Class: ImmuneCell

URI: cell_type:ImmuneCell

erDiagram ImmuneCell { 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 } ProteinOrComplex { string id string label } ImmuneCell ||--}o ProteinOrComplex : "has_surface_markers" ImmuneCell ||--|o CellOntologyTerm : "equivalent_to" ImmuneCell ||--}o CellOntologyTerm : "parents" ImmuneCell ||--}o CellOntologyTerm : "subtypes" ImmuneCell ||--}o AnatomicalStructure : "localizations" ImmuneCell ||--}o Gene : "genes" ImmuneCell ||--}o Disease : "diseases" ImmuneCell ||--}o BiologicalProcess : "roles"

Inheritance

CellType
- ImmuneCell

Slots

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

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ImmuneCell
from_schema: http://w3id.org/ontogpt/cell_type
is_a: CellType
attributes:
  has_surface_markers:
    name: has_surface_markers
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of proteins or complexes expressed on the
          surface of the cell
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    domain_of:
    - ImmuneCell
    range: ProteinOrComplex

Induced

name: ImmuneCell
from_schema: http://w3id.org/ontogpt/cell_type
is_a: CellType
attributes:
  has_surface_markers:
    name: has_surface_markers
    annotations:
      prompt:
        tag: prompt
        value: semicolon-separated list of proteins or complexes expressed on the
          surface of the cell
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    from_schema: http://w3id.org/ontogpt/cell_type
    rank: 1000
    multivalued: true
    alias: has_surface_markers
    owner: ImmuneCell
    domain_of:
    - ImmuneCell
    range: ProteinOrComplex
  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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    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: ImmuneCell
    domain_of:
    - CellType
    range: BiologicalProcess