Cassette

None

classDiagram Reagent <|-- Cassette Cassette : cassette_components Cassette : cassette_full_name Cassette : cassette_genomic_entity_associations Cassette : cassette_symbol Cassette : cassette_synonyms Cassette : cassette_transgenic_tool_associations Cassette : created_by Cassette : curie Cassette : data_provider Cassette : data_provider_cross_reference Cassette : date_created Cassette : date_updated Cassette : db_date_created Cassette : db_date_updated Cassette : internal Cassette : mod_internal_id Cassette : obsolete Cassette : placeholder Cassette : primary_external_id Cassette : references Cassette : related_notes Cassette : secondary_identifiers Cassette : unique_id Cassette : updated_by

URI: alliance:Cassette

Parent Classes

AuditedObject
- CurieObject
  - SubmittedObject
    - Reagent
      - Cassette

Slots

Name	Description
cassette_components	None
cassette_full_name	Holds between a Cassette and a full name.
cassette_genomic_entity_associations	None
cassette_symbol	Holds between a Cassette and the one current accepted symbol
cassette_synonyms	Holds between a Cassette and a list of synonyms.
cassette_transgenic_tool_associations	None
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obsolete	Entity is no longer current.
placeholder	A boolean property to indicate whether a data record/object/entity is intended to be a placeholder data object rather than a publicly displayed object with a proper ID, name and/or symbol, for example. For example, the Cassette class has been introduced to support FlyBase Cassette objects with IDs and names, but not every Alliance member has data tables/classes for these objects and any IDs or names/symbols would likely be derived and not helpful to end users. Data records/entities where the placeholder value is set to true would have various visible properties suppressed, so as not to confuse end users with private, internal or otherwise contrived representations.
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.
references	holds between an object and a list of references
related_notes	Holds between an object and a list of related Note objects.
secondary_identifiers	None
unique_id	A non-curie unique identifier for a thing.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: Cassette
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: Reagent
slots:
- cassette_symbol
- cassette_full_name
- cassette_synonyms
- cassette_genomic_entity_associations
- cassette_transgenic_tool_associations
- cassette_components
- references
rules:
- postconditions:
    description: At least one of cassette_genomic_entity_associations or cassette_components
      should be populated.
    any_of:
    - slot_conditions:
        cassette_genomic_entity_associations:
          name: cassette_genomic_entity_associations
          required: true
    - slot_conditions:
        cassette_components:
          name: cassette_components
          required: true

Induced

name: Cassette
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: Reagent
attributes:
  cassette_symbol:
    name: cassette_symbol
    description: Holds between a Cassette and the one current accepted symbol
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Cassette
    alias: cassette_symbol
    owner: Cassette
    domain_of:
    - Cassette
    range: CassetteSymbolSlotAnnotation
    required: false
    multivalued: false
  cassette_full_name:
    name: cassette_full_name
    description: Holds between a Cassette and a full name.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Cassette
    alias: cassette_full_name
    owner: Cassette
    domain_of:
    - Cassette
    range: CassetteFullNameSlotAnnotation
    required: false
    multivalued: false
  cassette_synonyms:
    name: cassette_synonyms
    description: Holds between a Cassette and a list of synonyms.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Cassette
    alias: cassette_synonyms
    owner: Cassette
    domain_of:
    - Cassette
    range: CassetteSynonymSlotAnnotation
    required: false
    multivalued: true
  cassette_genomic_entity_associations:
    name: cassette_genomic_entity_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Cassette
    alias: cassette_genomic_entity_associations
    owner: Cassette
    domain_of:
    - Cassette
    range: CassetteGenomicEntityAssociation
    multivalued: true
  cassette_transgenic_tool_associations:
    name: cassette_transgenic_tool_associations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Cassette
    alias: cassette_transgenic_tool_associations
    owner: Cassette
    domain_of:
    - Cassette
    range: CassetteTransgenicToolAssociation
    multivalued: true
  cassette_components:
    name: cassette_components
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Cassette
    alias: cassette_components
    owner: Cassette
    domain_of:
    - Cassette
    range: CassetteComponentSlotAnnotation
    multivalued: true
  references:
    name: references
    description: holds between an object and a list of references
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: reference
    alias: references
    owner: Cassette
    domain_of:
    - AffectedGenomicModel
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - Cassette
    - TransgenicTool
    - HTPExpressionDatasetAnnotation
    - Variant
    range: Reference
    multivalued: true
  unique_id:
    name: unique_id
    description: A non-curie unique identifier for a thing.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: unique_id
    owner: Cassette
    domain_of:
    - Person
    - Exon
    - CodingSequence
    - ExpressionExperiment
    - GeneInteraction
    - Reagent
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    range: string
    multivalued: false
  secondary_identifiers:
    name: secondary_identifiers
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - secondary_ids
    alias: secondary_identifiers
    owner: Cassette
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - Figure
    - Image
    - OntologyTerm
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
    multivalued: true
  related_notes:
    name: related_notes
    description: Holds between an object and a list of related Note objects.
    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: Cassette
    domain_of:
    - Allele
    - Gene
    - GeneChangeEventSlotAnnotation
    - ExpressionExperiment
    - Reagent
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - ConstructCassetteAssociation
    - CassetteComponentSlotAnnotation
    - CassetteGenomicEntityAssociation
    - CassetteTransgenicToolAssociation
    - Annotation
    - HTPExpressionDatasetSampleAnnotation
    - Variant
    range: Note
    multivalued: true
  placeholder:
    name: placeholder
    description: A boolean property to indicate whether a data record/object/entity
      is intended to be a placeholder data object rather than a publicly displayed
      object with a proper ID, name and/or symbol, for example. For example, the Cassette
      class has been introduced to support FlyBase Cassette objects with IDs and names,
      but not every Alliance member has data tables/classes for these objects and
      any IDs or names/symbols would likely be derived and not helpful to end users.
      Data records/entities where the placeholder value is set to true would have
      various visible properties suppressed, so as not to confuse end users with private,
      internal or otherwise contrived representations.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: placeholder
    owner: Cassette
    domain_of:
    - Reagent
    - ReagentDTO
    range: boolean
  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: Cassette
    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: Cassette
    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: Cassette
    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: Cassette
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
    multivalued: false
  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: Cassette
    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: Cassette
    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: Cassette
    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: Cassette
    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: Cassette
    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: Cassette
    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: Cassette
    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: Cassette
    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: Cassette
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
rules:
- postconditions:
    description: At least one of cassette_genomic_entity_associations or cassette_components
      should be populated.
    any_of:
    - slot_conditions:
        cassette_genomic_entity_associations:
          name: cassette_genomic_entity_associations
          required: true
    - slot_conditions:
        cassette_components:
          name: cassette_components
          required: true