added original ansrs schemas. copied exactly from lydia's original an…

…srs repo

linkml-schema/ansrs.yaml

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+id: https://w3id.org/my-org/ansrs-schema
+name: ansrs-schema
+title: ANSRS schema
+description: |-
+  Schema for ANSRS
+license: MIT
+see_also:
+  - https://my-org.github.io/ansrs-schema
+
+prefixes:
+  ANSRS: https://w3id.org/my-org/ansrs-schema/
+  linkml: https://w3id.org/linkml/
+  biolink: https://w3id.org/biolink/
+  schema: http://schema.org/
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  example: https://example.org/
+default_prefix: ANSRS
+default_range: string
+
+imports:
+  - linkml:types
+  - ansrs_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:
+        range: ImageDataset
+
+  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:
+        range: ImageDataset
+        description: >-
+          Reference to the specific image dataset used to define the anatomical space.
+        required: true
+    slot_usage:
+      revision_of:
+        range: AnatomicalSpace
+
+  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:
+        range: ParcellationTerminology
+
+  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:
+        range: ParcellationTerminology
+        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:
+        range: ParcellationTermSet
+        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:
+        range: ParcellationTermSet
+        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:
+        range: ParcellationTerm
+        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:
+        range: ParcellationTerminology
+        description: >-
+          Reference to the parcellation terminology for which the parcellation color scheme is in 
+          context of.
+        required: true
+    slot_usage:
+      revision_of:
+        range: ParcellationColorScheme
+
+  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:
+        range: ParcellationColorScheme
+        description: >-
+          Reference to the parcellation color scheme for which the color assignment is part of.
+        required: true
+      subject_parcellation_term:
+        range: ParcellationTerm
+        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:
+        range: AnatomicalSpace
+        description: >-
+          Reference to the anatomical space for which the anatomical annotation set is anchored
+        required: true
+    slot_usage:
+      revision_of:
+        range: AnatomicalAnnotationSet
+
+  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:
+        range: AnatomicalAnnotationSet
+        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:
+        range: ParcellationAnnotation
+        description: >-
+          Reference to the parcellation annotation that is the subject of the association.
+        required: true
+      subject_parcellation_term:
+        range: ParcellationTerm
+        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:
+        range: AnatomicalSpace
+        description: >-
+          Reference to the anatomical space component of the parcellation atlas
+        required: true
+      has_anatomical_annotation_set:
+        range: AnatomicalAnnotationSet
+        description: >-
+          Reference to the anatomical annotation set component of the parcellation atlas
+        required: true
+      has_parcellation_terminology:
+        range: ParcellationTerminology
+        description: >-
+          Reference to the parcellation terminology component of the parcellation atlas
+        required: true
+      specialization_of:
+        range: ParcellationAtlas
+        description: >-
+          Reference to the general (non versioned) parcellation atlas for which the parcellation atlas is a specific 
+          version release of.
+    slot_usage:
+      revision_of:
+        range: ParcellationAtlas
+
+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
+
+  DISTANCE_UNIT:
+    permissible_values:
+      mm:
+        title: millimeter
+      um:
+        title: micrometer
+      m:
+        title: meter

linkml-schema/ansrs_core.yaml

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+id: https://w3id.org/my-org/ansrs_core
+name: ANSRS-Core
+title: ANSRS schema Core Types
+description: |-
+  Core types for ANSRS schema
+
+prefixes:
+  ansrs_schema: https://w3id.org/my-org/ansrs-schema/
+  linkml: https://w3id.org/linkml/
+  biolink: https://w3id.org/biolink/
+  schema: http://schema.org/
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  example: https://example.org/
+default_prefix: ansrs
+default_range: string
+
+classes:
+    NamedThing:
+        description: >-
+            Core base entity for ANSRS schema representing an entity with an identifier 
+            name and description.
+        abstract: true
+        slots:
+            - id
+            - name
+            - description
+
+    VersionedNamedThing:
+        is_a: NamedThing
+        description: >-
+            Core base entity for ANSRS schema representing an versioned named thing.
+        abstract: true
+        slots:
+            - version
+            - revision_of
+slots:
+    id:
+        range: uriorcurie
+        identifier: true
+        required: true
+    name:
+        required: true
+    description:
+        required: true
+    version:
+        required: true
+    revision_of:
+        range: VersionedNamedThing