GeneDiseaseAnnotation

An annotation asserting an association between a gene and a disease supported by evidence.

classDiagram DiseaseAnnotation <|-- GeneDiseaseAnnotation GeneDiseaseAnnotation : annotation_type GeneDiseaseAnnotation : condition_relations GeneDiseaseAnnotation : created_by GeneDiseaseAnnotation : curie GeneDiseaseAnnotation : data_provider GeneDiseaseAnnotation : data_provider_cross_reference GeneDiseaseAnnotation : date_created GeneDiseaseAnnotation : date_updated GeneDiseaseAnnotation : db_date_created GeneDiseaseAnnotation : db_date_updated GeneDiseaseAnnotation : disease_annotation_object GeneDiseaseAnnotation : disease_annotation_subject GeneDiseaseAnnotation : disease_genetic_modifier_agms GeneDiseaseAnnotation : disease_genetic_modifier_alleles GeneDiseaseAnnotation : disease_genetic_modifier_genes GeneDiseaseAnnotation : disease_genetic_modifier_relation GeneDiseaseAnnotation : disease_qualifiers GeneDiseaseAnnotation : evidence_codes GeneDiseaseAnnotation : genetic_sex GeneDiseaseAnnotation : internal GeneDiseaseAnnotation : mod_internal_id GeneDiseaseAnnotation : negated GeneDiseaseAnnotation : obsolete GeneDiseaseAnnotation : primary_external_id GeneDiseaseAnnotation : related_notes GeneDiseaseAnnotation : relation GeneDiseaseAnnotation : secondary_data_provider GeneDiseaseAnnotation : secondary_data_provider_cross_reference GeneDiseaseAnnotation : sgd_strain_background GeneDiseaseAnnotation : single_reference GeneDiseaseAnnotation : unique_id GeneDiseaseAnnotation : updated_by GeneDiseaseAnnotation : with_or_from

URI: alliance:GeneDiseaseAnnotation

Parent Classes

AuditedObject
- Association
  - SingleReferenceAssociation
    - Annotation
      - DiseaseAnnotation
        
        GeneDiseaseAnnotation

Slots

Name	Description
annotation_type	The type of annotation classified according to curation method. Submitted value should be a vocabulary term from the 'Annotation types' vocabulary
condition_relations	None
created_by	The individual that created the entity.
curie	The Alliance-minted ID for the disease annotation. The ID is of the format AGRKB:100000000000001, where the first three digits represent the DiseaseAnnotation class code of "100", followed by a 12-digit identifier
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.
disease_annotation_object	The Disease Ontology term
disease_annotation_subject	The gene to which the disease ontology term is associated.
disease_genetic_modifier_agms	Specifies an affected genomic model (e.g. genotype) that modifies a disease model.
disease_genetic_modifier_alleles	Specifies an allele that modifies a disease model.
disease_genetic_modifier_genes	Specifies a gene that modifies a disease model.
disease_genetic_modifier_relation	A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary
disease_qualifiers	Submitted values should be vocabulary terms from the 'Disease qualifiers' Vocabulary
evidence_codes	ECO term IDs
genetic_sex	Submitted value should be a vocabulary term from the 'Genetic sexes' vocabulary
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 disease annotation. When available, this is used for determination of distinctness instead of the Unique ID field.
negated	The negative qualifier for the annotation.
obsolete	Entity is no longer current.
primary_external_id	The primary external (non-AGRKB) identifier/curie for the disease annotation. Currently only used by WormBase for disease annotations, e.g. "WBDOannot00000907"
related_notes	Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the "Disease annotation note types" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.
relation	The relationship between gene and disease. Submitted value should be a vocabulary term from the 'Gene disease relations' vocabulary
secondary_data_provider	Object representing organization (e.g. MOD) that provided the data directly to the Alliance, but not the original source
secondary_data_provider_cross_reference	CrossReference to the organization that provided the data to the Alliance
sgd_strain_background	None
single_reference	The reference in which the disease association was asserted/reported.
unique_id	Unique identifier for the disease annotation. Will be generated at AGR if not submitted by the MOD.
updated_by	The individual that last modified the entity.
with_or_from	A field for disease annotations that captures the human gene the implicated MOD gene is homologous or orthologous to when using the ISS (inferred from sequence similarity) evidence code or the ISO (inferred from sequence orthology) evidence code. The assertion would state that the MOD gene is implicated in the indicated disease based on sequence-similarity/sequence-orthology "with" some human gene. Currently used by SGD.

Mappings

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

LinkML Specification

Direct

name: GeneDiseaseAnnotation
description: An annotation asserting an association between a gene and a disease supported
  by evidence.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: DiseaseAnnotation
slots:
- sgd_strain_background
slot_usage:
  disease_annotation_subject:
    name: disease_annotation_subject
    description: The gene to which the disease ontology term is associated.
    domain_of:
    - DiseaseAnnotation
    range: Gene
    required: true
  relation:
    name: relation
    description: The relationship between gene and disease. Submitted value should
      be a vocabulary term from the 'Gene disease relations' vocabulary
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    range: VocabularyTerm
    required: true

Induced

name: GeneDiseaseAnnotation
description: An annotation asserting an association between a gene and a disease supported
  by evidence.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: DiseaseAnnotation
slot_usage:
  disease_annotation_subject:
    name: disease_annotation_subject
    description: The gene to which the disease ontology term is associated.
    domain_of:
    - DiseaseAnnotation
    range: Gene
    required: true
  relation:
    name: relation
    description: The relationship between gene and disease. Submitted value should
      be a vocabulary term from the 'Gene disease relations' vocabulary
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    range: VocabularyTerm
    required: true
attributes:
  sgd_strain_background:
    name: sgd_strain_background
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: sgd_strain_background
    owner: GeneDiseaseAnnotation
    domain_of:
    - GenePhenotypeAnnotation
    - GeneDiseaseAnnotation
    range: AffectedGenomicModel
  disease_annotation_subject:
    name: disease_annotation_subject
    description: The gene to which the disease ontology term is associated.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotation
    alias: disease_annotation_subject
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: Gene
    required: true
  negated:
    name: negated
    description: The negative qualifier for the annotation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: negated
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    - DiseaseAnnotationDTO
    - ExpressionAnnotation
    range: boolean
  evidence_codes:
    name: evidence_codes
    description: ECO term IDs
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: evidence_codes
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: ECOTerm
    required: true
  annotation_type:
    name: annotation_type
    description: The type of annotation classified according to curation method. Submitted
      value should be a vocabulary term from the 'Annotation types' vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: annotation_type
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: VocabularyTerm
    required: false
  with_or_from:
    name: with_or_from
    description: A field for disease annotations that captures the human gene the
      implicated MOD gene is homologous or orthologous to when using the ISS (inferred
      from sequence similarity) evidence code or the ISO (inferred from sequence orthology)
      evidence code. The assertion would state that the MOD gene is implicated in
      the indicated disease based on sequence-similarity/sequence-orthology "with"
      some human gene. Currently used by SGD.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: with_or_from
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: Gene
    required: false
  disease_qualifiers:
    name: disease_qualifiers
    description: Submitted values should be vocabulary terms from the 'Disease qualifiers'
      Vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: DiseaseAnnotation
    multivalued: true
    alias: disease_qualifiers
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: VocabularyTerm
  genetic_sex:
    name: genetic_sex
    description: Submitted value should be a vocabulary term from the 'Genetic sexes'
      vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: genetic_sex
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: VocabularyTerm
    required: false
  secondary_data_provider:
    name: secondary_data_provider
    description: Object representing organization (e.g. MOD) that provided the data
      directly to the Alliance, but not the original source
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: secondary_data_provider
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: Organization
  secondary_data_provider_cross_reference:
    name: secondary_data_provider_cross_reference
    description: CrossReference to the organization that provided the data to the
      Alliance
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: secondary_data_provider_cross_reference
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: CrossReference
  disease_genetic_modifier_genes:
    name: disease_genetic_modifier_genes
    description: Specifies a gene that modifies a disease model.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: disease_genetic_modifier_genes
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: Gene
    required: false
  disease_genetic_modifier_alleles:
    name: disease_genetic_modifier_alleles
    description: Specifies an allele that modifies a disease model.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: disease_genetic_modifier_alleles
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: Allele
    required: false
  disease_genetic_modifier_agms:
    name: disease_genetic_modifier_agms
    description: Specifies an affected genomic model (e.g. genotype) that modifies
      a disease model.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: disease_genetic_modifier_agms
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: AffectedGenomicModel
    required: false
  disease_genetic_modifier_relation:
    name: disease_genetic_modifier_relation
    description: A relation describing how the genetic modifier modifies the disease
      model. Submitted value should be a vocabulary term from the 'Disease genetic
      modifiers' vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: disease_genetic_modifier_relation
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: VocabularyTerm
  disease_annotation_object:
    name: disease_annotation_object
    description: The Disease Ontology term
    from_schema: https://github.com/alliance-genome/agr_persistent_schema/phenotypeAndDiseaseAnnotation.yaml
    alias: disease_annotation_object
    owner: GeneDiseaseAnnotation
    domain_of:
    - DiseaseAnnotation
    range: DOTerm
    required: true
  curie:
    name: curie
    description: The Alliance-minted ID for the disease annotation. The ID is of the
      format AGRKB:100000000000001, where the first three digits represent the DiseaseAnnotation
      class code of "100", followed by a 12-digit identifier
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: GeneDiseaseAnnotation
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  unique_id:
    name: unique_id
    description: Unique identifier for the disease annotation.  Will be generated
      at AGR if not submitted by the MOD.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: unique_id
    owner: GeneDiseaseAnnotation
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
    range: string
    required: false
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-AGRKB) identifier/curie for the disease
      annotation. Currently only used by WormBase for disease annotations, e.g. "WBDOannot00000907"
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: GeneDiseaseAnnotation
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
    required: false
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the disease
      annotation. When available, this is used for determination of distinctness instead
      of the Unique ID field.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: GeneDiseaseAnnotation
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
    required: false
  condition_relations:
    name: condition_relations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: condition_relations
    owner: GeneDiseaseAnnotation
    domain_of:
    - Annotation
    - ExpressionExperiment
    range: ConditionRelation
  related_notes:
    name: related_notes
    description: Valid note types are available for viewing in the A-Team curation
      tool Controlled Vocabulary Terms Table (in the "Disease annotation note types"
      vocabulary) on the production environment (curation.alliancegenome.org). New
      terms can be added as needed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: GeneDiseaseAnnotation
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  single_reference:
    name: single_reference
    description: The reference in which the disease association was asserted/reported.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_reference
    owner: GeneDiseaseAnnotation
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
    required: true
  relation:
    name: relation
    description: The relationship between gene and disease. Submitted value should
      be a vocabulary term from the 'Gene disease relations' vocabulary
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: association_slot
    alias: relation
    owner: GeneDiseaseAnnotation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    range: VocabularyTerm
    required: true
  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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    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: GeneDiseaseAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean