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GenomeAssembly

A set of chromosome assemblies, scaffolds and contigs that represent the haploid genome sequence of a species or strain.

classDiagram BiologicalEntity <|-- GenomeAssembly GenomeAssembly : created_by GenomeAssembly : cross_references GenomeAssembly : curie GenomeAssembly : data_provider GenomeAssembly : data_provider_cross_reference GenomeAssembly : date_created GenomeAssembly : date_updated GenomeAssembly : db_date_created GenomeAssembly : db_date_updated GenomeAssembly : internal GenomeAssembly : mod_internal_id GenomeAssembly : obsolete GenomeAssembly : primary_external_id GenomeAssembly : specimen_genomic_model GenomeAssembly : taxon GenomeAssembly : updated_by

URI: alliance:GenomeAssembly

Parent Classes

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.
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obsolete Entity is no longer current.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.
specimen_genomic_model The strain or genotype of origin for the genome sequence.
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:GenomeAssembly']
native ['alliance:GenomeAssembly']

LinkML Specification

Direct

name: GenomeAssembly
description: A set of chromosome assemblies, scaffolds and contigs that represent
  the haploid genome sequence of a species or strain.
notes:
- These should typically have an NCBI curie.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntity
slots:
- specimen_genomic_model
- cross_references
slot_usage:
  specimen_genomic_model:
    name: specimen_genomic_model
    description: The strain or genotype of origin for the genome sequence.
    domain_of:
    - GenomeAssembly
    - ExpressionExperiment

Induced

name: GenomeAssembly
description: A set of chromosome assemblies, scaffolds and contigs that represent
  the haploid genome sequence of a species or strain.
notes:
- These should typically have an NCBI curie.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: BiologicalEntity
slot_usage:
  specimen_genomic_model:
    name: specimen_genomic_model
    description: The strain or genotype of origin for the genome sequence.
    domain_of:
    - GenomeAssembly
    - ExpressionExperiment
attributes:
  specimen_genomic_model:
    name: specimen_genomic_model
    description: The strain or genotype of origin for the genome sequence.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: specimen_genomic_model
    owner: GenomeAssembly
    domain_of:
    - GenomeAssembly
    - ExpressionExperiment
    range: AffectedGenomicModel
  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
    multivalued: true
    alias: cross_references
    owner: GenomeAssembly
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  taxon:
    name: taxon
    description: The taxon from which the biological entity derives.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: taxon
    owner: GenomeAssembly
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
    required: true
  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: GenomeAssembly
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - 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: GenomeAssembly
    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
    multivalued: false
    alias: data_provider
    owner: GenomeAssembly
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
  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
    multivalued: false
    alias: data_provider_cross_reference
    owner: GenomeAssembly
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: 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/core.yaml
    multivalued: false
    alias: curie
    owner: GenomeAssembly
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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
    multivalued: false
    alias: created_by
    owner: GenomeAssembly
    domain_of:
    - AuditedObject
    range: Person
  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: GenomeAssembly
    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
    multivalued: false
    alias: updated_by
    owner: GenomeAssembly
    domain_of:
    - AuditedObject
    range: Person
  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: GenomeAssembly
    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: GenomeAssembly
    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: GenomeAssembly
    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: GenomeAssembly
    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: GenomeAssembly
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean