../Taxonomy"

        
      Taxon : title
        
      Taxon : weight

Inheritance

Resource
- Term
  - Taxon

Slots

Name	Cardinality and Range	Description	Inheritance
taxonomy	* recommended Taxonomy	The taxonomy release(s) in which this entity exists	direct
parentTaxon	0..1 recommended Taxon	Immediate broader taxon that contains the current taxon in the taxonomy hiera…	direct
rank	0..1 recommended TaxonomicRank	Relative level or position of the identified taxon in the taxonomy	direct
externalEquivalentTaxon	* Taxon	Any equivalent taxon in a different taxonomy if exists/known to serve as a br…	direct
taxonomicId	1 String	The taxonomic identifier as a persistent identifier accross releases	direct
taxonomicNodeId	0..1 recommended String	Identifier for the taxonomic node, unique to this taxon within the specific t…	direct
alternateName	* AlternateName	Any other name under which the entity can be known	direct
previouslyKnownAs	* Taxon	Any historic version of this taxon having a different name	direct
lineage	* String	An ordered list of textual taxon names representing the taxonomic lineage of …	direct
title	1 String	A name given to the resource	Term
description	0..1 recommended String	A short explanation of the characteristics, features, or nature of the curren…	Term
weight	0..1 recommended Integer	A numerical value indicating relative importance or priority, generally proce…	Term
inVocabulary	0..1 recommended Vocabulary	Terms belong to a specific vocabulary	Term
keyword	* String	A keyword or tag describing the resource	Resource
dateIssued	0..1 Datetime	Date of formal issuance (e	Resource
dateModified	0..1 Datetime	Most recent date on which the resource was changed, updated or modified	Resource
identifier	* String	A unique identifier of the resource being described or cataloged	Resource
iri	* Uri	International Resource Identifier (IRI) that uniquely identifies or refers to…	Resource
publisher	0..1 PersonOrOrganization	The entity responsible for making the resource available	Resource

Usages

used by	used in	type	used
Taxonomy	taxon	range	Taxon
PathogenIdentification	taxon	range	Taxon
Taxon	parentTaxon	range	Taxon
Taxon	externalEquivalentTaxon	range	Taxon
Taxon	previouslyKnownAs	range	Taxon
ClinicalGroup	taxon	range	Taxon

Comments

The taxonomic taxons connected to their parent so that a full lienage can be rebuild.
Use of Data provider recommended.

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/evorao/

Mappings

Mapping Type	Mapped Value
self	EVORAO:Taxon
native	EVORAO:Taxon
exact	schema:Taxon, schema:Taxon
close	wd:Q16521, dwc:Taxon, uniprotrdfs:Taxon, wd:Q16521, dwc:Taxon, uniprotrdfs:Taxon

LinkML Source

Direct

Induced

```yaml name: Taxon description: Conceptual entity that groups one or more populations of an organism or organisms, as seen by taxonomists, to form a unit. title: Taxon comments: - The taxonomic taxons connected to their parent so that a full lienage can be rebuild. - Use of Data provider recommended. from_schema: https://w3id.org/evorao/ exact_mappings: - schema:Taxon - schema:Taxon close_mappings: - wd:Q16521 - dwc:Taxon - uniprotrdfs:Taxon - wd:Q16521 - dwc:Taxon - uniprotrdfs:Taxon is_a: Term slot_usage: taxonomy: name: taxonomy description: The taxonomy release(s) in which this entity exists. title: taxonomy broad_mappings: - dct:isPartOf domain_of: - Taxon - TaxonomicRank range: Taxonomy required: false recommended: true multivalued: true parentTaxon: name: parentTaxon description: Immediate broader taxon that contains the current taxon in the taxonomy hierarchy. title: parent taxon exact_mappings: - schema:parentTaxon close_mappings: - wdp:P171 broad_mappings: - dwc:Taxon domain_of: - Taxon range: Taxon required: false recommended: true multivalued: false rank: name: rank description: Relative level or position of the identified taxon in the taxonomy. title: rank exact_mappings: - wdp:P105 close_mappings: - dwc:taxonRank - schema:taxonRank - biolink:has_taxonomic_rank related_mappings: - taxrank:1000000 - ncbitaxon:has_rank domain_of: - Taxon - Taxonomy range: TaxonomicRank required: false recommended: true multivalued: false externalEquivalentTaxon: name: externalEquivalentTaxon description: Any equivalent taxon in a different taxonomy if exists/known to serve as a bridge (e.g, ICTV towards NCBI). title: external equivalent taxon comments: - Could serve as a bridge between ICTV and NCBI as several providers currently uses NCBI Taxonomy. close_mappings: - dwc:taxonID related_mappings: - dct:references domain_of: - Taxon range: Taxon required: false multivalued: true taxonomicId: name: taxonomicId description: The taxonomic identifier as a persistent identifier accross releases. title: taxonomic ID exact_mappings: - dwc:taxonID narrow_mappings: - ncit:P331 broad_mappings: - schema:identifier - dct:identifier is_a: identifier domain_of: - Taxon range: string required: true multivalued: false taxonomicNodeId: name: taxonomicNodeId description: Identifier for the taxonomic node, unique to this taxon within the specific taxonomy release/version. title: taxonomic node ID comments: - NCBI does not have a taxon_node id, only a taxonomicID. Taxon_node id is Unique in ICTV= Key of the taxon node! close_mappings: - dwc:taxonID broad_mappings: - dct:identifier is_a: identifier domain_of: - Taxon range: string required: false recommended: true multivalued: false alternateName: name: alternateName description: Any other name under which the entity can be known. title: alternate name comments: - This includes previous names, acronyms, former taxonomic terms, and other variations. - This information can serve as keywords for search purposes and as a bridge with other projects that use different naming systems or taxonomies. exact_mappings: - schema:alternateName - dct:alternative - iao:0000118 close_mappings: - wdp:P4970 domain_of: - Taxon - CommonName - AlternateName - ClinicalGroup - Organization range: AlternateName required: false multivalued: true previouslyKnownAs: name: previouslyKnownAs description: Any historic version of this taxon having a different name. title: previously known as deprecated: Deprecated in favor of EVORAO:alternateName. Use EVORAO:alternateName for historical names, synonyms, and other alternative labels. EVORAO:previouslyKnownAs was limited to historical taxon names and required a Taxon value, which made it too narrow for broader naming use cases. deprecated_element_has_possible_replacement: EVORAO:alternateName related_mappings: - schema:alternateName broad_mappings: - dwc:Taxon domain_of: - Taxon range: Taxon required: false multivalued: true lineage: name: lineage description: An ordered list of textual taxon names representing the taxonomic lineage of the current taxon, normally from the highest known ancestor to the immediate parent. title: lineage comments: - This property is intended for display, indexing, and search optimisation purposes. It represents a denormalised view of the taxonomic lineage and is typically derived automatically from successive parentTaxon relations. It MUST NOT be considered authoritative for taxonomic reasoning. This property provides a flattened, display-oriented view of the lineage and does not replace the parentTaxon relation. domain_of: - Taxon range: string required: false multivalued: true attributes: taxonomy: name: taxonomy description: The taxonomy release(s) in which this entity exists. title: taxonomy from_schema: https://w3id.org/evorao/ broad_mappings: - dct:isPartOf rank: 1000 alias: taxonomy owner: Taxon domain_of: - Taxon - TaxonomicRank range: Taxonomy required: false recommended: true multivalued: true parentTaxon: name: parentTaxon description: Immediate broader taxon that contains the current taxon in the taxonomy hierarchy. title: parent taxon from_schema: https://w3id.org/evorao/ exact_mappings: - schema:parentTaxon close_mappings: - wdp:P171 broad_mappings: - dwc:Taxon rank: 1000 alias: parentTaxon owner: Taxon domain_of: - Taxon range: Taxon required: false recommended: true multivalued: false rank: name: rank description: Relative level or position of the identified taxon in the taxonomy. title: rank from_schema: https://w3id.org/evorao/ exact_mappings: - wdp:P105 close_mappings: - dwc:taxonRank - schema:taxonRank - biolink:has_taxonomic_rank related_mappings: - taxrank:1000000 - ncbitaxon:has_rank rank: 1000 alias: rank owner: Taxon domain_of: - Taxon - Taxonomy range: TaxonomicRank required: false recommended: true multivalued: false externalEquivalentTaxon: name: externalEquivalentTaxon description: Any equivalent taxon in a different taxonomy if exists/known to serve as a bridge (e.g, ICTV towards NCBI). title: external equivalent taxon comments: - Could serve as a bridge between ICTV and NCBI as several providers currently uses NCBI Taxonomy. from_schema: https://w3id.org/evorao/ close_mappings: - dwc:taxonID related_mappings: - dct:references rank: 1000 alias: externalEquivalentTaxon owner: Taxon domain_of: - Taxon range: Taxon required: false multivalued: true taxonomicId: name: taxonomicId description: The taxonomic identifier as a persistent identifier accross releases. title: taxonomic ID from_schema: https://w3id.org/evorao/ exact_mappings: - dwc:taxonID narrow_mappings: - ncit:P331 broad_mappings: - schema:identifier - dct:identifier rank: 1000 is_a: identifier alias: taxonomicId owner: Taxon domain_of: - Taxon range: string required: true multivalued: false taxonomicNodeId: name: taxonomicNodeId description: Identifier for the taxonomic node, unique to this taxon within the specific taxonomy release/version. title: taxonomic node ID comments: - NCBI does not have a taxon_node id, only a taxonomicID. Taxon_node id is Unique in ICTV= Key of the taxon node! from_schema: https://w3id.org/evorao/ close_mappings: - dwc:taxonID broad_mappings: - dct:identifier rank: 1000 is_a: identifier alias: taxonomicNodeId owner: Taxon domain_of: - Taxon range: string required: false recommended: true multivalued: false alternateName: name: alternateName description: Any other name under which the entity can be known. title: alternate name comments: - This includes previous names, acronyms, former taxonomic terms, and other variations. - This information can serve as keywords for search purposes and as a bridge with other projects that use different naming systems or taxonomies. from_schema: https://w3id.org/evorao/ exact_mappings: - schema:alternateName - dct:alternative - iao:0000118 close_mappings: - wdp:P4970 rank: 1000 alias: alternateName owner: Taxon domain_of: - Taxon - CommonName - AlternateName - ClinicalGroup - Organization range: AlternateName required: false multivalued: true previouslyKnownAs: name: previouslyKnownAs description: Any historic version of this taxon having a different name. title: previously known as deprecated: Deprecated in favor of EVORAO:alternateName. Use EVORAO:alternateName for historical names, synonyms, and other alternative labels. EVORAO:previouslyKnownAs was limited to historical taxon names and required a Taxon value, which made it too narrow for broader naming use cases. from_schema: https://w3id.org/evorao/ deprecated_element_has_possible_replacement: EVORAO:alternateName related_mappings: - schema:alternateName broad_mappings: - dwc:Taxon rank: 1000 alias: previouslyKnownAs owner: Taxon domain_of: - Taxon range: Taxon required: false multivalued: true lineage: name: lineage description: An ordered list of textual taxon names representing the taxonomic lineage of the current taxon, normally from the highest known ancestor to the immediate parent. title: lineage comments: - This property is intended for display, indexing, and search optimisation purposes. It represents a denormalised view of the taxonomic lineage and is typically derived automatically from successive parentTaxon relations. It MUST NOT be considered authoritative for taxonomic reasoning. This property provides a flattened, display-oriented view of the lineage and does not replace the parentTaxon relation. from_schema: https://w3id.org/evorao/ rank: 1000 alias: lineage owner: Taxon domain_of: - Taxon range: string required: false multivalued: true title: name: title description: A name given to the resource. title: title comments: - The title of the item should be as short and descriptive as possible. - 'E.g. for virus products it should basically be based on the following Pattern: ''Virus name'', ''virus host type'', ''collection year'', ''country of collection'' ex ''suspected epidemiological origin'', ''genotype'', ''strain'', ''variant name or specific feature.' from_schema: https://w3id.org/evorao/ exact_mappings: - schema:name - rdfs:label rank: 1000 slot_uri: dct:title alias: title owner: Taxon domain_of: - Term - Dataset - DataService - Publication - License - Certification - FundingSource range: string required: true multivalued: false description: name: description description: A short explanation of the characteristics, features, or nature of the current item. title: description comments: - Describe this item in few lines. This description will serve as a summary to present the resource. from_schema: https://w3id.org/evorao/ exact_mappings: - schema:description rank: 1000 slot_uri: dct:description alias: description owner: Taxon domain_of: - Term - Dataset - DataService - PersonOrOrganization - File - ContactPoint - License - Certification - FundingSource range: string required: false recommended: true multivalued: false weight: name: weight description: A numerical value indicating relative importance or priority, generally processed in ascending order. This weight helps prioritize content when organizing or processing data. Its value can be negative, with a default set to 0. title: weight comments: - The lowest weighted Data providers are triggered first. - This property may be usefull to populate at first entities that are referenced by others (e.g. Version ahead of Rank ahead of Taxon). from_schema: https://w3id.org/evorao/ close_mappings: - adms:status rank: 1000 ifabsent: int(0) alias: weight owner: Taxon domain_of: - Term - DataProvider range: integer required: false recommended: true multivalued: false inVocabulary: name: inVocabulary description: Terms belong to a specific vocabulary. title: in Vocabulary from_schema: https://w3id.org/evorao/ close_mappings: - wdp:P972 related_mappings: - dct:isReferencedBy broad_mappings: - dct:isPartOf rank: 1000 alias: inVocabulary owner: Taxon domain_of: - Term range: Vocabulary required: false recommended: true multivalued: false keyword: name: keyword description: A keyword or tag describing the resource. title: keyword from_schema: https://w3id.org/evorao/ rank: 1000 slot_uri: dcat:keyword alias: keyword owner: Taxon domain_of: - Resource range: string required: false multivalued: true dateIssued: name: dateIssued description: Date of formal issuance (e.g., publication) of the resource. title: date issued comments: - encoded using the relevant ISO 8601 Date and Time compliant string [DATETIME]. from_schema: https://w3id.org/evorao/ exact_mappings: - sepio:0000051 close_mappings: - schema:datePublished - schema:dateCreated rank: 1000 slot_uri: dct:issued alias: dateIssued owner: Taxon domain_of: - Resource range: datetime required: false multivalued: false dateModified: name: dateModified description: Most recent date on which the resource was changed, updated or modified. title: date modified comments: - encoded using the relevant ISO 8601 Date and Time compliant string [DATETIME]. from_schema: https://w3id.org/evorao/ exact_mappings: - sepio:0000036 close_mappings: - schema:dateModified rank: 1000 slot_uri: dct:modified alias: dateModified owner: Taxon domain_of: - Resource range: datetime required: false multivalued: false identifier: name: identifier description: A unique identifier of the resource being described or cataloged. title: identifier comments: - The identifier is a text string which is assigned to the resource to provide an unambiguous reference within a particular context. Persistent identifiers should be provided as HTTP URIs. from_schema: https://w3id.org/evorao/ exact_mappings: - schema:identifier rank: 1000 slot_uri: dct:identifier alias: identifier owner: Taxon domain_of: - Resource range: string required: false multivalued: true iri: name: iri description: International Resource Identifier (IRI) that uniquely identifies or refers to the resource. IRIs include URIs, and URIs include URLs. title: IRI comments: - An IRI is a global identifier standardized by IETF RFC 3987. It may or may not be resolvable on the web. IRIs include URIs, and URIs include URLs. from_schema: https://w3id.org/evorao/ close_mappings: - biolink:iri related_mappings: - mi:url narrow_mappings: - schema:url rank: 1000 is_a: identifier alias: iri owner: Taxon domain_of: - Resource range: uri required: false multivalued: true publisher: name: publisher description: The entity responsible for making the resource available. title: publisher comments: - Resources of type foaf:Agent like EVORAO:PersonOrOrganization are recommended as values for this property. from_schema: https://w3id.org/evorao/ rank: 1000 slot_uri: dct:publisher alias: publisher owner: Taxon domain_of: - Resource range: PersonOrOrganization required: false multivalued: false ```

This site is open source. Improve this page.