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Class: ParcellationAtlas

A parcellation atlas is a versioned release reference used to guide experiments or deal with the spatial relationship between objects or the location of objects within the context of some anatomical structure. An atlas is minimally defined by a notion of space (either implicit or explicit) and an annotation set. Reference atlases usually have additional parts that make them more useful in certain situations, such as a well defined coordinate system, delineations indicating the boundaries of various regions or cell populations, landmarks, and labels and names to make it easier to communicate about well known and useful locations (ref: ILX:0777109, RRID:SCR_023499).

URI: bican:ParcellationAtlas

classDiagram class ParcellationAtlas click ParcellationAtlas href "../ParcellationAtlas" VersionedNamedThing <|-- ParcellationAtlas click VersionedNamedThing href "../VersionedNamedThing" ParcellationAtlas : category ParcellationAtlas : deprecated ParcellationAtlas : description ParcellationAtlas : full_name ParcellationAtlas : has_attribute ParcellationAtlas --> "*" Attribute : has_attribute click Attribute href "../Attribute" ParcellationAtlas : has_anatomical_annotation_set ParcellationAtlas : has_anatomical_space ParcellationAtlas : has_parcellation_terminology ParcellationAtlas : id ParcellationAtlas : iri ParcellationAtlas : name ParcellationAtlas : provided_by ParcellationAtlas : revision_of ParcellationAtlas --> "0..1" VersionedNamedThing : revision_of click VersionedNamedThing href "../VersionedNamedThing" ParcellationAtlas : specialization_of ParcellationAtlas : synonym ParcellationAtlas : type ParcellationAtlas : version ParcellationAtlas : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_anatomical_space 1
String or 
AnatomicalSpace or 
String		 Reference to the anatomical space component of the parcellation atlas direct
has_anatomical_annotation_set 1
String or 
AnatomicalAnnotationSet or 
String		 Reference to the anatomical annotation set component of the parcellation atla... direct
has_parcellation_terminology 1
String or 
ParcellationTerminology or 
String		 Reference to the parcellation terminology component of the parcellation atlas direct
specialization_of 0..1
String or 
ParcellationAtlas or 
String		 Reference to the general (non versioned) parcellation atlas for which the par... direct
version 1
String		 VersionedNamedThing
revision_of 0..1
VersionedNamedThing or 
ParcellationAtlas or 
String		 VersionedNamedThing
id 1
String		 A unique identifier for an entity Entity, NamedThing
iri 0..1
IriType		 An IRI for an entity Entity, NamedThing
category *
Curie		 Name of the high level ontology class in which this entity is categorized Entity, NamedThing
type *
String		 Entity, NamedThing
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity, NamedThing
description 0..1
NarrativeText		 a human-readable description of an entity Entity, NamedThing
has_attribute *
Attribute		 connects any entity to an attribute Entity, NamedThing
deprecated 0..1
Boolean		 A boolean flag indicating that an entity is no longer considered current or v... Entity, NamedThing
provided_by *
String		 The value in this node property represents the knowledge provider that create... NamedThing
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing NamedThing
synonym *
LabelType		 Alternate human-readable names for a thing NamedThing

Usages

used by used in type used
ParcellationAtlas specialization_of any_of[range] ParcellationAtlas
ParcellationAtlas revision_of any_of[range] ParcellationAtlas

Identifier and Mapping Information

Schema Source

  • from schema: https:/w3id.org/brain-bican/bke-taxonomy

Mappings

Mapping Type Mapped Value
self bican:ParcellationAtlas
native bican:ParcellationAtlas

LinkML Source

Direct

name: ParcellationAtlas
description: 'A parcellation atlas is a versioned release reference used to guide
  experiments or deal with the spatial relationship between  objects or the location
  of objects within the context of some anatomical structure. An atlas is minimally
  defined by a notion  of space (either implicit or explicit) and an annotation set.
  Reference atlases usually have additional parts that make them  more useful in certain
  situations, such as a well defined coordinate system, delineations indicating the
  boundaries of various  regions or cell populations, landmarks, and labels and names
  to make it easier to communicate about well known and useful  locations (ref: ILX:0777109,
  RRID:SCR_023499).'
from_schema: https:/w3id.org/brain-bican/bke-taxonomy
is_a: VersionedNamedThing
slot_usage:
  revision_of:
    name: revision_of
    any_of:
    - range: ParcellationAtlas
    - range: string
attributes:
  has_anatomical_space:
    name: has_anatomical_space
    description: Reference to the anatomical space component of the parcellation atlas
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    domain_of:
    - ParcellationAtlas
    required: true
    any_of:
    - range: AnatomicalSpace
    - range: string
  has_anatomical_annotation_set:
    name: has_anatomical_annotation_set
    description: Reference to the anatomical annotation set component of the parcellation
      atlas
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    domain_of:
    - ParcellationAtlas
    required: true
    any_of:
    - range: AnatomicalAnnotationSet
    - range: string
  has_parcellation_terminology:
    name: has_parcellation_terminology
    description: Reference to the parcellation terminology component of the parcellation
      atlas
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    domain_of:
    - ParcellationAtlas
    required: true
    any_of:
    - range: ParcellationTerminology
    - range: string
  specialization_of:
    name: specialization_of
    description: Reference to the general (non versioned) parcellation atlas for which
      the parcellation atlas is a specific  version release of.
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    domain_of:
    - ParcellationAtlas
    any_of:
    - range: ParcellationAtlas
    - range: string

Induced

name: ParcellationAtlas
description: 'A parcellation atlas is a versioned release reference used to guide
  experiments or deal with the spatial relationship between  objects or the location
  of objects within the context of some anatomical structure. An atlas is minimally
  defined by a notion  of space (either implicit or explicit) and an annotation set.
  Reference atlases usually have additional parts that make them  more useful in certain
  situations, such as a well defined coordinate system, delineations indicating the
  boundaries of various  regions or cell populations, landmarks, and labels and names
  to make it easier to communicate about well known and useful  locations (ref: ILX:0777109,
  RRID:SCR_023499).'
from_schema: https:/w3id.org/brain-bican/bke-taxonomy
is_a: VersionedNamedThing
slot_usage:
  revision_of:
    name: revision_of
    any_of:
    - range: ParcellationAtlas
    - range: string
attributes:
  has_anatomical_space:
    name: has_anatomical_space
    description: Reference to the anatomical space component of the parcellation atlas
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    alias: has_anatomical_space
    owner: ParcellationAtlas
    domain_of:
    - ParcellationAtlas
    range: string
    required: true
    any_of:
    - range: AnatomicalSpace
    - range: string
  has_anatomical_annotation_set:
    name: has_anatomical_annotation_set
    description: Reference to the anatomical annotation set component of the parcellation
      atlas
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    alias: has_anatomical_annotation_set
    owner: ParcellationAtlas
    domain_of:
    - ParcellationAtlas
    range: string
    required: true
    any_of:
    - range: AnatomicalAnnotationSet
    - range: string
  has_parcellation_terminology:
    name: has_parcellation_terminology
    description: Reference to the parcellation terminology component of the parcellation
      atlas
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    alias: has_parcellation_terminology
    owner: ParcellationAtlas
    domain_of:
    - ParcellationAtlas
    range: string
    required: true
    any_of:
    - range: ParcellationTerminology
    - range: string
  specialization_of:
    name: specialization_of
    description: Reference to the general (non versioned) parcellation atlas for which
      the parcellation atlas is a specific  version release of.
    from_schema: https://identifiers.org/brain-bican/anatomical-structure-schema
    rank: 1000
    alias: specialization_of
    owner: ParcellationAtlas
    domain_of:
    - ParcellationAtlas
    range: string
    any_of:
    - range: ParcellationAtlas
    - range: string
  version:
    name: version
    definition_uri: https://w3id.org/biolink/vocab/version
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    broad_mappings:
    - pav:version
    - owl:versionInfo
    rank: 1000
    is_a: node property
    domain: dataset
    slot_uri: biolink:version
    alias: version
    owner: ParcellationAtlas
    domain_of:
    - VersionedNamedThing
    - GenomeAnnotation
    - GenomeAssembly
    range: string
    required: true
  revision_of:
    name: revision_of
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: revision_of
    owner: ParcellationAtlas
    domain_of:
    - VersionedNamedThing
    range: VersionedNamedThing
    any_of:
    - range: ParcellationAtlas
    - range: string
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/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/brain-bican/bke-taxonomy
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    alias: id
    owner: ParcellationAtlas
    domain_of:
    - ontology class
    - entity
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    - Abbreviation
    - ColorPalette
    - DisplayColor
    - attribute
    - named thing
    - taxonomic rank
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    required: true
  iri:
    name: iri
    definition_uri: https://w3id.org/biolink/vocab/iri
    description: An IRI for an entity. This is determined by the id using expansion
      rules.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    alias: iri
    owner: ParcellationAtlas
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: iri type
  category:
    name: category
    definition_uri: https://w3id.org/biolink/vocab/category
    description: 'Name of the high level ontology class in which this entity is categorized.
      Corresponds to the label for the biolink entity type class. In a neo4j database
      this MAY correspond to the neo4j label tag. In an RDF database it should be
      a biolink model class URI. This field is multi-valued. It should include values
      for ancestors of the biolink class; for example, a protein such as Shh would
      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
      In an RDF database, nodes will typically have an rdf:type triples. This can
      be to the most specific biolink class, or potentially to a class more specific
      than something in biolink. For example, a sequence feature `f` may have a rdf:type
      assertion to a SO class such as TF_binding_site, which is more specific than
      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
      biolink:NamedThing}. NOTE: The category slot was modified to have a curie range
      and a pattern for bican categories.'
    in_subset:
    - translator_minimal
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: ParcellationAtlas
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    is_class_field: true
    range: curie
    multivalued: true
    pattern: ^bican:[A-Z][A-Za-z]+$
  type:
    name: type
    definition_uri: https://w3id.org/biolink/vocab/type
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    alias: type
    owner: ParcellationAtlas
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    description: A human-readable name for an attribute or entity.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    aliases:
    - label
    - display name
    - title
    mappings:
    - rdfs:label
    exact_mappings:
    - gff3:Name
    - gpi:DB_Object_Name
    narrow_mappings:
    - dct:title
    - WIKIDATA_PROPERTY:P1476
    rank: 1000
    domain: entity
    slot_uri: rdfs:label
    alias: name
    owner: ParcellationAtlas
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    - ColorPalette
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene or gene product
    - gene
    - genome
    range: label type
  description:
    name: description
    definition_uri: https://w3id.org/biolink/vocab/description
    description: a human-readable description of an entity
    in_subset:
    - translator_minimal
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    aliases:
    - definition
    mappings:
    - dct:description
    exact_mappings:
    - IAO:0000115
    - skos:definitions
    narrow_mappings:
    - gff3:Description
    rank: 1000
    slot_uri: dct:description
    alias: description
    owner: ParcellationAtlas
    domain_of:
    - entity
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - ColorPalette
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: narrative text
  has attribute:
    name: has attribute
    definition_uri: https://w3id.org/biolink/vocab/has_attribute
    description: connects any entity to an attribute
    in_subset:
    - samples
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    exact_mappings:
    - SIO:000008
    close_mappings:
    - OBI:0001927
    narrow_mappings:
    - OBAN:association_has_subject_property
    - OBAN:association_has_object_property
    - CPT:has_possibly_included_panel_element
    - DRUGBANK:category
    - EFO:is_executed_in
    - HANCESTRO:0301
    - 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:R88
    - NCIT:eo_disease_has_property_or_attribute
    - NCIT:has_data_element
    - NCIT:has_pharmaceutical_administration_method
    - NCIT:has_pharmaceutical_basic_dose_form
    - NCIT:has_pharmaceutical_intended_site
    - NCIT:has_pharmaceutical_release_characteristics
    - NCIT:has_pharmaceutical_state_of_matter
    - NCIT:has_pharmaceutical_transformation
    - NCIT:is_qualified_by
    - NCIT:qualifier_applies_to
    - NCIT:role_has_domain
    - NCIT:role_has_range
    - INO:0000154
    - HANCESTRO:0308
    - OMIM:has_inheritance_type
    - orphanet:C016
    - orphanet:C017
    - RO:0000053
    - RO:0000086
    - RO:0000087
    - SNOMED:has_access
    - SNOMED:has_clinical_course
    - SNOMED:has_count_of_base_of_active_ingredient
    - SNOMED:has_dose_form_administration_method
    - SNOMED:has_dose_form_release_characteristic
    - SNOMED:has_dose_form_transformation
    - SNOMED:has_finding_context
    - SNOMED:has_finding_informer
    - SNOMED:has_inherent_attribute
    - SNOMED:has_intent
    - SNOMED:has_interpretation
    - SNOMED:has_laterality
    - SNOMED:has_measurement_method
    - SNOMED:has_method
    - SNOMED:has_priority
    - SNOMED:has_procedure_context
    - SNOMED:has_process_duration
    - SNOMED:has_property
    - SNOMED:has_revision_status
    - SNOMED:has_scale_type
    - SNOMED:has_severity
    - SNOMED:has_specimen
    - SNOMED:has_state_of_matter
    - SNOMED:has_subject_relationship_context
    - SNOMED:has_surgical_approach
    - SNOMED:has_technique
    - SNOMED:has_temporal_context
    - SNOMED:has_time_aspect
    - SNOMED:has_units
    - UMLS:has_structural_class
    - UMLS:has_supported_concept_property
    - UMLS:has_supported_concept_relationship
    - UMLS:may_be_qualified_by
    rank: 1000
    domain: entity
    slot_uri: biolink:has_attribute
    alias: has_attribute
    owner: ParcellationAtlas
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: attribute
    multivalued: true
  deprecated:
    name: deprecated
    definition_uri: https://w3id.org/biolink/vocab/deprecated
    description: A boolean flag indicating that an entity is no longer considered
      current or valid.
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: deprecated
    owner: ParcellationAtlas
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: boolean
  provided by:
    name: provided by
    definition_uri: https://w3id.org/biolink/vocab/provided_by
    description: The value in this node property represents the knowledge provider
      that created or assembled the node and all of its attributes.  Used internally
      to represent how a particular node made its way into a knowledge provider or
      graph.
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: ParcellationAtlas
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  xref:
    name: xref
    definition_uri: https://w3id.org/biolink/vocab/xref
    description: A database cross reference or alternative identifier for a NamedThing
      or edge between two NamedThings.  This property should point to a database record
      or webpage that supports the existence of the edge, or gives more detail about
      the edge. This property can be used on a node or edge to provide multiple URIs
      or CURIE cross references.
    in_subset:
    - translator_minimal
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    aliases:
    - dbxref
    - Dbxref
    - DbXref
    - record_url
    - source_record_urls
    narrow_mappings:
    - gff3:Dbxref
    - gpi:DB_Xrefs
    rank: 1000
    domain: named thing
    slot_uri: biolink:xref
    alias: xref
    owner: ParcellationAtlas
    domain_of:
    - named thing
    - gene
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    - ObservationMatrix
    - ObservationRow
    - Abbreviation
    - MatrixFile
    - ColorPalette
    - DisplayColor
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - genome
    range: uriorcurie
    multivalued: true
  full name:
    name: full name
    definition_uri: https://w3id.org/biolink/vocab/full_name
    description: a long-form human readable name for a thing
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: ParcellationAtlas
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
  synonym:
    name: synonym
    definition_uri: https://w3id.org/biolink/vocab/synonym
    description: Alternate human-readable names for a thing
    in_subset:
    - translator_minimal
    from_schema: https:/w3id.org/brain-bican/bke-taxonomy
    aliases:
    - alias
    narrow_mappings:
    - skos:altLabel
    - gff3:Alias
    - AGRKB:synonyms
    - gpi:DB_Object_Synonyms
    - HANCESTRO:0330
    - IAO:0000136
    - RXNORM:has_tradename
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:synonym
    alias: synonym
    owner: ParcellationAtlas
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
    multivalued: true