Class: CapTaxonomy

name: Cap_Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Taxonomy
slots:
- cap_publication_title
- cap_publication_description
- cap_publication_url
- cap_dataset_url
- publication_timestamp
- publication_version
slot_usage:
  annotations:
    name: annotations
    range: Cap_Annotation
  cellannotation_schema_version:
    name: cellannotation_schema_version
    required: true
  cellannotation_timestamp:
    name: cellannotation_timestamp
    required: true
  cellannotation_version:
    name: cellannotation_version
    required: true
  cellannotation_url:
    name: cellannotation_url
    required: true
class_uri: CAS:Taxonomy
tree_root: true

name: Cap_Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
is_a: Taxonomy
slot_usage:
  annotations:
    name: annotations
    range: Cap_Annotation
  cellannotation_schema_version:
    name: cellannotation_schema_version
    required: true
  cellannotation_timestamp:
    name: cellannotation_timestamp
    required: true
  cellannotation_version:
    name: cellannotation_version
    required: true
  cellannotation_url:
    name: cellannotation_url
    required: true
attributes:
  cap_publication_title:
    name: cap_publication_title
    description: 'The title of the publication on CAP (i.e. a published collection
      of datasets, the \"CAP Workspace\".). The title of the publication on CAP. (NOTE:
      the term \"publication\" refers to the workspace published on CAP with a version
      and timestamp.) This MUST be less than or equal to N characters, and this MUST
      be encoded as a single string.'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cap_publication_title
    owner: Cap_Taxonomy
    domain_of:
    - Cap_Taxonomy
    range: string
  cap_publication_description:
    name: cap_publication_description
    description: 'The description of the publication on CAP. The description of the
      publication on CAP. (NOTE: the term \"publication\" refers to the workspace
      published on CAP with a version and timestamp.) This MUST be less than or equal
      to N characters, and this MUST be encoded as a single string.'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cap_publication_description
    owner: Cap_Taxonomy
    domain_of:
    - Cap_Taxonomy
    range: string
  cap_publication_url:
    name: cap_publication_url
    description: 'A persistent URL of the publication on CAP. (NOTE: the term \"publication\"
      refers to the workspace published on CAP with a version and timestamp.)'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cap_publication_url
    owner: Cap_Taxonomy
    domain_of:
    - Cap_Taxonomy
    range: string
  cap_dataset_url:
    name: cap_dataset_url
    description: A persistent URL of the dataset on CAP.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cap_dataset_url
    owner: Cap_Taxonomy
    domain_of:
    - Cap_Taxonomy
    range: string
  publication_timestamp:
    name: publication_timestamp
    description: The timestamp of the CAP publication. This MUST be a string in the
      format %yyyy-%MM-%dd'T'%hh:%mm:%ss. This value will be overwritten by the newest
      timestamp upon a new publication.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: publication_timestamp
    owner: Cap_Taxonomy
    domain_of:
    - Cap_Taxonomy
    range: string
  publication_version:
    name: publication_version
    description: The (latest) version of the CAP publication. This value will be overwritten
      by the newest version upon a new publication (and automatically incremented).
      This versioning MUST follow the format 'v' + '[integer]', whereby newer versions
      must be naturally incremented.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: publication_version
    owner: Cap_Taxonomy
    domain_of:
    - Cap_Taxonomy
    range: string
  matrix_file_id:
    name: matrix_file_id
    description: A resolvable ID for a cell by gene matrix file in the form namespace:accession,
      e.g. CellXGene_dataset:8e10f1c4-8e98-41e5-b65f-8cd89a887122.  Please see https://github.com/cellannotation/cell-annotation-schema/registry/registry.json
      for supported namespaces.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: matrix_file_id
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: uriorcurie
  title:
    name: title
    description: The title of the dataset. This MUST be less than or equal to 200
      characters. e.g. 'Human retina cell atlas - retinal ganglion cells'.
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: title
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
    required: true
  description:
    name: description
    description: The description of the dataset. e.g. 'A total of 15 retinal ganglion
      cell clusters were identified from over 99K retinal ganglion cell nuclei in
      the current atlas. Utilizing previous characterized markers from macaque, 5
      clusters can be annotated.'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    slot_uri: IAO:0000115
    alias: description
    owner: Cap_Taxonomy
    domain_of:
    - Labelset
    - Taxonomy
    range: string
  cellannotation_schema_version:
    name: cellannotation_schema_version
    description: 'The schema version, the cell annotation open standard. Current version
      MUST follow 0.1.0

      This versioning MUST follow the format `''[MAJOR].[MINOR].[PATCH]''` as defined
      by Semantic Versioning 2.0.0, https://semver.org/'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cellannotation_schema_version
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
    required: true
  cellannotation_timestamp:
    name: cellannotation_timestamp
    description: The timestamp of all cell annotations published (per dataset). This
      MUST be a string in the format `'%yyyy-%mm-%dd %hh:%mm:%ss'`
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cellannotation_timestamp
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
    required: true
  cellannotation_version:
    name: cellannotation_version
    description: The version for all cell annotations published (per dataset). This
      MUST be a string. The recommended versioning format is `'[MAJOR].[MINOR].[PATCH]'`
      as defined by Semantic Versioning 2.0.0, https://semver.org/
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cellannotation_version
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
    required: true
  cellannotation_url:
    name: cellannotation_url
    description: A persistent URL of all cell annotations published (per dataset).
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: cellannotation_url
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
    required: true
  author_list:
    name: author_list
    description: This field stores a list of users who are included in the project
      as collaborators, regardless of their specific role. An example list; '['John
      Smith', 'Cody Miller', 'Sarah Jones']'
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: author_list
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
  author_name:
    name: author_name
    description: Primary author's name. This MUST be a string in the format `[FIRST
      NAME] [LAST NAME]`
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: author_name
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
    required: true
  author_contact:
    name: author_contact
    description: Primary author's contact. This MUST be a valid email address of the
      author
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: author_contact
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
  orcid:
    name: orcid
    description: Primary author's orcid. This MUST be a valid ORCID for the author
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: orcid
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: string
  labelsets:
    name: labelsets
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: labelsets
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: Labelset
    required: true
    multivalued: true
    inlined_as_list: true
  annotations:
    name: annotations
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: annotations
    owner: Cap_Taxonomy
    domain_of:
    - Taxonomy
    range: Cap_Annotation
    required: true
    multivalued: true
    inlined_as_list: true
class_uri: CAS:Taxonomy
tree_root: true