figure1.yaml

id: https://www.biorxiv.org/content/10.1101/2023.01.22.525049v1
name: figure1
prefixes:
  linkml: https://w3id.org/linkml/
imports:
  - linkml:types
default_range: string

classes:
  NamedThing:
    slots:
      - id
      - label

  CellClass:
    is_a: NamedThing
    description: >-
      Class division in Figure 1, also found in Supplementary Materials: Table 7
    attributes:
      category:
        required: true
        range: CellCategory
      has_hierarchical_relationships:
        multivalued: true
        range: HierarchicalRelationship
        inlined_as_list: true

  CellSubclass:
    is_a: NamedThing
    description: >-
      Subclass division in Figure 1
    attributes:
      has_hierarchical_relationships:
        multivalued: true
        range: HierarchicalRelationship
        inlined_as_list: true
      division:
        range: Division
      nt_type:
        range: NTType

  Cluster:
    is_a: NamedThing
    description: >-
      Cluster in Supplementary Materials: Table 7
    attributes:
      has_hierarchical_relationships:
        multivalued: true
        range: HierarchicalRelationship
        inlined_as_list: true
      has_group_relationships:
        multivalued: true
        range: GroupRelationship
        inlined_as_list: true

  Cell:
    is_a: NamedThing
    description: >-
      Cell, a member of a cluster
    attributes:
      has_group_relationships:
        multivalued: true
        range: GroupRelationship
        inlined_as_list: true
      broad_region:
        range: BroadRegion

#    Supertype:
#      description: >- # TODO: under Cluster class?
#        Supertype in Supplementary Materials: Table 7
#      attributes:
#        id:
#          identifier: true  # unique key
#        label:
#          required: true
#
#  Division:
#    is_a: NamedThing
#    description: >-
#      Division in Figure 1, also found in Supplementary Materials: Table 7
#
#    NTType:
#      description: >-
#        Neurotransmitter Type in Figure 1
#      attributes:
#        label:
#          required: true
#        combo_label:
#          required: true
#
#    BroadRegion:
#      description: >-
#        Broad Region in Figure 1
#      attributes:
#        label:
#          required: true
#
#    Region:
#      description: >-
#        Region in Figure 1
#      attributes:
#        label:
#          required: true

  Relationship:
    abstract: true
    attributes:
      related_to:
        range: NamedThing
        required: true
#      relationship_type:

  HierarchicalRelationship:
    is_a: Relationship
    attributes:
      relationship_type:
        range: HierarchicalRelationshipType

  GroupRelationship:
    is_a: Relationship
    attributes:
      relationship_type:
        range: GroupRelationshipType

  Container:
    tree_root: true
    attributes:
      subclasses:
        multivalued: true
        inlined_as_list: true
        range: CellSubclass
      classes:
        multivalued: true
        inlined_as_list: true
        range: CellClass
      cells:
        multivalued: true
        inlined_as_list: true
        range: Cell
      clusters:
        multivalued: true
        inlined_as_list: true
        range: Cluster

slots:
  id:
    identifier: true
  label:

enums:
  CellCategory:
    permissible_values: # table 4
      NEURON:
      OTHER_IMN:
      OTHER_VASCULAR:
      NEUROGLIAL:

  BroadRegion:
    permissible_values:
      PALL:
      CNU:
      TH:
      HY:
      MB:
      HB:
      CB:

  Division:
    permissible_values:
      Pallium glutamatergic:
      Subpallium GABAergic:
      PAL−sAMY−TH−HY −MB−HB neuronal:
      CBX−MOB−other neuronal:
      Neuroglial:
      Vascular:
      Immune:

  NTType:
    permissible_values:
      Glut:
      GABA:
      Glut−GABA:
      GABA−Glyc:
      Chol:
      Dopa:
      Sero:
      Nora:
      Hist:
      NA:

  HierarchicalRelationshipType:
    permissible_values:
      PARENT_OF:
      CHILD_OF:

  GroupRelationshipType:
    permissible_values:
      CONSISTS_OF:
      MEMBER_OF: