AGMPhenotypeAnnotation

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

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

URI: alliance:AGMPhenotypeAnnotation

Parent Classes

AuditedObject
- Association
  - SingleReferenceAssociation
    - Annotation
      - PhenotypeAnnotation
        
        AGMPhenotypeAnnotation

Slots

Name	Description
asserted_alleles	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.
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_allele	The allele to which the phenotype is inferred to be associated.
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 AGM 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:AGMPhenotypeAnnotation']
native	['alliance:AGMPhenotypeAnnotation']

LinkML Specification

Direct

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

Induced

name: AGMPhenotypeAnnotation
description: An annotation asserting an association between an AGM 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 AGM to which the phenotype ontology term is associated.
    range: AffectedGenomicModel
  inferred_gene:
    name: inferred_gene
    description: The gene to which the phenotype is inferred to be associated.
    range: Gene
    required: false
  inferred_allele:
    name: inferred_allele
    description: The allele to which the phenotype is inferred to be associated.
    range: Allele
    required: false
  asserted_genes:
    name: asserted_genes
    required: false
  asserted_alleles:
    name: asserted_alleles
    required: false
attributes:
  inferred_allele:
    name: inferred_allele
    description: The allele to which the phenotype is inferred to be associated.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: inferred_allele
    owner: AGMPhenotypeAnnotation
    domain_of:
    - AGMPhenotypeAnnotation
    - AGMDiseaseAnnotation
    range: Allele
    required: false
  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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    domain_of:
    - AllelePhenotypeAnnotation
    - AGMPhenotypeAnnotation
    - AlleleDiseaseAnnotation
    - AGMDiseaseAnnotation
    range: Gene
    required: false
    multivalued: true
  asserted_alleles:
    name: asserted_alleles
    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_alleles
    owner: AGMPhenotypeAnnotation
    domain_of:
    - AGMPhenotypeAnnotation
    - AGMDiseaseAnnotation
    range: Allele
    required: false
    multivalued: true
  phenotype_annotation_subject:
    name: phenotype_annotation_subject
    description: The AGM 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: AGMPhenotypeAnnotation
    domain_of:
    - PhenotypeAnnotation
    range: AffectedGenomicModel
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    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: AGMPhenotypeAnnotation
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean