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PhenotypeAnnotation

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

classDiagram Annotation <|-- PhenotypeAnnotation PhenotypeAnnotation : condition_relations PhenotypeAnnotation : created_by PhenotypeAnnotation : cross_reference PhenotypeAnnotation : curie PhenotypeAnnotation : data_provider PhenotypeAnnotation : data_provider_cross_reference PhenotypeAnnotation : date_created PhenotypeAnnotation : date_updated PhenotypeAnnotation : db_date_created PhenotypeAnnotation : db_date_updated PhenotypeAnnotation : internal PhenotypeAnnotation : mod_internal_id PhenotypeAnnotation : obsolete PhenotypeAnnotation : phenotype_annotation_object PhenotypeAnnotation : phenotype_annotation_subject PhenotypeAnnotation : phenotype_terms PhenotypeAnnotation : primary_external_id PhenotypeAnnotation : related_notes PhenotypeAnnotation : relation PhenotypeAnnotation : single_reference PhenotypeAnnotation : unique_id PhenotypeAnnotation : updated_by

URI: alliance:PhenotypeAnnotation

Parent Classes

Children

Slots

Name Description
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.
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
obsolete Entity is no longer current.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 biological entity (e.g. gene, allele, genotype) to which the phenotype is associated, by direct curation.
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.
single_reference The reference in which the phenotype association was asserted/reported.
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:PhenotypeAnnotation']
native ['alliance:PhenotypeAnnotation']

LinkML Specification

Direct

name: PhenotypeAnnotation
description: An annotation asserting an association between a biological entity and
  a phenotype supported by evidence.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: Annotation
slots:
- phenotype_annotation_subject
- phenotype_terms
- cross_reference
slot_usage:
  phenotype_terms:
    name: phenotype_terms
    examples:
    - value: HP:0002487
      description: Hyperkinesis
    - value: WBPhenotype:0000180
      description: axon morphology variant
    - value: MP:0001569
      description: abnormal circulating bilirubin level
    values_from:
    - HP
    - MP
    - WBPhenotype
    - ZP
    - APO
    - FBcv
    domain_of:
    - PhenotypeAnnotation
    range: PhenotypeTerm
  single_reference:
    name: single_reference
    description: The reference in which the phenotype association was asserted/reported.
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
  date_created:
    name: date_created
    description: The date of curation at the source (MOD) database.
    multivalued: false
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    required: 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.
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
attributes:
  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
    range: string
    required: true

Induced

name: PhenotypeAnnotation
description: An annotation asserting an association between a biological entity and
  a phenotype supported by evidence.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: Annotation
slot_usage:
  phenotype_terms:
    name: phenotype_terms
    examples:
    - value: HP:0002487
      description: Hyperkinesis
    - value: WBPhenotype:0000180
      description: axon morphology variant
    - value: MP:0001569
      description: abnormal circulating bilirubin level
    values_from:
    - HP
    - MP
    - WBPhenotype
    - ZP
    - APO
    - FBcv
    domain_of:
    - PhenotypeAnnotation
    range: PhenotypeTerm
  single_reference:
    name: single_reference
    description: The reference in which the phenotype association was asserted/reported.
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
  date_created:
    name: date_created
    description: The date of curation at the source (MOD) database.
    multivalued: false
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    required: 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.
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
attributes:
  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: PhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: string
    required: true
  phenotype_annotation_subject:
    name: phenotype_annotation_subject
    description: The biological entity (e.g. gene, allele, genotype) to which the
      phenotype is associated, by direct curation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: PhenotypeAnnotation
    alias: phenotype_annotation_subject
    owner: PhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: BiologicalEntity
    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
    multivalued: true
    alias: phenotype_terms
    owner: PhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: PhenotypeTerm
  cross_reference:
    name: cross_reference
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: cross_reference
    owner: PhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    - ExpressionExperiment
    range: CrossReference
    inlined: 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/core.yaml
    multivalued: false
    alias: curie
    owner: PhenotypeAnnotation
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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
    multivalued: false
    alias: unique_id
    owner: PhenotypeAnnotation
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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
    multivalued: true
    alias: condition_relations
    owner: PhenotypeAnnotation
    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 "Phenotype 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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  single_reference:
    name: single_reference
    description: The reference in which the phenotype association was asserted/reported.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: single_reference
    owner: PhenotypeAnnotation
    domain_of:
    - SingleReferenceAssociation
    - Figure
    - ConditionRelation
    - SourceVariantGenomicLocationAssociation
    - SourceVariantTranscriptLocationAssociation
    - SourceVariantPolypeptideLocationAssociation
    - GeneToGeneOrthologyCurated
    - ExpressionExperiment
    - FunctionalGeneSet
    range: Reference
    required: true
  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
    is_a: association_slot
    alias: relation
    owner: PhenotypeAnnotation
    domain_of:
    - ConstructComponentSlotAnnotation
    - Association
    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
    multivalued: false
    alias: created_by
    owner: PhenotypeAnnotation
    domain_of:
    - AuditedObject
    range: Person
  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
    multivalued: false
    alias: date_created
    owner: PhenotypeAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
    required: true
  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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean