AffectedGenomicModel

Includes inbred strains, stocks, disease models and mutant genotypes

classDiagram GenomicEntity <|-- AffectedGenomicModel AffectedGenomicModel : agm_secondary_ids AffectedGenomicModel : components AffectedGenomicModel : created_by AffectedGenomicModel : cross_references AffectedGenomicModel : curie AffectedGenomicModel : data_provider AffectedGenomicModel : data_provider_cross_reference AffectedGenomicModel : date_created AffectedGenomicModel : date_updated AffectedGenomicModel : db_date_created AffectedGenomicModel : db_date_updated AffectedGenomicModel : internal AffectedGenomicModel : mod_internal_id AffectedGenomicModel : name AffectedGenomicModel : obsolete AffectedGenomicModel : parental_populations AffectedGenomicModel : primary_external_id AffectedGenomicModel : references AffectedGenomicModel : sequence_targeting_reagents AffectedGenomicModel : subtype AffectedGenomicModel : taxon AffectedGenomicModel : updated_by

URI: alliance:AffectedGenomicModel

Parent Classes

AuditedObject
- CurieObject
  - SubmittedObject
    - BiologicalEntity
      - GenomicEntity
        
        AffectedGenomicModel

Slots

Name	Description
agm_secondary_ids	Secondary IDs of a given AGM
components	Collection of genomic components that make up a model, i.e. 'allele', each with a zygosity
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
name	a human-readable name for an entity
obsolete	Entity is no longer current.
parental_populations	None
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
sequence_targeting_reagents	None
subtype	Subtype of affected genomic model - permissible values: strain / genotype / fish
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:AffectedGenomicModel']
native	['alliance:AffectedGenomicModel']

LinkML Specification

Direct

name: AffectedGenomicModel
description: Includes inbred strains, stocks, disease models and mutant genotypes
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
slots:
- name
- subtype
- agm_secondary_ids
- components
- sequence_targeting_reagents
- parental_populations
- references
slot_usage:
  name:
    name: name
    notes:
    - May want to convert this into a slot that uses NameSlotAnnotation.
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad

Induced

name: AffectedGenomicModel
description: Includes inbred strains, stocks, disease models and mutant genotypes
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: GenomicEntity
slot_usage:
  name:
    name: name
    notes:
    - May want to convert this into a slot that uses NameSlotAnnotation.
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
attributes:
  name:
    name: name
    description: a human-readable name for an entity
    notes:
    - May want to convert this into a slot that uses NameSlotAnnotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: name
    owner: AffectedGenomicModel
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    range: string
  subtype:
    name: subtype
    description: 'Subtype of affected genomic model - permissible values: strain /
      genotype / fish'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AffectedGenomicModel
    alias: subtype
    owner: AffectedGenomicModel
    domain_of:
    - AffectedGenomicModel
    range: VocabularyTerm
    required: true
  agm_secondary_ids:
    name: agm_secondary_ids
    description: Secondary IDs of a given AGM
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AffectedGenomicModel
    multivalued: true
    alias: agm_secondary_ids
    owner: AffectedGenomicModel
    domain_of:
    - AffectedGenomicModel
    range: AgmSecondaryIdSlotAnnotation
  components:
    name: components
    description: Collection of genomic components that make up a model, i.e. 'allele',
      each with a zygosity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: component
    domain: AffectedGenomicModel
    multivalued: true
    alias: components
    owner: AffectedGenomicModel
    domain_of:
    - AffectedGenomicModel
    range: AffectedGenomicModelComponent
  sequence_targeting_reagents:
    name: sequence_targeting_reagents
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: sequence_targeting_reagent
    domain: AffectedGenomicModel
    multivalued: true
    alias: sequence_targeting_reagents
    owner: AffectedGenomicModel
    domain_of:
    - AffectedGenomicModel
    range: SequenceTargetingReagent
  parental_populations:
    name: parental_populations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: parental_population
    domain: AffectedGenomicModel
    alias: parental_populations
    owner: AffectedGenomicModel
    domain_of:
    - AffectedGenomicModel
    range: uriorcurie
  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
    multivalued: true
    alias: references
    owner: AffectedGenomicModel
    domain_of:
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - AffectedGenomicModel
    - Variant
    - HTPExpressionDatasetAnnotation
    range: Reference
  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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    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: AffectedGenomicModel
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean