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Class: Taxonomy

URI: cell_annotation_schema:Taxonomy

classDiagram class Taxonomy click Taxonomy href "../Taxonomy" Taxonomy <|-- BicanTaxonomy click BicanTaxonomy href "../BicanTaxonomy" Taxonomy : annotations Taxonomy --> "1..*" Annotation : annotations click Annotation href "../Annotation" Taxonomy : author_contact Taxonomy : author_list Taxonomy : author_name Taxonomy : cellannotation_schema_version Taxonomy : cellannotation_timestamp Taxonomy : cellannotation_url Taxonomy : cellannotation_version Taxonomy : description Taxonomy : labelsets Taxonomy --> "1..*" Labelset : labelsets click Labelset href "../Labelset" Taxonomy : matrix_file_id Taxonomy : orcid Taxonomy : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
matrix_file_id 0..1
Uriorcurie		 A resolvable ID for a cell by gene matrix file in the form namespace:accessio... direct
title 1
String		 The title of the dataset direct
description 0..1
String		 The description of the dataset direct
cellannotation_schema_version 0..1
String		 The schema version, the cell annotation open standard direct
cellannotation_timestamp 0..1
String		 The timestamp of all cell annotations published (per dataset) direct
cellannotation_version 0..1
String		 The version for all cell annotations published (per dataset) direct
cellannotation_url 0..1
String		 A persistent URL of all cell annotations published (per dataset) direct
author_list 0..1
String		 This field stores a list of users who are included in the project as collabor... direct
author_name 1
String		 Primary author's name direct
author_contact 0..1
String		 Primary author's contact direct
orcid 0..1
String		 Primary author's orcid direct
labelsets 1..*
Labelset		 direct
annotations 1..*
Annotation		 direct

Identifier and Mapping Information

Schema Source

  • from schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS

Mappings

Mapping Type Mapped Value
self cell_annotation_schema:Taxonomy
native cell_annotation_schema:Taxonomy

LinkML Source

Direct

name: Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
slots:
- matrix_file_id
- title
- description
- cellannotation_schema_version
- cellannotation_timestamp
- cellannotation_version
- cellannotation_url
- author_list
- author_name
- author_contact
- orcid
- labelsets
- annotations

Induced

name: Taxonomy
from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
attributes:
  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: 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: 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: 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: Taxonomy
    domain_of:
    - Taxonomy
    range: string
  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: Taxonomy
    domain_of:
    - Taxonomy
    range: string
  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: Taxonomy
    domain_of:
    - Taxonomy
    range: string
  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: Taxonomy
    domain_of:
    - Taxonomy
    range: string
  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: 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: 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: 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: Taxonomy
    domain_of:
    - Taxonomy
    range: string
  labelsets:
    name: labelsets
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: labelsets
    owner: Taxonomy
    domain_of:
    - Taxonomy
    range: Labelset
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  annotations:
    name: annotations
    from_schema: https://cellular-semantics.sanger.ac.uk/ontology/CAS
    rank: 1000
    alias: annotations
    owner: Taxonomy
    domain_of:
    - Taxonomy
    range: Annotation
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true