SingleCellExpressionCellCluster

A cluster of cells derived algorithmically from single cell expression (e.g. scRNA-seq) data. This typically represents a cluster of individual cells sequenced that have similar expression profiles.

classDiagram SubmittedObject <|-- SingleCellExpressionCellCluster SingleCellExpressionCellCluster : cell_count SingleCellExpressionCellCluster : cell_type SingleCellExpressionCellCluster : created_by SingleCellExpressionCellCluster : curie SingleCellExpressionCellCluster : data_provider SingleCellExpressionCellCluster : data_provider_cross_reference SingleCellExpressionCellCluster : date_created SingleCellExpressionCellCluster : date_updated SingleCellExpressionCellCluster : db_date_created SingleCellExpressionCellCluster : db_date_updated SingleCellExpressionCellCluster : internal SingleCellExpressionCellCluster : mod_internal_id SingleCellExpressionCellCluster : obsolete SingleCellExpressionCellCluster : primary_external_id SingleCellExpressionCellCluster : related_notes SingleCellExpressionCellCluster : symbol SingleCellExpressionCellCluster : title SingleCellExpressionCellCluster : updated_by

URI: alliance:SingleCellExpressionCellCluster

Parent Classes

AuditedObject
- CurieObject
  - SubmittedObject
    - SingleCellExpressionCellCluster

Slots

Name	Description
cell_count	The count of cells that are part of an analysis or cell cluster
cell_type	The type of cell that is represented in a given single-cell expression cluster
created_by	The individual that created the entity.
curie	A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
data_provider	The organization (e.g. MOD) from which the data was sourced
data_provider_cross_reference	CrossReference to the organization from which the data was sourced
date_created	The date on which an entity was created. This can be applied to nodes or edges.
date_updated	Date on which an entity was last modified.
db_date_created	The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated	Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
internal	Classifies the entity as private (for internal use) or not (for public use).
mod_internal_id	The model organism database (MOD) internal identifier for the object
obsolete	Entity is no longer current.
primary_external_id	The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
related_notes	Valid note types are available for viewing in the A-Team curation tool (curation.alliancegenome.org) Controlled Vocabulary Terms Table (in the Note Type vocabulary). The subset of terms applicable for a particular entity type are listed in the Vocabulary Term Sets table (e.g. Allele Note Type). New terms can be added as needed.
symbol	The free text symbol (human-readable) for an entity or record
title	The free text title for an entity or record
updated_by	The individual that last modified the entity.

Mappings

Mapping Type	Mapped Value
self	['alliance:SingleCellExpressionCellCluster']
native	['alliance:SingleCellExpressionCellCluster']

LinkML Specification

Direct

name: SingleCellExpressionCellCluster
description: A cluster of cells derived algorithmically from single cell expression
  (e.g. scRNA-seq) data. This typically represents a cluster of individual cells sequenced
  that have similar expression profiles.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
slots:
- cell_count
- symbol
- title
attributes:
  cell_type:
    name: cell_type
    description: The type of cell that is represented in a given single-cell expression
      cluster
    from_schema: https://github.com/alliance-genome/agr_persistent_schema/src/schema/highThroughputExpression.yaml
    domain_of:
    - SingleCellExpressionCellCluster
    range: AnatomyTerm

Induced

name: SingleCellExpressionCellCluster
description: A cluster of cells derived algorithmically from single cell expression
  (e.g. scRNA-seq) data. This typically represents a cluster of individual cells sequenced
  that have similar expression profiles.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: SubmittedObject
attributes:
  cell_type:
    name: cell_type
    description: The type of cell that is represented in a given single-cell expression
      cluster
    from_schema: https://github.com/alliance-genome/agr_persistent_schema/src/schema/highThroughputExpression.yaml
    alias: cell_type
    owner: SingleCellExpressionCellCluster
    domain_of:
    - SingleCellExpressionCellCluster
    range: AnatomyTerm
  cell_count:
    name: cell_count
    description: The count of cells that are part of an analysis or cell cluster
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cell_count
    owner: SingleCellExpressionCellCluster
    domain_of:
    - SingleCellExpressionAnalysis
    - SingleCellExpressionCellCluster
    range: integer
    multivalued: false
  symbol:
    name: symbol
    description: The free text symbol (human-readable) for an entity or record
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: symbol
    owner: SingleCellExpressionCellCluster
    domain_of:
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - SingleCellExpressionAnalysis
    - SingleCellExpressionCellCluster
    range: string
    multivalued: false
  title:
    name: title
    description: The free text title for an entity or record
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: title
    owner: SingleCellExpressionCellCluster
    domain_of:
    - Reference
    - SingleCellExpressionAnalysis
    - SingleCellExpressionCellCluster
    - Resource
    range: string
    multivalued: false
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-Alliance) database identifier/curie for
      the object. Note that this may be an external (non-Alliance member) identifier
      for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance
      member's primary key for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: SingleCellExpressionCellCluster
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: SingleCellExpressionCellCluster
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider:
    name: data_provider
    description: The organization (e.g. MOD) from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: data_provider
    owner: SingleCellExpressionCellCluster
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
    multivalued: false
  data_provider_cross_reference:
    name: data_provider_cross_reference
    description: CrossReference to the organization from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: data_provider_cross_reference
    owner: SingleCellExpressionCellCluster
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
    multivalued: false
  related_notes:
    name: related_notes
    description: Valid note types are available for viewing in the A-Team curation
      tool (curation.alliancegenome.org) Controlled Vocabulary Terms Table (in the
      Note Type vocabulary).  The subset of terms applicable for a particular entity
      type are listed in the Vocabulary Term Sets table (e.g. Allele Note Type). New
      terms can be added as needed.
    notes:
    - The original name suggested for this slot was simply notes, but I think that
      label is reserved in LinkML for internal descriptions of objects, hence the
      related_notes label used here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_notes
    owner: SingleCellExpressionCellCluster
    domain_of:
    - SubmittedObject
    - Gene
    - GeneChangeEventSlotAnnotation
    - ExpressionExperiment
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - ConstructCassetteAssociation
    - CassetteComponentSlotAnnotation
    - CassetteGenomicEntityAssociation
    - CassetteTransgenicToolAssociation
    - CassetteStrAssociation
    - Annotation
    - HTPExpressionDatasetSampleAnnotation
    range: Note
    multivalued: true
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: curie
    owner: SingleCellExpressionCellCluster
    domain_of:
    - Laboratory
    - CurieObject
    - Identifier
    - GeneNomenclatureSet
    - OntologyTerm
    - Annotation
    - ExternalDataBaseEntityDTO
    range: uriorcurie
    multivalued: false
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    alias: created_by
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    alias: updated_by
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: SingleCellExpressionCellCluster
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean