Class: CapAnnotation

name: Cap_Annotation
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Annotation
slots:
- canonical_marker_genes
- cell_ontology_exists
- category_fullname
- category_cell_ontology_exists
- category_cell_ontology_term_id
- category_cell_ontology_term
- cell_ontology_assessment
class_uri: PCL:0010001

name: Cap_Annotation
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Annotation
attributes:
  canonical_marker_genes:
    name: canonical_marker_genes
    description: A list of gene names considered to be canonical markers for the biological
      entity used in the cell annotation.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: canonical_marker_genes
    owner: Cap_Annotation
    domain_of:
    - Cap_Annotation
    range: string
    multivalued: true
  cell_ontology_exists:
    name: cell_ontology_exists
    description: Decision by user whether this biological entity exists in the current
      Cell Ontology or not (at the given time of publication).
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cell_ontology_exists
    owner: Cap_Annotation
    domain_of:
    - Cap_Annotation
    range: boolean
  category_fullname:
    name: category_fullname
    description: Any term denoting a biological entity which the author associates
      as the nearest \"class\" or \"broader term\" (or \"parent term\") for the value/term
      in the field.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: category_fullname
    owner: Cap_Annotation
    domain_of:
    - Cap_Annotation
    range: string
  category_cell_ontology_exists:
    name: category_cell_ontology_exists
    description: Decision by user whether this biological entity exists in the current
      Cell Ontology or not (at the given time of publication).
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: category_cell_ontology_exists
    owner: Cap_Annotation
    domain_of:
    - Cap_Annotation
    range: boolean
  category_cell_ontology_term_id:
    name: category_cell_ontology_term_id
    description: The ID from either the Cell Ontology or from some ontology that extends
      it by classifying cell types under terms from the Cell Ontology.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: category_cell_ontology_term_id
    owner: Cap_Annotation
    domain_of:
    - Cap_Annotation
    range: string
  category_cell_ontology_term:
    name: category_cell_ontology_term
    description: The human-readable name assigned to the value of 'category_cell_ontology_term_id'.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: category_cell_ontology_term
    owner: Cap_Annotation
    domain_of:
    - Cap_Annotation
    range: string
  cell_ontology_assessment:
    name: cell_ontology_assessment
    description: Free-text field for researchers to express disagreements with any
      aspect of the Cell Ontology for this cell annotation.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cell_ontology_assessment
    owner: Cap_Annotation
    domain_of:
    - Cap_Annotation
    range: string
  labelset:
    name: labelset
    description: "The unique name of the set of cell annotations. \nEach cell within\
      \ the AnnData/Seurat file MUST be associated with a 'cell_label' value in order\
      \ for this to be a valid 'cellannotation_setname'."
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    slot_uri: CAS:has_labelset
    alias: labelset
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
    required: true
  cell_label:
    name: cell_label
    description: "This denotes any free-text term which the author uses to annotate\
      \ cells, i.e. the preferred cell label name used by the author. Abbreviations\
      \ are exceptable in this field; refer to 'cell_fullname' for related details.\
      \ \nCertain key words have been reserved:\n- `'doublets'` is reserved for encoding\
      \ cells defined as doublets based on some computational analysis\n- `'junk'`\
      \ is reserved for encoding cells that failed sequencing for some reason, e.g.\
      \ few genes detected, high fraction of mitochondrial reads\n- `'unknown'` is\
      \ explicitly reserved for unknown or 'author does not know'\n- `'NA'` is incomplete,\
      \ i.e. no cell annotation was provided"
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    slot_uri: rdfs:label
    alias: cell_label
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
    required: true
  cell_fullname:
    name: cell_fullname
    description: "This MUST be the full-length name for the biological entity listed\
      \ in `cell_label` by the author. (If the value in `cell_label` is the full-length\
      \ term, this field will contain the same value.) \nNOTE: any reserved word used\
      \ in the field 'cell_label' MUST match the value of this field. \n\nEXAMPLE\
      \ 1: Given the matching terms 'LC' and 'luminal cell' used to annotate the same\
      \ cell(s), then users could use either terms as values in the field 'cell_label'.\
      \ However, the abbreviation 'LC' CANNOT be provided in the field 'cell_fullname'.\
      \ \n\nEXAMPLE 2: Either the abbreviation 'AC' or the full-length term intended\
      \ by the author 'GABAergic amacrine cell' MAY be placed in the field 'cell_label',\
      \ but as full-length term naming this biological entity, 'GABAergic amacrine\
      \ cell' MUST be placed in the field 'cell_fullname'."
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    slot_uri: skos:preflabel
    alias: cell_fullname
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
  cell_ontology_term_id:
    name: cell_ontology_term_id
    description: 'This MUST be a term from either the Cell Ontology (https://www.ebi.ac.uk/ols/ontologies/cl)
      or from some ontology that extends it by classifying cell types under terms
      from the Cell Ontology

      e.g. the Provisional Cell Ontology (https://www.ebi.ac.uk/ols/ontologies/pcl)
      or the Drosophila Anatomy Ontology (DAO) (https://www.ebi.ac.uk/ols4/ontologies/fbbt).


      NOTE: The closest available ontology term matching the value within the field
      ''cell_label'' (at the time of publication) MUST be used.

      For example, if the value of ''cell_label'' is ''relay interneuron'', but this
      entity does not yet exist in the ontology, users must choose the closest available
      term in the CL ontology. In this case, it''s the broader term ''interneuron''
      i.e.  https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:0000099.'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    slot_uri: RO:0002473
    alias: cell_ontology_term_id
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: CellTypeEnum
  cell_ontology_term:
    name: cell_ontology_term
    description: This MUST be the human-readable name assigned to the value of 'cell_ontology_term_id'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cell_ontology_term
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
  cell_ids:
    name: cell_ids
    description: Cell barcode sequences/UUIDs used to uniquely identify the cells
      within the AnnData/Seurat matrix. Any and all cell barcode sequences/UUIDs MUST
      be included in the AnnData/Seurat matrix.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    slot_uri: CAS:has_cellid
    alias: cell_ids
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
    multivalued: true
  rationale:
    name: rationale
    description: "The free-text rationale which users provide as justification/evidence\
      \ for their cell annotations. \nResearchers are encouraged to use this field\
      \ to cite relevant publications in-line using standard academic citations of\
      \ the form `(Zheng et al., 2020)` This human-readable free-text MUST be encoded\
      \ as a single string.\nAll references cited SHOULD be listed using DOIs under\
      \ rationale_dois. There MUST be a 2000-character limit."
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: rationale
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
  rationale_dois:
    name: rationale_dois
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: rationale_dois
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
    multivalued: true
  marker_gene_evidence:
    name: marker_gene_evidence
    description: Gene names explicitly used as evidence, which MUST be in the matrix
      of the AnnData/Seurat file
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: marker_gene_evidence
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
    multivalued: true
  synonyms:
    name: synonyms
    description: List of synonyms
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: synonyms
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: string
    multivalued: true
  reviews:
    name: reviews
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: reviews
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: Review
    multivalued: true
  author_annotation_fields:
    name: author_annotation_fields
    description: A dictionary of author defined key value pairs annotating the cell
      set. The names and aims of these fields MUST not clash with official annotation
      fields.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: author_annotation_fields
    owner: Cap_Annotation
    domain_of:
    - Annotation
    range: Any
class_uri: PCL:0010001