AGMDiseaseAnnotation
An annotation asserting an association between an AGM and a disease supported by evidence.
classDiagram
DiseaseAnnotation <|-- AGMDiseaseAnnotation
AGMDiseaseAnnotation : annotation_type
AGMDiseaseAnnotation : asserted_allele
AGMDiseaseAnnotation : asserted_genes
AGMDiseaseAnnotation : condition_relations
AGMDiseaseAnnotation : created_by
AGMDiseaseAnnotation : curie
AGMDiseaseAnnotation : data_provider
AGMDiseaseAnnotation : data_provider_cross_reference
AGMDiseaseAnnotation : date_created
AGMDiseaseAnnotation : date_updated
AGMDiseaseAnnotation : db_date_created
AGMDiseaseAnnotation : db_date_updated
AGMDiseaseAnnotation : disease_annotation_object
AGMDiseaseAnnotation : disease_annotation_subject
AGMDiseaseAnnotation : disease_genetic_modifier_agms
AGMDiseaseAnnotation : disease_genetic_modifier_alleles
AGMDiseaseAnnotation : disease_genetic_modifier_genes
AGMDiseaseAnnotation : disease_genetic_modifier_relation
AGMDiseaseAnnotation : disease_qualifiers
AGMDiseaseAnnotation : evidence_codes
AGMDiseaseAnnotation : genetic_sex
AGMDiseaseAnnotation : inferred_allele
AGMDiseaseAnnotation : inferred_gene
AGMDiseaseAnnotation : internal
AGMDiseaseAnnotation : mod_internal_id
AGMDiseaseAnnotation : negated
AGMDiseaseAnnotation : obsolete
AGMDiseaseAnnotation : primary_external_id
AGMDiseaseAnnotation : related_notes
AGMDiseaseAnnotation : relation
AGMDiseaseAnnotation : secondary_data_provider
AGMDiseaseAnnotation : secondary_data_provider_cross_reference
AGMDiseaseAnnotation : single_reference
AGMDiseaseAnnotation : unique_id
AGMDiseaseAnnotation : updated_by
AGMDiseaseAnnotation : with_or_from
URI: alliance:AGMDiseaseAnnotation
Parent Classes
- AuditedObject
- Association
- SingleReferenceAssociation
- Annotation
- DiseaseAnnotation
- AGMDiseaseAnnotation
- DiseaseAnnotation
- Annotation
- SingleReferenceAssociation
- Association
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 |
asserted_allele | The allele to which something is manually asserted to be associated. |
asserted_genes | The gene(s) to which something is manually asserted to be associated. |
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 AGM 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 |
inferred_allele | The allele to which the disease is inferred to be associated. |
inferred_gene | The gene to which the disease is inferred to be associated. |
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 AGM and disease. Submitted value should be a vocabulary term from the 'AGM 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 |
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:AGMDiseaseAnnotation'] |
native | ['alliance:AGMDiseaseAnnotation'] |
LinkML Specification
Direct
name: AGMDiseaseAnnotation
description: An annotation asserting an association between an AGM and a disease supported
by evidence.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: DiseaseAnnotation
slots:
- inferred_allele
- inferred_gene
- asserted_genes
- asserted_allele
slot_usage:
disease_annotation_subject:
name: disease_annotation_subject
description: The AGM to which the disease ontology term is associated.
domain_of:
- DiseaseAnnotation
range: AffectedGenomicModel
relation:
name: relation
description: The relationship between AGM and disease. Submitted value should
be a vocabulary term from the 'AGM disease relations' vocabulary
domain_of:
- ConstructComponentSlotAnnotation
- Association
range: VocabularyTerm
required: true
inferred_gene:
name: inferred_gene
description: The gene to which the disease is inferred to be associated.
domain_of:
- AllelePhenotypeAnnotation
- AGMPhenotypeAnnotation
- AlleleDiseaseAnnotation
- AGMDiseaseAnnotation
range: Gene
required: false
inferred_allele:
name: inferred_allele
description: The allele to which the disease is inferred to be associated.
domain_of:
- AGMPhenotypeAnnotation
- AGMDiseaseAnnotation
range: Allele
required: false
asserted_genes:
name: asserted_genes
domain_of:
- AllelePhenotypeAnnotation
- AGMPhenotypeAnnotation
- AlleleDiseaseAnnotation
- AGMDiseaseAnnotation
required: false
asserted_allele:
name: asserted_allele
domain_of:
- AGMPhenotypeAnnotation
- AGMDiseaseAnnotation
required: false
Induced
name: AGMDiseaseAnnotation
description: An annotation asserting an association between an AGM 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 AGM to which the disease ontology term is associated.
domain_of:
- DiseaseAnnotation
range: AffectedGenomicModel
relation:
name: relation
description: The relationship between AGM and disease. Submitted value should
be a vocabulary term from the 'AGM disease relations' vocabulary
domain_of:
- ConstructComponentSlotAnnotation
- Association
range: VocabularyTerm
required: true
inferred_gene:
name: inferred_gene
description: The gene to which the disease is inferred to be associated.
domain_of:
- AllelePhenotypeAnnotation
- AGMPhenotypeAnnotation
- AlleleDiseaseAnnotation
- AGMDiseaseAnnotation
range: Gene
required: false
inferred_allele:
name: inferred_allele
description: The allele to which the disease is inferred to be associated.
domain_of:
- AGMPhenotypeAnnotation
- AGMDiseaseAnnotation
range: Allele
required: false
asserted_genes:
name: asserted_genes
domain_of:
- AllelePhenotypeAnnotation
- AGMPhenotypeAnnotation
- AlleleDiseaseAnnotation
- AGMDiseaseAnnotation
required: false
asserted_allele:
name: asserted_allele
domain_of:
- AGMPhenotypeAnnotation
- AGMDiseaseAnnotation
required: false
attributes:
inferred_allele:
name: inferred_allele
description: The allele to which the disease is inferred to be associated.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
alias: inferred_allele
owner: AGMDiseaseAnnotation
domain_of:
- AGMPhenotypeAnnotation
- AGMDiseaseAnnotation
range: Allele
required: false
inferred_gene:
name: inferred_gene
description: The gene to which the disease is inferred to be associated.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
alias: inferred_gene
owner: AGMDiseaseAnnotation
domain_of:
- AllelePhenotypeAnnotation
- AGMPhenotypeAnnotation
- AlleleDiseaseAnnotation
- AGMDiseaseAnnotation
range: Gene
required: false
asserted_genes:
name: asserted_genes
description: The gene(s) to which something is manually asserted to be associated.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
singular_name: asserted_gene
multivalued: true
alias: asserted_genes
owner: AGMDiseaseAnnotation
domain_of:
- AllelePhenotypeAnnotation
- AGMPhenotypeAnnotation
- AlleleDiseaseAnnotation
- AGMDiseaseAnnotation
range: Gene
required: false
asserted_allele:
name: asserted_allele
description: 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
owner: AGMDiseaseAnnotation
domain_of:
- AGMPhenotypeAnnotation
- AGMDiseaseAnnotation
range: Allele
required: false
disease_annotation_subject:
name: disease_annotation_subject
description: The AGM 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: AGMDiseaseAnnotation
domain_of:
- DiseaseAnnotation
range: AffectedGenomicModel
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
domain_of:
- SingleReferenceAssociation
- Figure
- ConditionRelation
- SourceVariantGenomicLocationAssociation
- SourceVariantTranscriptLocationAssociation
- SourceVariantPolypeptideLocationAssociation
- GeneToGeneOrthologyCurated
- ExpressionExperiment
- FunctionalGeneSet
range: Reference
required: true
relation:
name: relation
description: The relationship between AGM and disease. Submitted value should
be a vocabulary term from the 'AGM disease relations' vocabulary
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: association_slot
alias: relation
owner: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
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: AGMDiseaseAnnotation
domain_of:
- AuditedObject
- AuditedObjectDTO
range: boolean