anatomical_structure.yaml

id: https://w3id.org/my-org/anatomical-structure-schema
name: anatomical-structure-schema
title: Anatomical Structure Schema
description: |-
  The Anatomical Structure schema is designed to represent types and relationships of anatomical brain structures. 
license: MIT

prefixes:
  AnS: https://w3id.org/my-org/anatomical-structure-schema/
  linkml: https://w3id.org/linkml/
  biolink: https://w3id.org/biolink/
  schema: http://schema.org/
  PATO: http://purl.obolibrary.org/obo/PATO_
default_prefix: AnS
default_range: string

imports:
  - linkml:types
  - anatomical_structure_core

settings:
  PositiveFloat: ^[+]?\d*\.?\d+$
  ColorHexTriplet: "#[0-9a-fA-F]{6}"

classes:
  ImageDataset:
    is_a: VersionedNamedThing
    description: >-
      An image dataset is versioned release of a multidimensional regular grid of measurements 
      and metadata required for a morphological representation of an entity such as an anatomical 
      structure (ref: OBI_0003327, RRID:SCR_006266)
    attributes:
      x_direction:
        range: ANATOMICAL_DIRECTION
        description: >-
          A controlled vocabulary attribute defining the x axis direction in terms of anatomical 
          direction.
      y_direction:
        range: ANATOMICAL_DIRECTION
        description: >-
          A controlled vocabulary attribute defining the y axis direction in terms of anatomical 
          direction.
      z_direction:
        range: ANATOMICAL_DIRECTION
        description: >-
          A controlled vocabulary attribute defining the z axis direction in terms of anatomical 
          direction.
      x_size:
        range: integer
        description: The number of pixels/voxels (size) along the x axis.
        minimum_value: 1
      y_size:
        range: integer
        description: The number of pixels/voxels (size) along the y axis.
        minimum_value: 1
      z_size:
        range: integer
        description: The number of pixels/voxels (size) along the y axis.
        minimum_value: 1
      x_resolution:
        range: float
        description: >-
          The resolution (length / pixel) in along the x axis (numerical value part).
        structured_pattern:
          syntax: "{PositiveFloat}"
      y_resolution:
        range: float
        description: >-
          The resolution (length / pixel) in along the y axis (numerical value part).
        structured_pattern:
          syntax: "{PositiveFloat}"
      z_resolution:
        range: float
        description: >-
          The resolution (length / pixel) in along the z axis (numerical value part).
        structured_pattern:
          syntax: "{PositiveFloat}"
      unit:
        range: DISTANCE_UNIT
        description: >-
          A controlled vocabulary attribute defining the length unit of the x, y, and z 
          resolution values.
    slot_usage:
      revision_of:
        any_of:
          - range: ImageDataset
          - range: string

  AnatomicalSpace:
    is_a: VersionedNamedThing
    description: >-
      An anatomical space is versioned release of a mathematical space with a defined mapping 
      between the anatomical axes and the mathematical axes. An anatomical space may be defined by 
      a reference image chosen as the biological reference for an anatomical structure of interest 
      derived from a single or multiple specimens (ref: ILX:0777106, RRID:SCR_023499)
    attributes:
      measures:
        any_of:
          - range: ImageDataset
          - range: string
        description: >-
          Reference to the specific image dataset used to define the anatomical space.
        required: true
    slot_usage:
      revision_of:
        any_of:
          - range: AnatomicalSpace
          - range: string

  ParcellationTerminology:
    is_a: VersionedNamedThing
    description: >-
      A parcellation terminology is a versioned release set of terms that can be used to label 
      annotations in an atlas, providing human readability and context and allowing communication 
      about brain locations and structural properties. Typically, a terminology is a set of 
      descriptive anatomical terms following a specific naming convention and/or approach to 
      organization scheme. The terminology may be a flat list of controlled vocabulary, a taxonomy 
      and partonomy, or an ontology (ref: ILX:0777107, RRID:SCR_023499)
    slot_usage:
      revision_of:
        any_of:
          - range: ParcellationTerminology
          - range: string

  ParcellationTermSet:
    is_a: NamedThing
    description: >-
      A parcellation term set is the set of parcellation terms within a specific parcellation terminology. 
      A parcellation term set belongs to one and only one parcellation terminology and each parcellation 
      term in a parcellation terminology belongs to one and only one term set. 
      If the parcellation terminology is a taxonomy, parcellation term sets can be used to represent 
      taxonomic ranks. For consistency, if the terminology does not have the notion of taxonomic ranks, 
      all terms are grouped into a single parcellation term set.
    attributes:
      part_of_parcellation_terminology:
        any_of:
          - range: ParcellationTerminology
          - range: string
        description: >-
          Reference to the parcellation terminology for which the parcellation term set partitions.
        required: true
      ordinal:
        range: integer
        description: >-
          Ordinal of the parcellation term set among other term sets within the context of the 
          associated parcellation terminology.
        minimum_value: 0
      has_parent_parcellation_term_set:
        any_of:
          - range: ParcellationTermSet
          - range: string
        description: >-
          Reference to the parent parcellation term set for which the parcellation term set is a child 
          (lower taxonomic rank) of.

  ParcellationTerm:
    is_a: NamedThing
    description: >-
      A parcellation term is an individual term within a specific parcellation terminology describing a 
      single anatomical entity by a persistent identifier, name, symbol and description.  A parcellation 
      term is a unique and exclusive member of a versioned release parcellation terminology. Although term 
      identifiers must be unique within the context of one versioned release of a parcellation terminology, 
      they can be reused in different parcellation terminology versions enabling the representation of 
      terminology updates and modifications over time.
    attributes:
      symbol:
        description: Symbol representing a parcellation term.
      part_of_parcellation_term_set:
        any_of:
          - range: ParcellationTermSet
          - range: string
        description: >-
          Reference to the parcellation term set for which the parcellation term is part of.
        required: true
      ordinal:
        range: integer
        description: >-
          Ordinal of the parcellation term among other terms within the context of the associated 
          parcellation terminology.
        minimum_value: 0
      has_parent_parcellation_term:
        any_of:
          - range: ParcellationTerm
          - range: string
        description: >-
          Reference to the parent parcellation term for which the parcellation term is a child (
          spatially part) of

  ParcellationColorScheme:
    is_a: VersionedNamedThing
    description: >-
      A parcellation color scheme is a versioned release color palette that can be used to visualize a 
      parcellation terminology or its related parcellation annotation. A parcellation terminology may 
      have zero or more parcellation color schemes and each color scheme is in context of a specific 
      parcellation terminology, where each parcellation term is assigned a hex color value. A parcellation 
      color scheme is defined as a part of one and only one parcellation terminology.
    attributes:
      subject_parcellation_terminology:
        any_of:
          - range: ParcellationTerminology
          - range: string
        description: >-
          Reference to the parcellation terminology for which the parcellation color scheme is in 
          context of.
        required: true
    slot_usage:
      revision_of:
        any_of:
          - range: ParcellationColorScheme
          - range: string

  ParcellationColorAssignment:
    description: >-
      The parcellation color assignment associates hex color value to a parcellation term within a 
      versioned release of a color scheme. A parcellation term is uniquely denoted by a parcellation 
      term identifier and the parcellation terminology it belongs to.
    attributes:
      part_of_parcellation_color_scheme:
        any_of:
          - range: ParcellationColorScheme
          - range: string
        description: >-
          Reference to the parcellation color scheme for which the color assignment is part of.
        required: true
      subject_parcellation_term:
        any_of:
          - range: ParcellationTerm
          - range: string
        description: >-
          Reference to the parcellation term identifier for which the color assignment is about.
        required: true
      color:
        range: string
        description: A string representing to hex triplet code of a color
        structured_pattern:
          syntax: "{ColorHexTriplet}"

  AnatomicalAnnotationSet:
    is_a: VersionedNamedThing
    description: >-
      An anatomical annotation set is a versioned release of a set of anatomical annotations anchored 
      in the same anatomical space that divides the space into distinct segments following some annotation 
      criteria or parcellation scheme. For example, the anatomical annotation set of 3D image based 
      reference atlases (e.g. Allen Mouse CCF) can be expressed as a set of label indices of single 
      multi-valued image annotations or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499)
    attributes:
      parameterizes:
        any_of:
          - range: AnatomicalSpace
          - range: string
        description: >-
          Reference to the anatomical space for which the anatomical annotation set is anchored
        required: true
    slot_usage:
      revision_of:
        any_of:
          - range: AnatomicalAnnotationSet
          - range: string

  ParcellationAnnotation:
    description: >-
      A parcellation annotation defines a specific segment of an anatomical space denoted by an internal 
      identifier and is a unique and exclusive member of a versioned release anatomical annotation set. 
      For example, in the case where the anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF),
      a specific annotation corresponds to a specific label index (internal identifier) in the mask.
    attributes:
      part_of_anatomical_annotation_set:
        any_of:
          - range: AnatomicalAnnotationSet
          - range: string
        description:
        required: true
      internal_identifier:
        description: >-
          An identifier that uniquely denotes a specific parcellation annotation within the context of an anatomical annotation set
        required: true
      voxel_count:
        range: integer
        description: >-
          The number of voxels (3D pixels) spanned by the parcellation annotation (optional).
        minimum_value: 0

  ParcellationAnnotationTermMap:
    description: >-
      The parcellation annotation term map table defines the relationship between parcellation annotations and parcellation terms. 
      A parcellation term is uniquely denoted by a parcellation term identifier and the parcellation terminology it belongs to. 
      A parcellation term can be spatially parameterized by the union of one or more parcellation annotations within a versioned 
      release of an anatomical annotation set. For example, annotations defining individual cortical layers in cortical region 
      R (R1, R2/3, R4, etc) can be combined to define the parent region R.
    attributes:
      subject_parcellation_annotation:
        any_of:
          - range: ParcellationAnnotation
          - range: string
        description: >-
          Reference to the parcellation annotation that is the subject of the association.
        required: true
      subject_parcellation_term:
        any_of:
          - range: ParcellationTerm
          - range: string
        description: >-
          Reference to the parcellation term that is the subject of the association.
        required: true

  ParcellationAtlas:
    is_a: VersionedNamedThing
    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).
    attributes:
      has_anatomical_space:
        any_of:
          - range: AnatomicalSpace
          - range: string
        description: >-
          Reference to the anatomical space component of the parcellation atlas
        required: true
      has_anatomical_annotation_set:
        any_of:
          - range: AnatomicalAnnotationSet
          - range: string
        description: >-
          Reference to the anatomical annotation set component of the parcellation atlas
        required: true
      has_parcellation_terminology:
        any_of:
          - range: ParcellationTerminology
          - range: string
        description: >-
          Reference to the parcellation terminology component of the parcellation atlas
        required: true
      specialization_of:
        any_of:
          - range: ParcellationAtlas
          - range: string
        description: >-
          Reference to the general (non versioned) parcellation atlas for which the parcellation atlas is a specific 
          version release of.
    slot_usage:
      revision_of:
        any_of:
          - range: ParcellationAtlas
          - range: string

enums:
  ANATOMICAL_DIRECTION:
    description: >-
      A controlled vocabulary term defining axis direction in terms of anatomical direction.
    permissible_values:
      left_to_right:
        title: left-to-right
      posterior_to_anterior:
        title: posterior-to-anterior
      inferior_to_superior:
        title: inferior-to-superior
      superior_to_inferior: 
        title: superior-to-inferior
      anterior_to_posterior: 
        title: anterior-to-posterior

  DISTANCE_UNIT:
    permissible_values:
      mm:
        title: millimeter
      um:
        title: micrometer
      m:
        title: meter