AssemblyComponent

A scaffold component of a genome assembly, including chromosomal pseudo-molecule sequences, unplaced/unlocalized scaffolds and contigs, and organelle genomes.

classDiagram GenomicEntity <|-- AssemblyComponent AssemblyComponent : created_by AssemblyComponent : cross_references AssemblyComponent : curie AssemblyComponent : data_provider AssemblyComponent : data_provider_cross_reference AssemblyComponent : date_created AssemblyComponent : date_updated AssemblyComponent : db_date_created AssemblyComponent : db_date_updated AssemblyComponent : genome_assembly AssemblyComponent : internal AssemblyComponent : maps_to_chromosome AssemblyComponent : mod_internal_id AssemblyComponent : name AssemblyComponent : obsolete AssemblyComponent : primary_external_id AssemblyComponent : related_notes AssemblyComponent : taxon AssemblyComponent : updated_by

URI: alliance:AssemblyComponent

Parent Classes

AuditedObject
- CurieObject
  - SubmittedObject
    - BiologicalEntity
      - GenomicEntity
        
        AssemblyComponent

Slots

Name	Description
created_by	The individual that created the entity.
cross_references	Holds between an object and its CrossReferences.
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.
genome_assembly	The GenomeAssembly to which a AssemblyComponent belongs.
internal	Classifies the entity as private (for internal use) or not (for public use).
maps_to_chromosome	The chromosome(s) to which a chromosome assembly or unlocalized scaffold or contig maps.
mod_internal_id	The model organism database (MOD) internal identifier for the object
name	a human-readable name for an entity
obsolete	Entity is no longer current.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.
taxon	The taxon from which the biological entity derives.
updated_by	The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: AssemblyComponent
description: A scaffold component of a genome assembly, including chromosomal pseudo-molecule
  sequences, unplaced/unlocalized scaffolds and contigs, and organelle genomes.
notes:
- In the context of this model, this entity is used as a landmark for the location
  of other genomic entities.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
slots:
- name
- genome_assembly
- maps_to_chromosome
slot_usage:
  name:
    name: name
    required: true
defining_slots:
- name
- genome_assembly

Induced

name: AssemblyComponent
description: A scaffold component of a genome assembly, including chromosomal pseudo-molecule
  sequences, unplaced/unlocalized scaffolds and contigs, and organelle genomes.
notes:
- In the context of this model, this entity is used as a landmark for the location
  of other genomic entities.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
slot_usage:
  name:
    name: name
    required: true
attributes:
  name:
    name: name
    description: a human-readable name for an entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: name
    owner: AssemblyComponent
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - BulkLoadGroup
    - BulkLoad
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - CurationReportGroup
    - CurationReport
    - Antibody
    - AntibodyDTO
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    range: string
    required: true
    multivalued: false
  genome_assembly:
    name: genome_assembly
    description: The GenomeAssembly to which a AssemblyComponent belongs.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AssemblyComponent
    alias: genome_assembly
    owner: AssemblyComponent
    domain_of:
    - AssemblyComponent
    - Species
    range: GenomeAssembly
    required: true
    multivalued: false
  maps_to_chromosome:
    name: maps_to_chromosome
    description: The chromosome(s) to which a chromosome assembly or unlocalized scaffold
      or contig maps.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AssemblyComponent
    alias: maps_to_chromosome
    owner: AssemblyComponent
    domain_of:
    - AssemblyComponent
    range: Chromosome
    required: false
    multivalued: false
  cross_references:
    name: cross_references
    description: Holds between an object and its CrossReferences.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - xrefs
    singular_name: cross_reference
    alias: cross_references
    owner: AssemblyComponent
    domain_of:
    - GenomicEntity
    - GenomeAssembly
    - ExpressionExperiment
    - GeneExpressionAnnotation
    - AuthorReference
    - GeneInteraction
    - Antibody
    - TransgenicTool
    - OntologyTerm
    - ExternalDataBaseEntity
    range: CrossReference
    multivalued: true
  taxon:
    name: taxon
    description: The taxon from which the biological entity derives.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: taxon
    owner: AssemblyComponent
    domain_of:
    - BiologicalEntity
    - Chromosome
    - Species
    - Antibody
    - ConstructComponentSlotAnnotation
    - CassetteComponentSlotAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
    required: true
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    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: AssemblyComponent
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
defining_slots:
- name
- genome_assembly