AGMDiseaseAnnotationDTO

Ingest class for an association between an AGM and a disease

classDiagram DiseaseAnnotationDTO <|-- AGMDiseaseAnnotationDTO AGMDiseaseAnnotationDTO : agm_identifier AGMDiseaseAnnotationDTO : annotation_type_name AGMDiseaseAnnotationDTO : asserted_allele_identifier AGMDiseaseAnnotationDTO : asserted_gene_identifiers AGMDiseaseAnnotationDTO : condition_relation_dtos AGMDiseaseAnnotationDTO : created_by_curie AGMDiseaseAnnotationDTO : data_provider_dto AGMDiseaseAnnotationDTO : date_created AGMDiseaseAnnotationDTO : date_updated AGMDiseaseAnnotationDTO : db_date_created AGMDiseaseAnnotationDTO : db_date_updated AGMDiseaseAnnotationDTO : disease_genetic_modifier_identifiers AGMDiseaseAnnotationDTO : disease_genetic_modifier_relation_name AGMDiseaseAnnotationDTO : disease_qualifier_names AGMDiseaseAnnotationDTO : disease_relation_name AGMDiseaseAnnotationDTO : do_term_curie AGMDiseaseAnnotationDTO : evidence_code_curies AGMDiseaseAnnotationDTO : genetic_sex_name AGMDiseaseAnnotationDTO : inferred_allele_identifier AGMDiseaseAnnotationDTO : inferred_gene_identifier AGMDiseaseAnnotationDTO : internal AGMDiseaseAnnotationDTO : mod_internal_id AGMDiseaseAnnotationDTO : negated AGMDiseaseAnnotationDTO : note_dtos AGMDiseaseAnnotationDTO : obsolete AGMDiseaseAnnotationDTO : primary_external_id AGMDiseaseAnnotationDTO : reference_curie AGMDiseaseAnnotationDTO : secondary_data_provider_dto AGMDiseaseAnnotationDTO : updated_by_curie AGMDiseaseAnnotationDTO : with_gene_identifiers

URI: alliance:AGMDiseaseAnnotationDTO

Parent Classes

AuditedObjectDTO
- SingleReferenceAssociationDTO
  - AnnotationDTO
    - DiseaseAnnotationDTO
      - AGMDiseaseAnnotationDTO

Slots

Name	Description
agm_identifier	None
annotation_type_name	Name of the VocabularyTerm describing the annotation type selected from the 'Annotation types' Vocabulary
asserted_allele_identifier	Identifier (curie/primary_external_id/mod_internal_id) of the allele to which something is manually asserted to be associated
asserted_gene_identifiers	Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated
condition_relation_dtos	None
created_by_curie	Curie of the Person object representing the individual that created the entity
data_provider_dto	Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site
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.
disease_genetic_modifier_identifiers	Identifiers (curie/primary_external_id/mod_internal_id) of Gene, Allele or AGM that modifies the disease model
disease_genetic_modifier_relation_name	Name of the VocabularyTerm that describes how the genetic modifier modifies the disease model, selected from the 'Disease genetic modifier relations' Vocabulary.
disease_qualifier_names	Names of terms from the 'Disease qualifiers' vocabulary
disease_relation_name	Name of term from 'Disease Relation Vocabulary' vocabulary
do_term_curie	Curie of DOTerm describing the disease
evidence_code_curies	List of ECOTerm curies
genetic_sex_name	Name of term from the 'Genetic sexes' vocabulary
inferred_allele_identifier	Identifier (curie/primary_external_id/mod_internal_id) of allele to which something is inferred to be associated via an automated pipeline
inferred_gene_identifier	Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline
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
negated	if set to true, then the association is negated i.e. is not true
note_dtos	None
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.
reference_curie	External reference curie used for ingest
secondary_data_provider_dto	Ingest object representing organization (e.g. MOD) that provided the data directly to the Alliance, but not the original source, and a CrossReference to that organisation's site
updated_by_curie	Curie of the Person object representing the individual that updated the entity
with_gene_identifiers	Identifier (curie/primary_external_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8

Mappings

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

LinkML Specification

Direct

name: AGMDiseaseAnnotationDTO
description: Ingest class for an association between an AGM and a disease
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: DiseaseAnnotationDTO
slots:
- agm_identifier
- inferred_gene_identifier
- asserted_gene_identifiers
- inferred_allele_identifier
- asserted_allele_identifier

Induced

name: AGMDiseaseAnnotationDTO
description: Ingest class for an association between an AGM and a disease
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: DiseaseAnnotationDTO
attributes:
  agm_identifier:
    name: agm_identifier
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: agm_identifier
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AlleleOriginAssociationDTO
    - AGMPhenotypeAnnotationDTO
    - AGMDiseaseAnnotationDTO
    - BioSampleGenomicInformationDTO
    range: string
    required: true
  inferred_gene_identifier:
    name: inferred_gene_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of gene to
      which something is inferred to be associated via an automated pipeline
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: inferred_gene_identifier
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AllelePhenotypeAnnotationDTO
    - AGMPhenotypeAnnotationDTO
    - AlleleDiseaseAnnotationDTO
    - AGMDiseaseAnnotationDTO
    range: string
  asserted_gene_identifiers:
    name: asserted_gene_identifiers
    description: Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s)
      to which something is manually asserted to be associated
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: asserted_gene_identifiers
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AllelePhenotypeAnnotationDTO
    - AGMPhenotypeAnnotationDTO
    - AlleleDiseaseAnnotationDTO
    - AGMDiseaseAnnotationDTO
    range: string
  inferred_allele_identifier:
    name: inferred_allele_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of allele
      to which something is inferred to be associated via an automated pipeline
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: inferred_allele_identifier
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AGMPhenotypeAnnotationDTO
    - AGMDiseaseAnnotationDTO
    range: string
  asserted_allele_identifier:
    name: asserted_allele_identifier
    description: Identifier (curie/primary_external_id/mod_internal_id) of the allele
      to which something is manually asserted to be associated
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: asserted_allele_identifier
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AGMPhenotypeAnnotationDTO
    - AGMDiseaseAnnotationDTO
    range: string
  disease_relation_name:
    name: disease_relation_name
    description: Name of term from 'Disease Relation Vocabulary' vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotationDTO
    alias: disease_relation_name
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
    required: true
  do_term_curie:
    name: do_term_curie
    description: Curie of DOTerm describing the disease
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotationDTO
    alias: do_term_curie
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
    required: true
  negated:
    name: negated
    description: if set to true, then the association is negated i.e. is not true
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: negated
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotation
    - DiseaseAnnotationDTO
    - ExpressionAnnotation
    range: boolean
  evidence_code_curies:
    name: evidence_code_curies
    description: List of ECOTerm curies
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence_code_curies
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
  annotation_type_name:
    name: annotation_type_name
    description: Name of the VocabularyTerm describing the annotation type selected
      from the 'Annotation types' Vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotationDTO
    alias: annotation_type_name
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
  with_gene_identifiers:
    name: with_gene_identifiers
    description: Identifier (curie/primary_external_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: with_gene_identifiers
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
  disease_qualifier_names:
    name: disease_qualifier_names
    description: Names of terms from the 'Disease qualifiers' vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotationDTO
    multivalued: true
    alias: disease_qualifier_names
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
  genetic_sex_name:
    name: genetic_sex_name
    description: Name of term from the 'Genetic sexes' vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotationDTO
    alias: genetic_sex_name
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
  secondary_data_provider_dto:
    name: secondary_data_provider_dto
    description: Ingest object representing organization (e.g. MOD) that provided
      the data directly to the Alliance, but not the original source, and a CrossReference
      to that organisation's site
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: secondary_data_provider_dto
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: DataProviderDTO
    inlined: true
  disease_genetic_modifier_identifiers:
    name: disease_genetic_modifier_identifiers
    description: Identifiers (curie/primary_external_id/mod_internal_id) of Gene,
      Allele or AGM that modifies the disease model
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotationDTO
    multivalued: true
    alias: disease_genetic_modifier_identifiers
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    range: string
  disease_genetic_modifier_relation_name:
    name: disease_genetic_modifier_relation_name
    description: Name of the VocabularyTerm that describes how the genetic modifier
      modifies the disease model, selected from the 'Disease genetic modifier relations'
      Vocabulary.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotationDTO
    multivalued: false
    alias: disease_genetic_modifier_relation_name
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - DiseaseAnnotationDTO
    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: AGMDiseaseAnnotationDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  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: AGMDiseaseAnnotationDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: note_dtos
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    inlined: true
    inlined_as_list: true
  data_provider_dto:
    name: data_provider_dto
    description: Ingest object representing the organization (e.g. MOD) from which
      the data was sourced and a CrossReference to that organisation's site
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider_dto
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    inlined: true
  condition_relation_dtos:
    name: condition_relation_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: condition_relation_dtos
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AnnotationDTO
    range: ConditionRelationDTO
    inlined: true
    inlined_as_list: true
  reference_curie:
    name: reference_curie
    description: External reference curie used for ingest
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: reference_curie
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - SourceVariantGenomicLocationAssociationDTO
    - SourceVariantTranscriptLocationAssociationDTO
    - SourceVariantPolypeptideLocationAssociationDTO
    - SingleReferenceAssociationDTO
    - ConditionRelationDTO
    range: string
    required: true
  created_by_curie:
    name: created_by_curie
    description: Curie of the Person object representing the individual that created
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: created_by_curie
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AGMDiseaseAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by_curie:
    name: updated_by_curie
    description: Curie of the Person object representing the individual that updated
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: updated_by_curie
    owner: AGMDiseaseAnnotationDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AGMDiseaseAnnotationDTO
    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: AGMDiseaseAnnotationDTO
    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: AGMDiseaseAnnotationDTO
    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: AGMDiseaseAnnotationDTO
    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: AGMDiseaseAnnotationDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean