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Class: Genotype

Description: An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background
classDiagram class Genotype PhysicalEssence <|-- Genotype GenomicEntity <|-- Genotype OntologyClass <|-- Genotype BiologicalEntity <|-- Genotype Genotype : category Genotype : deprecated Genotype : description Genotype : full_name Genotype : has_attribute Genotype --|> Attribute : has_attribute Genotype : has_biological_sequence Genotype : has_zygosity Genotype --|> Zygosity : has_zygosity Genotype : id Genotype : in_taxon Genotype --|> OrganismTaxon : in_taxon Genotype : in_taxon_label Genotype : iri Genotype : name Genotype : provided_by Genotype : synonym Genotype : type Genotype : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
has_zygosity:
None
0..1
Zygosity		 direct
has_biological_sequence:
connects a genomic feature to its sequence 		0..1
BiologicalSequence		 GenomicEntity
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 OntologyClass, Entity
in_taxon:
connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon' 		*
OrganismTaxon		 ThingWithTaxon
in_taxon_label:
The human readable scientific name for the taxon of the entity. 		0..1
LabelType		 ThingWithTaxon
provided_by:
The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph. 		*
String		 NamedThing
xref:
A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references. 		*
Uriorcurie		 NamedThing
full_name:
a long-form human readable name for a thing 		0..1
LabelType		 NamedThing
synonym:
Alternate human-readable names for a thing 		*
LabelType		 NamedThing
iri:
An IRI for an entity. This is determined by the id using expansion rules. 		0..1
IriType		 Entity
category:
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing} 		1..*
Uriorcurie		 Entity
type:
None 		*
String		 Entity
name:
A human-readable name for an attribute or entity. 		0..1
LabelType		 Entity
description:
a human-readable description of an entity 		0..1
NarrativeText		 Entity
has_attribute:
connects any entity to an attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

Usages

used by used in type used
GenotypeToGenotypePartAssociation subject range Genotype
GenotypeToGenotypePartAssociation object range Genotype
GenotypeToGeneAssociation subject range Genotype
GenotypeToVariantAssociation subject range Genotype
GenotypeToEntityAssociationMixin subject range Genotype
GenotypeToPhenotypicFeatureAssociation subject range Genotype
GenotypeToDiseaseAssociation subject range Genotype
GenotypeAsAModelOfDiseaseAssociation subject range Genotype

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:

ID Prefix Usage
ZFIN Gene
Genotype
SequenceVariant
FB Pathway
Gene
Transcript
Polypeptide
Protein
GeneFamily
Genotype
SequenceVariant

LinkML Source

name: genotype
id_prefixes:
- ZFIN
- FB
description: An information content entity that describes a genome by specifying the
  total variation in genomic sequence and/or gene expression, relative to some established
  background
comments:
- Consider renaming as genotypic entity
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- GENO:0000536
- SIO:001079
is_a: biological entity
mixins:
- physical essence
- genomic entity
- ontology class
slots:
- has zygosity