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Class: GenomicBackgroundExposure

Description: A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.
classDiagram class GenomicBackgroundExposure GeneGroupingMixin <|-- GenomicBackgroundExposure PhysicalEssence <|-- GenomicBackgroundExposure GenomicEntity <|-- GenomicBackgroundExposure ThingWithTaxon <|-- GenomicBackgroundExposure OntologyClass <|-- GenomicBackgroundExposure ExposureEvent <|-- GenomicBackgroundExposure GenomicBackgroundExposure : category GenomicBackgroundExposure : deprecated GenomicBackgroundExposure : description GenomicBackgroundExposure : equivalent_identifiers GenomicBackgroundExposure : exposure_additional_condition GenomicBackgroundExposure : exposure_duration GenomicBackgroundExposure : exposure_end_age GenomicBackgroundExposure : exposure_magnitude GenomicBackgroundExposure : exposure_route GenomicBackgroundExposure : exposure_start_age GenomicBackgroundExposure : exposure_type GenomicBackgroundExposure : exposure_vehicle GenomicBackgroundExposure : full_name GenomicBackgroundExposure : has_attribute GenomicBackgroundExposure --|> Attribute : has_attribute GenomicBackgroundExposure : has_biological_sequence GenomicBackgroundExposure : has_gene_or_gene_product GenomicBackgroundExposure --|> Gene : has_gene_or_gene_product GenomicBackgroundExposure : id GenomicBackgroundExposure : in_taxon GenomicBackgroundExposure --|> OrganismTaxon : in_taxon GenomicBackgroundExposure : in_taxon_label GenomicBackgroundExposure : information_content GenomicBackgroundExposure : iri GenomicBackgroundExposure : name GenomicBackgroundExposure : provided_by GenomicBackgroundExposure : synonym GenomicBackgroundExposure : taxon GenomicBackgroundExposure : timepoint GenomicBackgroundExposure : type GenomicBackgroundExposure : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
has_gene_or_gene_product:
connects an entity with one or more gene or gene products
*
Gene		 GeneGroupingMixin
has_biological_sequence:
connects a genomic feature to its sequence 		0..1
BiologicalSequence		 GenomicEntity
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
id:
Could generally be a CURIE from a suitable exposure ontology like ECTO. 		1
String		 Entity, OntologyClass
timepoint:
a point in time 		0..1
TimeType		 ExposureEvent
exposure_type:
Type of exposure 		0..1
String		 ExposureEvent
exposure_vehicle:
Type of an exposure event. 		0..1
String		 ExposureEvent
exposure_route:
Route of exposure. 		0..1
String		 ExposureEvent
exposure_start_age:
Starting age of an exposure event. 		0..1
Integer		 ExposureEvent
exposure_end_age:
Ending stage of an exposure event. 		0..1
Integer		 ExposureEvent
exposure_duration:
Duration of an exposure event. 		0..1
Time		 ExposureEvent
exposure_magnitude:
Magnitude of an exposure event, e.g, parts per million of a toxic chemical. 		0..1
String		 ExposureEvent
exposure_additional_condition:
Additional conditions impacting an exposure event. 		0..1
String		 ExposureEvent
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
equivalent_identifiers:
A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources. 		*
Uriorcurie		 NamedThing
information_content:
Information content (IC) value for a term, primarily from Automats. 		0..1
Float		 NamedThing
taxon:
A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology. 		0..1
Uriorcurie		 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

LinkML Source

name: genomic background exposure
description: A genomic background exposure is where an individual's specific genomic
  background of genes, sequence variants or other pre-existing genomic conditions
  constitute a kind of 'exposure' to the organism, leading to or influencing an outcome.
from_schema: https://w3id.org/biolink/vocab/
is_a: exposure event
mixins:
- gene grouping mixin
- physical essence
- genomic entity
- thing with taxon
- ontology class