Link Search Menu Expand Document

Class: MolecularEntity

A molecular entity is a chemical entity composed of individual or covalently bonded atoms.

URI: biolink:MolecularEntity


img


Identifier prefixes

  • PUBCHEM.COMPOUND
  • CHEMBL.COMPOUND
  • UNII
  • CHEBI
  • DRUGBANK
  • MESH
  • CAS
  • DrugCentral
  • GTOPDB
  • HMDB
  • KEGG.COMPOUND
  • ChemBank
  • PUBCHEM.SUBSTANCE
  • SIDER.DRUG
  • INCHI
  • INCHIKEY
  • KEGG.GLYCAN
  • KEGG.DRUG
  • KEGG.ENVIRON
  • KEGG
  • UMLS

Parents

  • is_a: ChemicalEntity - A chemical entity is a physical entity that pertains to chemistry or biochemistry.

Children

  • 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.
  • SmallMolecule - A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).

Referenced by class

Attributes

Own

  • is metabolite 0..1
    • Description: indicates whether a molecular entity is a metabolite
    • Range: Boolean

Inherited from chemical entity:

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}
  • type 0..*
  • 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 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 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}

Domain for slot:

  • is metabolite 0..1
    • Description: indicates whether a molecular entity is a metabolite
    • Range: Boolean

Other properties

     
In Subsets:   translator_minimal
Narrow Mappings:   STY:T088
    STY:T085
    CHEBI:23367
    bioschemas:MolecularEntity