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Class: AccessibleDnaRegion

Description: A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose

Aliases: dnase-seq accessible region, atac-seq accessible region

classDiagram class AccessibleDnaRegion GenomicEntity <|-- AccessibleDnaRegion ChemicalEntityOrGeneOrGeneProduct <|-- AccessibleDnaRegion PhysicalEssence <|-- AccessibleDnaRegion OntologyClass <|-- AccessibleDnaRegion RegulatoryRegion <|-- AccessibleDnaRegion AccessibleDnaRegion : category AccessibleDnaRegion : deprecated AccessibleDnaRegion : description AccessibleDnaRegion : full_name AccessibleDnaRegion : has_attribute AccessibleDnaRegion --|> Attribute : has_attribute AccessibleDnaRegion : has_biological_sequence AccessibleDnaRegion : id AccessibleDnaRegion : in_taxon AccessibleDnaRegion --|> OrganismTaxon : in_taxon AccessibleDnaRegion : in_taxon_label AccessibleDnaRegion : iri AccessibleDnaRegion : name AccessibleDnaRegion : provided_by AccessibleDnaRegion : synonym AccessibleDnaRegion : type AccessibleDnaRegion : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
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

LinkML Source

name: accessible dna region
description: A region (or regions) of a chromatinized genome that has been measured
  to be more accessible to an enzyme such as DNase-I or Tn5 Transpose
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- dnase-seq accessible region
- atac-seq accessible region
exact_mappings:
- SO:0002231
is_a: regulatory region
mixins:
- genomic entity
- chemical entity or gene or gene product
- physical essence
- ontology class