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Class: TaxonToTaxonAssociation

URI: base:TaxonToTaxonAssociation

classDiagram class TaxonToTaxonAssociation Association <|-- TaxonToTaxonAssociation TaxonToTaxonAssociation : aggregator_knowledge_source TaxonToTaxonAssociation : category TaxonToTaxonAssociation : description TaxonToTaxonAssociation : has_attribute TaxonToTaxonAssociation : has_evidence TaxonToTaxonAssociation : id TaxonToTaxonAssociation : iri TaxonToTaxonAssociation : knowledge_source TaxonToTaxonAssociation : name TaxonToTaxonAssociation : negated TaxonToTaxonAssociation : object TaxonToTaxonAssociation : predicate TaxonToTaxonAssociation : primary_knowledge_source TaxonToTaxonAssociation : publications TaxonToTaxonAssociation : qualifiers TaxonToTaxonAssociation : subject TaxonToTaxonAssociation : timepoint TaxonToTaxonAssociation : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
primary_knowledge_source 0..1
InformationResource		 The most upstream source of the knowledge expressed in an Association that an... Association
qualifiers 0..*
OntologyClass		 connects an association to qualifiers that modify or qualify the meaning of t... Association
publications 0..*
Publication		 One or more publications that report the statement expressed in an Associatio... Association
aggregator_knowledge_source 0..*
InformationResource		 An intermediate aggregator resource from which knowledge expressed in an Asso... Association
id 1..1
NONE		 A unique identifier for an entity Entity
knowledge_source 0..1
InformationResource		 An Information Resource from which the knowledge expressed in an Association ... Association
type 0..1
NONE		 Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute Entity
predicate 1..1
PredicateType		 A high-level grouping for the relationship type Association
subject 1..1
NamedThing		 connects an association to the subject of the association Association
timepoint 0..1
TimeType		 a point in time Association
object 1..1
NamedThing		 connects an association to the object of the association Association
negated 0..1
xsd:boolean		 if set to true, then the association is negated i Association
iri 0..1
IriType		 An IRI for an entity Entity
has_evidence 0..*
EvidenceType		 connects an association to an instance of supporting evidence Association
description 0..1
NarrativeText		 a human-readable description of an entity Entity
category 0..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lmodel/base

Mappings

Mapping Type Mapped Value
self base:TaxonToTaxonAssociation
native base:TaxonToTaxonAssociation

LinkML Source

Direct

name: taxon to taxon association
from_schema: https://w3id.org/lmodel/base
rank: 1000
is_a: association
slot_usage:
  subject:
    name: subject
    domain_of:
    - association
    - association
    - association
    range: system taxon
  object:
    name: object
    description: An association between individuals of different taxa.
    domain_of:
    - association
    - association
    - association
    range: system taxon
defining_slots:
- subject
- predicate
- object

Induced

name: taxon to taxon association
from_schema: https://w3id.org/lmodel/base
rank: 1000
is_a: association
slot_usage:
  subject:
    name: subject
    domain_of:
    - association
    - association
    - association
    range: system taxon
  object:
    name: object
    description: An association between individuals of different taxa.
    domain_of:
    - association
    - association
    - association
    range: system taxon
attributes:
  subject:
    name: subject
    description: connects an association to the subject of the association. For example,
      in a class-to-observable feature association, the class is subject and observable
      feature is object.
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    is_a: association slot
    domain: association
    slot_uri: rdf:subject
    alias: subject
    owner: taxon to taxon association
    domain_of:
    - association
    - association
    range: system taxon
    required: true
  predicate:
    name: predicate
    local_names:
      translator:
        local_name_source: translator
        local_name_value: predicate
    description: A high-level grouping for the relationship type. AKA minimal predicate.
      This is analogous to category for nodes.
    notes:
    - Has a value from the Baselink related_to hierarchy. In RDF,  this corresponds
      to rdf:predicate and in Neo4j this corresponds to the relationship type. The
      convention is for an edge label in snake_case form. For example, base:related_to,
      base:causes, base:restores
    from_schema: https://w3id.org/lmodel/base
    exact_mappings:
    - owl:annotatedProperty
    - sumo:Predicate
    rank: 1000
    is_a: association slot
    domain: association
    slot_uri: rdf:predicate
    alias: predicate
    owner: taxon to taxon association
    domain_of:
    - association
    range: predicate type
    required: true
  object:
    name: object
    description: An association between individuals of different taxa.
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    is_a: association slot
    domain: association
    slot_uri: rdf:object
    alias: object
    owner: taxon to taxon association
    domain_of:
    - association
    - association
    range: system taxon
    required: true
  negated:
    name: negated
    description: if set to true, then the association is negated i.e. is not true
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    is_a: association slot
    domain: association
    alias: negated
    owner: taxon to taxon association
    domain_of:
    - association
    range: boolean
  qualifiers:
    name: qualifiers
    description: connects an association to qualifiers that modify or qualify the
      meaning of that association
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    is_a: association slot
    singular_name: qualifier
    domain: association
    multivalued: true
    alias: qualifiers
    owner: taxon to taxon association
    domain_of:
    - association
    range: ontology class
  publications:
    name: publications
    description: One or more publications that report the statement expressed in an
      Association, or provide information used as evidence supporting this statement.
    from_schema: https://w3id.org/lmodel/base
    aliases:
    - supporting publications
    rank: 1000
    is_a: supporting documents
    singular_name: publication
    domain: association
    multivalued: true
    alias: publications
    owner: taxon to taxon association
    domain_of:
    - association
    range: publication
  has evidence:
    name: has evidence
    description: connects an association to an instance of supporting evidence
    from_schema: https://w3id.org/lmodel/base
    exact_mappings:
    - RO:0002558
    - SIO:000772
    broad_mappings:
    - csrc:evidence
    - sumo:evidence
    rank: 1000
    is_a: association slot
    domain: association
    multivalued: true
    alias: has_evidence
    owner: taxon to taxon association
    domain_of:
    - association
    range: evidence type
  knowledge source:
    name: knowledge source
    description: An Information Resource from which the knowledge expressed in an
      Association was retrieved, directly or indirectly. This can be any resource
      through which the knowledge passed on its way to its currently serialized form.
      In practice, implementers should use one of the more specific subtypes of this
      generic property.
    from_schema: https://w3id.org/lmodel/base
    close_mappings:
    - pav:providedBy
    rank: 1000
    is_a: association slot
    domain: association
    alias: knowledge_source
    owner: taxon to taxon association
    domain_of:
    - association
    range: information resource
  primary knowledge source:
    name: primary knowledge source
    description: The most upstream source of the knowledge expressed in an Association
      that an implementer can identify.  Performing a rigorous analysis of upstream
      data providers is expected; every effort is made to catalog the most upstream
      source of data in this property.  Only one data source should be declared primary
      in any association.  "aggregator knowledge source" can be used to capture non-primary
      sources.
    notes:
    - ''
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    is_a: knowledge source
    domain: association
    multivalued: false
    alias: primary_knowledge_source
    owner: taxon to taxon association
    domain_of:
    - association
    range: information resource
  aggregator knowledge source:
    name: aggregator knowledge source
    description: An intermediate aggregator resource from which knowledge expressed
      in an Association was retrieved downstream of the original source, on its path
      to its current serialized form.
    notes:
    - ''
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    is_a: knowledge source
    domain: association
    multivalued: true
    alias: aggregator_knowledge_source
    owner: taxon to taxon association
    domain_of:
    - association
    range: information resource
  timepoint:
    name: timepoint
    description: a point in time
    from_schema: https://w3id.org/lmodel/base
    aliases:
    - duration
    exact_mappings:
    - sumo:TimePoint
    - WIKIDATA_PROPERTY:P585
    narrow_mappings:
    - dwc:eventTime
    - SAN:ActuatingTime
    - sosa:phenomenonTime
    - sosa:resultTime
    rank: 1000
    alias: timepoint
    owner: taxon to taxon association
    domain_of:
    - geographic location at time
    - exposure event
    - association
    range: time type
  id:
    name: id
    description: A unique identifier for an entity. Must be either a CURIE shorthand
      for a URI or a complete URI
    in_subset:
    - translator_minimal
    from_schema: https://w3id.org/lmodel/base
    exact_mappings:
    - dct:identifier
    - EDAM-DATA:0842
    - EFO:id
    - REPR:id
    - schema:identifier
    - SIO:000115
    - sumo:Identifier
    narrow_mappings:
    - dwc:eventID
    - dwc:parentEventID
    - dwc:identificationID
    - dwc:systemID
    - CSO:bicm-id
    - SIO:000672
    - SIO:000674
    - ERO:0000044
    - ERO:0000480
    - NCIT:C94069
    - REPR:doi
    - SIO:000328
    - SIO:000729
    - schema:productID
    - schema:taxID
    - sumo:AccountID
    - sumo:AlphaIDString
    - sumo:AlphaNumericIDString
    - sumo:AgentID
    - sumo:CountryID
    - sumo:CustomerID
    - sumo:currencyCode
    - sumo:DistrictID
    - sumo:EmployeeID
    - sumo:IsoCode
    - sumo:LocalizablePlaceID
    - sumo:userIDString
    - sumo:urlString
    - sumo:UniformResourceLocator
    - WIKIDATA_PROPERTY:P3743
    broad_mappings:
    - CSO:catalogue_identifiers
    - IAO:0000603
    - IAO:0000119
    - sumo:identityElement
    rank: 1000
    identifier: true
    alias: id
    owner: taxon to taxon association
    domain_of:
    - NamedThing
    - ontology class
    - entity
    range: string
    required: true
  iri:
    name: iri
    description: An IRI for an entity. This is determined by the id using expansion
      rules.
    comments:
    - see also https://url.spec.whatwg.org/#goals
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://w3id.org/lmodel/base
    exact_mappings:
    - rr:IRI
    - WIKIDATA_PROPERTY:P854
    - WIKIDATA:Q424583
    - XAPI:IRI
    close_mappings:
    - NCIT:C165071
    - sumo:UniformResourceLocator
    related_mappings:
    - dwc:usewithiri
    narrow_mappings:
    - RO:0002617
    rank: 1000
    alias: iri
    owner: taxon to taxon association
    domain_of:
    - attribute
    - entity
    range: iri type
  category:
    name: category
    description: "Name of the high level ontology class in which this entity is categorized.\
      \ Corresponds to the label for the base entity type class.\n * In a neo4j database\
      \ this MAY correspond to the neo4j label tag.\n * In an RDF database it should\
      \ be a base model class URI.\nThis field is multi-valued. It should include\
      \ values for ancestors of the base class\nIn an RDF database, nodes will typically\
      \ have an rdf:type triples. This can be to the most specific base class, or\
      \ potentially to a class more specific than something in base."
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    is_a: type
    domain: entity
    multivalued: true
    designates_type: true
    alias: category
    owner: taxon to taxon association
    domain_of:
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    is_class_field: true
    range: category type
    required: false
  type:
    name: type
    description: rdf:type of base:Association should be fixed at rdf:Statement
    from_schema: https://w3id.org/lmodel/base
    rank: 1000
    slot_uri: rdf:type
    alias: type
    owner: taxon to taxon association
    domain_of:
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    - entity
    range: string
  name:
    name: name
    description: A human-readable name for an attribute or entity.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://w3id.org/lmodel/base
    aliases:
    - label
    - display name
    - title
    exact_mappings:
    - CSO:named_entity
    - gr:name
    - OM:name
    - REPR:name
    - schema:name
    - SIO:000116
    - sumo:Name
    - WIKIDATA_PROPERTY:P2561
    close_mappings:
    - IAO:0000111
    - IAO:0000118
    - skos:altLabel
    - sumo:originalTitle
    narrow_mappings:
    - AML:hasAttributeName
    - dct:title
    - NCIT:P386
    - WIKIDATA_PROPERTY:P1476
    - rr:column
    - rr:tableName
    - schema:recordLabel
    broad_mappings:
    - CSO:named_entity
    rank: 1000
    slot_uri: rdfs:label
    alias: name
    owner: taxon to taxon association
    domain_of:
    - NamedThing
    - attribute
    - entity
    - assembly mixin
    range: label type
  description:
    name: description
    description: a human-readable description of an entity
    in_subset:
    - translator_minimal
    from_schema: https://w3id.org/lmodel/base
    aliases:
    - definition
    exact_mappings:
    - dct:description
    - IAO:0000115
    - schema:description
    - skos:definitions
    - sumo:NarrativeText
    - WIKIDATA:Q1200750
    close_mappings:
    - sumo:Descriptor
    narrow_mappings:
    - csrc:architecture_description
    - CSO:architecture_description
    - CSO:concept_description
    - CSO:shape_description
    - OM:longcomment
    rank: 1000
    slot_uri: dct:description
    alias: description
    owner: taxon to taxon association
    domain_of:
    - NamedThing
    - entity
    range: narrative text
  has attribute:
    name: has attribute
    description: connects any entity to an attribute
    in_subset:
    - samples
    from_schema: https://w3id.org/lmodel/base
    exact_mappings:
    - AML:hasAttribute
    - CTRL:hasParameter
    - ssn:hasProperty
    - SIO:000008
    close_mappings:
    - sumo:hasVariable
    - sumo:property
    narrow_mappings:
    - AML:hasAttributeName
    - AML:hasDescription
    - AML:hasICID
    - AML:hasName
    - AML:hasProject
    - AML:hasUnit
    - AML:hasSchemaVersion
    - AML:hasVersionSUC
    - AML:hasWriterVersion
    - schema:hasPart
    - CDAO:has_Character
    - CDAO:has_Root
    - CDAO:has_First_Coordinate_Item
    - CDAO:has_Coordinate
    - CDAO:has_Change_Component
    - CDAO:has_Datum
    - CDAO:has_Node
    - CDAO:has_Annotation
    - CDAO:has_Remaining_Coordinate_List
    - CDAO:has_State
    - CDAO:has_Element
    - CTRL:hasApplicationLogic
    - CTRL:hasInput
    - CTRL:hasMedium
    - CTRL:hasOutput
    - CTRL:isConnectedTo
    - CTRL:isSupervisedBy
    - dct:hasPart
    - dct:hasFormat
    - dct:hasVersion
    - EFO:is_executed_in
    - EFO:0006351
    - geolink:hasAuthoritativeDigitalRepository
    - geolink:hasRelatedSample
    - geolink:hasAffiliation
    - geolink:hasAuthor
    - geolink:hasCollector
    - geolink:hasContact
    - geolink:hasContributor
    - geolink:hasCollectionEndDate
    - geolink:hasCollectionStartDate
    - geolink:hasCreator
    - geolink:hasDataset
    - geolink:hasEditor
    - geolink:hasEducator
    - geolink:hasFirstAppearance
    - geolink:hasIdentifierScheme
    - geolink:hasObserver
    - geolink:hasObservationArea
    - geolink:hasOwner
    - geolink:hasParticipant
    - geolink:hasParticipationEndTime
    - geolink:hasParticipationStartTime
    - geolink:hasPart
    - geolink:hasPublicationDate
    - geolink:hasRegistrationDate
    - geolink:hasStartDate
    - geolink:hasRepository
    - geolink:hasRightsHolder
    - geolink:hasScheduler
    - geolink:hasTimeStamp
    - geolink:hasVendor
    - gr:hasBusinessFunction
    - gr:hasBrand
    - gr:hasCurrency
    - gr:hasEligibleQuantity
    - gr:hasGlobalLocationNumber
    - gr:hasInventoryLevel
    - gr:hasManufacturer
    - gr:hasMakeAndModel
    - gr:hasNext
    - gr:hasPrevious
    - gr:hasUnitOfMeasurement
    - gr:hasValue
    - IAO:0000039
    - IAO:0000407
    - LOINC:has_action_guidance
    - LOINC:has_adjustment
    - LOINC:has_aggregation_view
    - LOINC:has_approach_guidance
    - LOINC:has_divisor
    - LOINC:has_exam
    - LOINC:has_method
    - LOINC:has_modality_subtype
    - LOINC:has_object_guidance
    - LOINC:has_scale
    - LOINC:has_suffix
    - LOINC:has_time_aspect
    - LOINC:has_time_modifier
    - LOINC:has_timing_of
    - NCIT:is_qualified_by
    - NCIT:qualifier_applies_to
    - NCIT:has_data_element
    - NCIT:role_has_domain
    - NCIT:role_has_range
    - NCIT:C62618
    - OM:hasPhenomenon
    - RO:0002002
    - RO:0000053
    - RO:0000086
    - RO:0000087
    - RO:0002520
    - RO:0002018
    - RO:0002017
    - RO:0002013
    - RO:0002016
    - RO:0002025
    - RO:0002521
    - RO:0002348
    - RO:0002566
    - RO:0002002
    - RO:0002338
    - RO:0002339
    - RO:0002573
    - RO:0009004
    - SAN:hasActuatingCapability
    - SAN:hasActuatingProperty
    - SAN:hasDateTime
    - SAN:hasEffect
    - SAN:hasWriter
    - SIO:000011
    - SIO:000586
    - SIO:001277
    - SIO:000671
    - SIO:000312
    - SIO:000552
    - SIO:000420
    - SIO:000253
    - SIO:000132
    - SIO:000255
    - SIO:000008
    - SIO:000364
    - SIO:000230
    - SIO:000235
    - SIO:000234
    - SIO:000228
    - SIO:000229
    - SIO:000900
    - SIO:000905
    - SIO:000221
    - SIO:000225
    - SIO:000223
    - SIO:000217
    - SIO:000291
    - SIO:000054
    - SIO:000059
    - SIO:000028
    - SIO:000139
    - SIO:000772
    - SIO:000641
    - SIO:000635
    - SIO:000066
    - SIO:001279
    - SIO:000300
    - SIO:001278
    - SIO:000680
    - SIO:000681
    - SIO:000679
    - SIO:000673
    - SIO:000369
    - SIO:000053
    - SIO:000972
    - SIO:000971
    - SIO:000273
    - SIO:000644
    - SIO:000974
    - SIO:000553
    - SIO:000145
    - SWO:0004000
    - sosa:hasFeatureOfInterest
    - sosa:hasSample
    - ssn:hasSubSystem
    - ssn:isProxyFor
    - ssn-system:hasSystemCapability
    - ssn-system:hasSystemProperty
    - ssn-system:hasOperatingRange
    - ssn-system:hasOperatingProperty
    - ssn-system:hasSurvivalRange
    - ssn-system:hasSurvivalProperty
    - ssn-system:inCondition
    - sumo:hasAcrossVariable
    - sumo:hasAccount
    - sumo:hasAward
    - sumo:hasDependency
    - sumo:hasDimension
    - sumo:hasExpertise
    - sumo:hasGUEState
    - sumo:hasOccupation
    - sumo:hasPurpose
    - sumo:hasPurposeForAgent
    - sumo:hasSkill
    - sumo:hasThroughVariable
    - sumo:hasUniform
    - sumo:hasVariable
    - sumo:holdsRight
    - SWO:9001002
    - SWO:0004001
    - SWO:9000067
    - SWO:0004002
    - SWO:0000087
    - SWO:0000086
    - SWO:0004004
    - SWO:0000741
    - SWO:0004002
    - SWO:3000054
    - SWO:0004000
    rank: 1000
    domain: entity
    multivalued: true
    alias: has_attribute
    owner: taxon to taxon association
    domain_of:
    - entity
    range: attribute
defining_slots:
- subject
- predicate
- object