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Class: CellType

Represents a cell type

URI: cell_type:CellType

erDiagram CellType { uriorcurie id string label string definition } BiologicalProcess { string id string label } Disease { string id string label } Gene { string id string label } AnatomicalStructure { string id string label } CellOntologyTerm { string id string label } CellType ||--|o CellOntologyTerm : "equivalent_to" CellType ||--}o CellOntologyTerm : "parents" CellType ||--}o CellOntologyTerm : "subtypes" CellType ||--}o AnatomicalStructure : "localizations" CellType ||--}o Gene : "genes" CellType ||--}o Disease : "diseases" CellType ||--}o BiologicalProcess : "roles"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
id 1..1
Uriorcurie		 direct
label 0..1
String		 the concise name of the cell type direct
equivalent_to 0..1
CellOntologyTerm		 the the cell type described direct
definition 0..1
String		 direct
parents 0..*
CellOntologyTerm		 categorization direct
subtypes 0..*
CellOntologyTerm		 direct
localizations 0..*
AnatomicalStructure		 direct
genes 0..*
Gene		 direct
diseases 0..*
Disease		 direct
roles 0..*
BiologicalProcess		 direct

Identifier and Mapping Information

Schema Source

  • from schema: http://w3id.org/ontogpt/cell_type

Mappings

Mapping Type Mapped Value
self cell_type:CellType
native cell_type:CellType

LinkML Source

Direct

name: CellType
description: Represents a cell type
from_schema: http://w3id.org/ontogpt/cell_type
attributes:
  id:
    name: id
    annotations:
      prompt.skip:
        tag: prompt.skip
        value: true
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: rdf:Resource
    identifier: true
    range: uriorcurie
    required: true
  label:
    name: label
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    description: the concise name of the cell type
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: rdfs:label
    range: string
  equivalent_to:
    name: equivalent_to
    annotations:
      prompt:
        tag: prompt
        value: the cell type described in the text
      owl:
        tag: owl
        value: AnnotationAssertion
    description: the the cell type described
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: skos:exactMatch
    range: CellOntologyTerm
  definition:
    name: definition
    annotations:
      prompt:
        tag: prompt
        value: A concise textual definition in genus-differentia form, i.e  'A <genus>
          that <differentiating characteristics>'
      owl:
        tag: owl
        value: AnnotationProperty, AnnotationAssertion
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: IAO:0000115
  parents:
    name: parents
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of parent (broader) cell types
      owl:
        tag: owl
        value: SubClassOf
    description: categorization
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    range: CellOntologyTerm
  subtypes:
    name: subtypes
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of the subtypes (subclasses) of this cell
          type. Use concise terms, and separate elements in a list using semicolon
          (;)
      owl.template:
        tag: owl.template
        value: '{% for subtype in subtypes %}

          SubClassOf( {{ tr(subtype) }} {{ id }} )

          {% endfor %}

          '
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    range: CellOntologyTerm
  localizations:
    name: localizations
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of anatomical structures in which this cell
          type is localized
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: BFO:0000050
    multivalued: true
    range: AnatomicalStructure
  genes:
    name: genes
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of genes expressed in cells of this type
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: RO:0002292
    multivalued: true
    range: Gene
  diseases:
    name: diseases
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of diseases in which this cell type is implicated
      owl.template:
        tag: owl.template
        value: '{% for disease in diseases %}

          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}
          ))

          {% endfor %}

          '
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    range: Disease
  roles:
    name: roles
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of roles (e.g. biological processes) that
          this cell type plays. These should be short descriptive terms corresponding
          to ontology terms in the GO biological process hierarchy.
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: RO:0002215
    multivalued: true
    range: BiologicalProcess
tree_root: true

Induced

name: CellType
description: Represents a cell type
from_schema: http://w3id.org/ontogpt/cell_type
attributes:
  id:
    name: id
    annotations:
      prompt.skip:
        tag: prompt.skip
        value: true
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: rdf:Resource
    identifier: true
    alias: id
    owner: CellType
    domain_of:
    - CellType
    - NamedEntity
    - Publication
    range: uriorcurie
    required: true
  label:
    name: label
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    description: the concise name of the cell type
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: rdfs:label
    alias: label
    owner: CellType
    domain_of:
    - CellType
    - NamedEntity
    range: string
  equivalent_to:
    name: equivalent_to
    annotations:
      prompt:
        tag: prompt
        value: the cell type described in the text
      owl:
        tag: owl
        value: AnnotationAssertion
    description: the the cell type described
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: skos:exactMatch
    alias: equivalent_to
    owner: CellType
    domain_of:
    - CellType
    range: CellOntologyTerm
  definition:
    name: definition
    annotations:
      prompt:
        tag: prompt
        value: A concise textual definition in genus-differentia form, i.e  'A <genus>
          that <differentiating characteristics>'
      owl:
        tag: owl
        value: AnnotationProperty, AnnotationAssertion
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: IAO:0000115
    alias: definition
    owner: CellType
    domain_of:
    - CellType
    range: string
  parents:
    name: parents
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of parent (broader) cell types
      owl:
        tag: owl
        value: SubClassOf
    description: categorization
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    alias: parents
    owner: CellType
    domain_of:
    - CellType
    range: CellOntologyTerm
  subtypes:
    name: subtypes
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of the subtypes (subclasses) of this cell
          type. Use concise terms, and separate elements in a list using semicolon
          (;)
      owl.template:
        tag: owl.template
        value: '{% for subtype in subtypes %}

          SubClassOf( {{ tr(subtype) }} {{ id }} )

          {% endfor %}

          '
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    alias: subtypes
    owner: CellType
    domain_of:
    - CellType
    range: CellOntologyTerm
  localizations:
    name: localizations
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of anatomical structures in which this cell
          type is localized
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: BFO:0000050
    multivalued: true
    alias: localizations
    owner: CellType
    domain_of:
    - CellType
    range: AnatomicalStructure
  genes:
    name: genes
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of genes expressed in cells of this type
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: RO:0002292
    multivalued: true
    alias: genes
    owner: CellType
    domain_of:
    - CellType
    range: Gene
  diseases:
    name: diseases
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of diseases in which this cell type is implicated
      owl.template:
        tag: owl.template
        value: '{% for disease in diseases %}

          SubClassOf( {{ tr(disease) }} ObjectSomeValuesFrom( RO:0004026 {{ id }}
          ))

          {% endfor %}

          '
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    alias: diseases
    owner: CellType
    domain_of:
    - CellType
    range: Disease
  roles:
    name: roles
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of roles (e.g. biological processes) that
          this cell type plays. These should be short descriptive terms corresponding
          to ontology terms in the GO biological process hierarchy.
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    slot_uri: RO:0002215
    multivalued: true
    alias: roles
    owner: CellType
    domain_of:
    - CellType
    range: BiologicalProcess
tree_root: true