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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 : evidence_item 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 : 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.
evidence_item Single item of evidence that supports some assertion.
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obsolete Entity is no longer current.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.
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
    range: PhenotypeTerm
  single_reference:
    name: single_reference
    description: The reference in which the phenotype association was asserted/reported.
  date_created:
    name: date_created
    description: The date of curation at the source (MOD) database.
    required: true
    multivalued: false
  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.
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
    domain_of:
    - PhenotypeAnnotation
    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
    range: PhenotypeTerm
  single_reference:
    name: single_reference
    description: The reference in which the phenotype association was asserted/reported.
  date_created:
    name: date_created
    description: The date of curation at the source (MOD) database.
    required: true
    multivalued: false
  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.
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
    alias: phenotype_terms
    owner: PhenotypeAnnotation
    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: PhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: CrossReference
    multivalued: false
    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/alliance_schema
    alias: curie
    owner: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: 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
    alias: condition_relations
    owner: PhenotypeAnnotation
    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: PhenotypeAnnotation
    domain_of:
    - Allele
    - Gene
    - GeneChangeEventSlotAnnotation
    - ExpressionExperiment
    - Reagent
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - ConstructCassetteAssociation
    - CassetteComponentSlotAnnotation
    - CassetteGenomicEntityAssociation
    - CassetteTransgenicToolAssociation
    - CassetteStrAssociation
    - Annotation
    - HTPExpressionDatasetSampleAnnotation
    - Variant
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    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: PhenotypeAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
    required: true
    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: PhenotypeAnnotation
    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: 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