ccn2.yaml

id: CCN2 # TODO: what should be here
name: CCN2
prefixes:
  linkml: https://w3id.org/linkml/
  ccn2: https://github.com/brain-bican/CCN2
default_prefix: ccn2
imports:
  - linkml:types
default_range: string


slots:
  cell set accession:
    description: >-
      Primary identifier for cell set.
  cell type name:
    description: >-
      The primary name/symbol to be used for the cell type defined by this cell set.
    aliases: [ "primary_cell_type_alias" ] #todo: alliases can be used for ccn1_mapping? doesn't show in json
  parent cell set accession:
    description: >-
      The cell set accession of the parent cell set in the taxonomy. This field should be programmatically assigned, not edited.
  synonyms:
    description: >-  #
      A list of alternative names for this cell type. Separate entries with a '|'. Do not use terms with a scope that is much narrower or broader than the cell type being described.
  synonym provenance:
    description: >-
      Each entry in the synonyms field should have a corresponding entry here, either the DOI of a supporting publication (in the form the form doi:10.1126/journal.abj6641) or the editor's ORCID (in the form: ORCID:01243-234-678). Multiple entries should be separated by a '|'.
  description:
    description: >-
      Optional free text description of the cluster. This could be particularly useful for describing the properties of cells clustered from techniques that provide data on morphology, function and connectivity, e.g. patch-seq & epi-retro-seq.
  classifying ontology term id:
    description: >-
      The ID of an ontology term that classifies the cell type defined by this node.
  classifying ontology term name:
    description: >-
      The name of the ontology term in the classification_id column
  classification provenance:
    description: >-
      Either the DOI(s) of a supporting publication (in the form the form doi:10.1126/journal.abj6641) or the editor's ORCID (in the form: ORCID:01243-234-678). Multiple entries should be separated by a '|'.
  classification comment:
    description: >-
      A free text comment describing the evidence for this classification.
  rank:
    description: >-
      Algorithmically generated hierarchical taxonomies can be complex, with many nodes between root and leaf and branches of variable depth. To simplify this for display and discussion it can be useful to assign nodes to a 3 level hierarchy, with leaf nodes at the bottom.
    range: Rank
  mapped cell set accession:
    description: >-
      The accession (ID) of a cell set in a second taxonomy that this cell set maps to.
  mapped cell type name:
    description: >-
      The name of the cell type corresponding to the mapped_cell_set_accession.
  evidence comment:
    description: >-
      A free text description of the evidence.
  similarity score:
    description: >-
      A score recording the similarity between mapped nodes.
    range: float
    minimum_value: 0
    maximum_value: 1
  provenance:
    description: >-
      ORCID of the person doing the mapping using the syntax ORCID:0123-4567-890. Optionally include supporting publications using DOIs of the form doi:10.1126/journal.abj6641.
  location ontology term id:
    description: >-
      The ID of an ontology term that refers to a brain region that this cell type is located in. Ideally this should be the ID of a term defined as a region in a standard atlas.
  location ontology term name:
    description: >-
      Name of the term whose ID is recorded in the ontology_term_id field.
  supporting data:
    description: >-
      A link to data supporting this location mapping.
  sample:
    description: >-
      Cell sample identifier.
  cell accessions:
    description: >-
      List of cell set accession identifiers.
    multivalued: true
  # range: string
  # inlined_as_list: true

classes:
  taxonomy:
    slots:
      - cell set accession
      - cell type name
      - parent cell set accession
      - synonyms
      - synonym provenance
      - description
      - classifying ontology term id
      - classifying ontology term name
      - classification provenance
      - classification comment
      - rank
    slot_usage:
      cell set accession:
        description: >-
          Primary identifier of the cell set. This field should be programmatically assigned, not edited.
        required: true
        readonly: true #todo
      cell type name:
        description: >-
          The primary name/symbol to be used for the (provisional) cell type defined by this cell set. This is left optional, but is strongly encouraged for every node that is linked.
      parent cell set accession:
        required: true
      classifying ontology term name:
        required: true
      classification provenance:
        required: true


  cross taxonomy mapping:
    slots:
      - cell set accession
      - cell type name
      - mapped cell set accession
      - mapped cell type name
      - evidence comment
      - similarity score
      - provenance
    slot_usage:
      cell set accession:
        required: true
      cell type name:
        required: true
      mapped cell set accession:
        required: true
      mapped cell type name:
        required: true
      evidence comment:
        description: >-
          A free text description of the evidence supporting this mapping. If a similarity_score is include, please also include details of how this was calculated.
        required: true

  location mapping:
    slots:
      - cell set accession
      - cell type name
      - location ontology term id
      - location ontology term name
      - evidence comment
      - supporting data
      - provenance
    slot_usage:
      cell set accession:
        required: true
      cell type name:
        required: true
      location ontology term id:
        required: true
      location ontology term name:
        required: true
      evidence comment:
        description: >-
          A comment describing the evidence for this location mapping
      provenance:
        required: true


  cell set accession to cell mapping:
    slots:
      - sample
      - cell accessions
    slot_usage:
      sample:
        required: true
      cell accessions:
        required: true

enums:
  Rank:
    permissible_values:
      leaf_node:
      family:
      gross: