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AllelePhenotypeAnnotation

An annotation asserting an association between an allele and a phenotype supported by evidence.

classDiagram PhenotypeAnnotation <|-- AllelePhenotypeAnnotation AllelePhenotypeAnnotation : asserted_genes AllelePhenotypeAnnotation : condition_relations AllelePhenotypeAnnotation : created_by AllelePhenotypeAnnotation : cross_reference AllelePhenotypeAnnotation : curie AllelePhenotypeAnnotation : data_provider AllelePhenotypeAnnotation : data_provider_cross_reference AllelePhenotypeAnnotation : date_created AllelePhenotypeAnnotation : date_updated AllelePhenotypeAnnotation : db_date_created AllelePhenotypeAnnotation : db_date_updated AllelePhenotypeAnnotation : evidence_item AllelePhenotypeAnnotation : inferred_gene AllelePhenotypeAnnotation : internal AllelePhenotypeAnnotation : mod_internal_id AllelePhenotypeAnnotation : negated AllelePhenotypeAnnotation : obsolete AllelePhenotypeAnnotation : phenotype_annotation_object AllelePhenotypeAnnotation : phenotype_annotation_subject AllelePhenotypeAnnotation : phenotype_terms AllelePhenotypeAnnotation : primary_external_id AllelePhenotypeAnnotation : related_notes AllelePhenotypeAnnotation : relation AllelePhenotypeAnnotation : unique_id AllelePhenotypeAnnotation : updated_by

URI: alliance:AllelePhenotypeAnnotation

Parent Classes

Slots

Name Description
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.
cross_reference None
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 of curation at the source (MOD) database.
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.
evidence_item Single item of evidence that supports some assertion.
inferred_gene The gene to which the phenotype 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 object
negated if set to true, then the association is negated i.e. is not true
obsolete Entity is no longer current.
phenotype_annotation_object phenotype statement: The label of an individual phenotype term from a phenotype ontology or the post-composed statement of the phenotype from a post-composed terminology
phenotype_annotation_subject The allele to which the phenotype ontology term is associated.
phenotype_terms The phenotype ontology term used to describe the phenotype of an organism or a set of organisms.
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.
related_notes Valid note types are available for viewing in the A-Team curation tool Controlled Vocabulary Terms Table (in the "Phenotype annotation note types" vocabulary) on the production environment (curation.alliancegenome.org). New terms can be added as needed.
relation A high-level grouping for the relationship type. This is analogous to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type.
unique_id A non-curie unique identifier for a thing.
updated_by The individual that last modified the entity.

Mappings

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

LinkML Specification

Direct

name: AllelePhenotypeAnnotation
description: An annotation asserting an association between an allele and a phenotype
  supported by evidence.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: PhenotypeAnnotation
slots:
- inferred_gene
- asserted_genes
slot_usage:
  phenotype_annotation_subject:
    name: phenotype_annotation_subject
    description: The allele to which the phenotype ontology term is associated.
    range: Allele
  inferred_gene:
    name: inferred_gene
    description: The gene to which the phenotype is inferred to be associated.
    range: Gene
    required: false
  asserted_genes:
    name: asserted_genes
    required: false

Induced

name: AllelePhenotypeAnnotation
description: An annotation asserting an association between an allele and a phenotype
  supported by evidence.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: PhenotypeAnnotation
slot_usage:
  phenotype_annotation_subject:
    name: phenotype_annotation_subject
    description: The allele to which the phenotype ontology term is associated.
    range: Allele
  inferred_gene:
    name: inferred_gene
    description: The gene to which the phenotype is inferred to be associated.
    range: Gene
    required: false
  asserted_genes:
    name: asserted_genes
    required: false
attributes:
  inferred_gene:
    name: inferred_gene
    description: The gene to which the phenotype is inferred to be associated.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: inferred_gene
    owner: AllelePhenotypeAnnotation
    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
    alias: asserted_genes
    owner: AllelePhenotypeAnnotation
    domain_of:
    - AllelePhenotypeAnnotation
    - AGMPhenotypeAnnotation
    - AlleleDiseaseAnnotation
    - AGMDiseaseAnnotation
    range: Gene
    required: false
    multivalued: true
  phenotype_annotation_subject:
    name: phenotype_annotation_subject
    description: The allele to which the phenotype ontology term is associated.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: PhenotypeAnnotation
    alias: phenotype_annotation_subject
    owner: AllelePhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: Allele
    required: true
  phenotype_terms:
    name: phenotype_terms
    description: The phenotype ontology term used to describe the phenotype of an
      organism or a set of organisms.
    examples:
    - value: HP:0002487
      description: Hyperkinesis
    - value: WBPhenotype:0000180
      description: axon morphology variant
    - value: MP:0001569
      description: abnormal circulating bilirubin level
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    values_from:
    - HP
    - MP
    - WBPhenotype
    - ZP
    - APO
    - FBcv
    alias: phenotype_terms
    owner: AllelePhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: PhenotypeTerm
    multivalued: true
  cross_reference:
    name: cross_reference
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: cross_reference
    owner: AllelePhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: CrossReference
    multivalued: false
    inlined: 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: AllelePhenotypeAnnotation
    domain_of:
    - ExpressionAnnotation
    - PhenotypeAnnotation
    - PhenotypeAnnotationDTO
    - DiseaseAnnotation
    - DiseaseAnnotationDTO
    range: boolean
  phenotype_annotation_object:
    name: phenotype_annotation_object
    description: 'phenotype statement: The label of an individual phenotype term from
      a phenotype ontology or the post-composed statement of the phenotype from a
      post-composed terminology'
    from_schema: https://github.com/alliance-genome/agr_persistent_schema/phenotypeAndDiseaseAnnotation.yaml
    alias: phenotype_annotation_object
    owner: AllelePhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: string
    required: true
  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/alliance_schema
    alias: curie
    owner: AllelePhenotypeAnnotation
    domain_of:
    - Laboratory
    - CurieObject
    - Identifier
    - GeneNomenclatureSet
    - OntologyTerm
    - Annotation
    - ExternalDataBaseEntityDTO
    range: uriorcurie
    multivalued: false
  unique_id:
    name: unique_id
    description: A non-curie unique identifier for a thing.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: unique_id
    owner: AllelePhenotypeAnnotation
    domain_of:
    - Person
    - Exon
    - CodingSequence
    - ExpressionExperiment
    - GeneInteraction
    - Reagent
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    range: string
    multivalued: false
  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: AllelePhenotypeAnnotation
    domain_of:
    - Person
    - SubmittedObject
    - SubmittedObjectDTO
    - 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: AllelePhenotypeAnnotation
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  condition_relations:
    name: condition_relations
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: condition_relations
    owner: AllelePhenotypeAnnotation
    domain_of:
    - ExpressionExperiment
    - Annotation
    range: ConditionRelation
    multivalued: true
  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 "Phenotype annotation note types"
      vocabulary) on the production environment (curation.alliancegenome.org). New
      terms can be added as needed.
    notes:
    - The original name suggested for this slot was simply notes, but I think that
      label is reserved in LinkML for internal descriptions of objects, hence the
      related_notes label used here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: related_notes
    owner: AllelePhenotypeAnnotation
    domain_of:
    - SubmittedObject
    - Gene
    - GeneChangeEventSlotAnnotation
    - ExpressionExperiment
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - ConstructCassetteAssociation
    - CassetteComponentSlotAnnotation
    - CassetteGenomicEntityAssociation
    - CassetteTransgenicToolAssociation
    - CassetteStrAssociation
    - Annotation
    - HTPExpressionDatasetSampleAnnotation
    range: Note
    multivalued: true
  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
    alias: data_provider
    owner: AllelePhenotypeAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
    multivalued: false
  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
    alias: data_provider_cross_reference
    owner: AllelePhenotypeAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
    multivalued: false
  evidence_item:
    name: evidence_item
    description: Single item of evidence that supports some assertion.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: evidence_item
    owner: AllelePhenotypeAnnotation
    domain_of:
    - SingleReferenceAssociation
    range: InformationContentEntity
  relation:
    name: relation
    description: A high-level grouping for the relationship type. This is analogous
      to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j
      this corresponds to the relationship type.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    exact_mappings:
    - biolink:predicate
    is_a: association_slot
    alias: relation
    owner: AllelePhenotypeAnnotation
    domain_of:
    - Association
    - ConstructComponentSlotAnnotation
    - CassetteComponentSlotAnnotation
    range: string
    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
    alias: created_by
    owner: AllelePhenotypeAnnotation
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  date_created:
    name: date_created
    description: The date of curation at the source (MOD) database.
    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: AllelePhenotypeAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
    multivalued: false
  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
    alias: updated_by
    owner: AllelePhenotypeAnnotation
    domain_of:
    - AuditedObject
    range: Person
    multivalued: false
  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: AllelePhenotypeAnnotation
    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: AllelePhenotypeAnnotation
    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: AllelePhenotypeAnnotation
    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: AllelePhenotypeAnnotation
    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: AllelePhenotypeAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean