Class: NucleicAcidEntity

A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.

URI: biolink:NucleicAcidEntity

---

---

Identifier prefixes

• PUBCHEM.COMPOUND
• CHEMBL.COMPOUND
• UNII
• CHEBI
• MESH
• CAS
• GTOPDB
• HMDB
• KEGG
• KEGG.COMPOUND
• ChemBank
• PUBCHEM.SUBSTANCE
• INCHI
• INCHIKEY
• KEGG.GLYCAN
• KEGG.ENVIRON

Parents

• is_a: MolecularEntity - A molecular entity is a chemical entity composed of individual or covalently bonded atoms.

Uses Mixins

• mixin: GenomicEntity
• mixin: ThingWithTaxon - A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes
• mixin: PhysicalEssence - Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.
• mixin: OntologyClass - a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.

Children

• CodingSequence
• Exon - A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
• Transcript - An RNA synthesized on a DNA or RNA template by an RNA polymerase.

Referenced by class

• GenomicSequenceLocalization object _1..1 NucleicAcidEntity
• GenomicSequenceLocalization subject _1..1 NucleicAcidEntity
• NucleicAcidEntity has sequence location _0..* NucleicAcidEntity
• SequenceFeatureRelationship object _1..1 NucleicAcidEntity
• SequenceFeatureRelationship subject _1..1 NucleicAcidEntity
• NucleicAcidEntity sequence location of _0..* NucleicAcidEntity

Attributes

Inherited from chemical entity:

• trade name _0..1
  • Range: ChemicalEntity
• available from _0..*
  • Range: DrugAvailabilityEnum
• max tolerated dose _0..1
  • Description: The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.
  • Range: String
• is toxic _0..1
  • Range: Boolean
• has chemical role _0..*
  • Description: A role is particular behaviour which a chemical entity may exhibit.
  • Range: ChemicalRole

Inherited from entity:

• id _1..1
  • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
  • Range: String
  • in subsets: (translator_minimal)
• iri _0..1
  • Description: An IRI for an entity. This is determined by the id using expansion rules.
  • Range: IriType
  • in subsets: (translator_minimal,samples)
• category _0..*
  • Description: 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)
• type _0..*
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• has attribute _0..*
  • Description: connects any entity to an attribute
  • Range: Attribute
  • in subsets: (samples)

Inherited from epigenomic entity:

• has biological sequence _0..1
  • Description: connects a genomic feature to its sequence
  • Range: BiologicalSequence

Inherited from gene product mixin:

• xref _0..*
  • Description: 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.
  • Range: Uriorcurie
  • in subsets: (translator_minimal)

Inherited from macromolecular machine mixin:

• name _0..1
  • Description: A human-readable name for an attribute or entity.
  • Range: LabelType
  • in subsets: (translator_minimal,samples)

Inherited from molecular entity:

• is metabolite _0..1
  • Description: indicates whether a molecular entity is a metabolite
  • Range: Boolean

Inherited from named thing:

• provided by _0..*
  • Description: 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.
  • Range: String
• category _0..*
  • Description: 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)

Inherited from thing with taxon:

• in taxon _0..*
  • Description: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
  • Range: OrganismTaxon
  • in subsets: (translator_minimal)
• in taxon label _0..1
  • Description: The human readable scientific name for the taxon of the entity.
  • Range: LabelType
  • in subsets: (translator_minimal)

Other properties