Class: Annotation

name: Annotation
description: 'A collection of fields recording a cell type/class/state annotation
  on some set of cells, supporting evidence and provenance. As this is intended as
  a general schema, compulsory fields are kept to a minimum. However, tools using
  this schema are encouarged to specify a larger set of compulsory fields for publication.    Note:
  This schema deliberately allows for additional fields in order to support ad hoc
  user fields, new formal schema extensions and project/tool specific metadata.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
slots:
- labelset
- cell_label
- cell_fullname
- cell_ontology_term_id
- cell_ontology_term
- cell_ids
- rationale
- rationale_dois
- marker_gene_evidence
- synonyms
- reviews
- author_annotation_fields
class_uri: PCL:0010001

name: Annotation
description: 'A collection of fields recording a cell type/class/state annotation
  on some set of cells, supporting evidence and provenance. As this is intended as
  a general schema, compulsory fields are kept to a minimum. However, tools using
  this schema are encouarged to specify a larger set of compulsory fields for publication.    Note:
  This schema deliberately allows for additional fields in order to support ad hoc
  user fields, new formal schema extensions and project/tool specific metadata.'
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
attributes:
  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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: Annotation
    domain_of:
    - Annotation
    range: Any
class_uri: PCL:0010001