Class: NucleicAcidEntity
Description: 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.
Aliases: sequence feature, genomic entity
classDiagram
class NucleicAcidEntity
GenomicEntity <|-- NucleicAcidEntity
ThingWithTaxon <|-- NucleicAcidEntity
PhysicalEssence <|-- NucleicAcidEntity
OntologyClass <|-- NucleicAcidEntity
MolecularEntity <|-- NucleicAcidEntity
NucleicAcidEntity : available_from
NucleicAcidEntity --|> DrugAvailabilityEnum : available_from
NucleicAcidEntity : category
NucleicAcidEntity : deprecated
NucleicAcidEntity : description
NucleicAcidEntity : full_name
NucleicAcidEntity : has_attribute
NucleicAcidEntity --|> Attribute : has_attribute
NucleicAcidEntity : has_biological_sequence
NucleicAcidEntity : has_chemical_role
NucleicAcidEntity --|> ChemicalRole : has_chemical_role
NucleicAcidEntity : id
NucleicAcidEntity : in_taxon
NucleicAcidEntity --|> OrganismTaxon : in_taxon
NucleicAcidEntity : in_taxon_label
NucleicAcidEntity : iri
NucleicAcidEntity : is_metabolite
NucleicAcidEntity : is_toxic
NucleicAcidEntity : max_tolerated_dose
NucleicAcidEntity : name
NucleicAcidEntity : provided_by
NucleicAcidEntity : synonym
NucleicAcidEntity : trade_name
NucleicAcidEntity : type
NucleicAcidEntity : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| 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: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1 String |
OntologyClass, Entity | |
| is_metabolite: indicates whether a molecular entity is a metabolite |
0..1 Boolean |
MolecularEntity | |
| trade_name: |
0..1 String |
ChemicalEntity | |
| available_from: |
* DrugAvailabilityEnum |
ChemicalEntity | |
| max_tolerated_dose: 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. |
0..1 String |
ChemicalEntity | |
| is_toxic: |
0..1 Boolean |
ChemicalEntity | |
| has_chemical_role: A role is particular behaviour which a chemical entity may exhibit. |
* ChemicalRole |
ChemicalEntity | |
| 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 |
|---|---|---|---|
| Genotype | has_zygosity | domain | NucleicAcidEntity |
| GenomicSequenceLocalization | subject | range | NucleicAcidEntity |
| GenomicSequenceLocalization | object | range | NucleicAcidEntity |
| SequenceFeatureRelationship | subject | range | NucleicAcidEntity |
| SequenceFeatureRelationship | object | range | NucleicAcidEntity |
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
LinkML Source
name: nucleic acid entity
id_prefixes:
- PUBCHEM.COMPOUND
- CHEMBL.COMPOUND
- UNII
- CHEBI
- MESH
- CAS
- GTOPDB
- HMDB
- KEGG
- KEGG.COMPOUND
- ChemBank
- PUBCHEM.SUBSTANCE
- INCHI
- INCHIKEY
- KEGG.GLYCAN
- KEGG.ENVIRON
- ChemBank
- SIDER.DRUG
- BIGG.METABOLITE
- foodb.compound
- UMLS
description: 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.
in_subset:
- model_organism_database
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- sequence feature
- genomic entity
exact_mappings:
- SO:0000110
narrow_mappings:
- STY:T086
- STY:T114
is_a: molecular entity
mixins:
- genomic entity
- thing with taxon
- physical essence
- ontology class