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MolecularEntity (Type)

Version: 0.3-RELEASE-2019_09_02 (2019-09-02)


If you spot any errors or omissions with this type, please file an issue in our GitHub.


Contributors

The following people have been involved in the creation of this specification document. They are all members of the Chemicals group.

Group Leader(s)
Other team members

Canonical URL

https://bioschemas.org/MolecularEntity

Schema.org hierarchy

This is a new Type that fits into the schema.org hierarchy as follows:
Thing > BioChemEntity > MolecularEntity

Description

Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. (Source: ChEBI:23367)

Latest types

Latest release: 0.3-RELEASE-2019_09_02

Previous types

Previous version: 0.2-RELEASE-2019_06_23

Previous release: 0.2-RELEASE-2019_06_23

Group Task & Issues
Chemicals



Key to specification table

Schema.org properties where the Expected Types have been changed, or new (i.e., Bioschemas created) properties/types are green.

Schema.org properties/types are red.

Pending Schema.org properties/types are blue.

External (i.e., from 3rd party ontology) properties/types are black.


CD = Cardinality


PropertyExpected TypeDescription
Properties from MolecularEntity
chemicalRole DefinedTerm A role played by the BioChemEntity within a chemical context.
inChI Text Non-proprietary identifier for molecular entity that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.
inChIKey Text InChIKey is a hashed version of the full InChI (using the SHA-256 algorithm).
iupacName Text Systematic method of naming chemical compounds as recommended by the International Union of Pure and Applied Chemistry (IUPAC).
molecularFormula Text The empirical formula is the simplest whole number ratio of all the atoms in a molecule.
molecularWeight QuantitativeValue  or
Text 
This is the molecular weight of the entity being described, not of the parent. Units should be included in the form '<Number> <unit>', for example '12 amu' or as '<QuantitativeValue>.
monoisotopicMolecularWeight QuantitativeValue  or
Text 
The monoisotopic mass is the sum of the masses of the atoms in a molecule using the unbound, ground-state, rest mass of the principal (most abundant) isotope for each element instead of the isotopic average mass. Please include the units the form '<Number> <unit>', for example '770.230488 g/mol' or as '<QuantitativeValue>.
potentialUse DefinedTerm Intended use of the BioChemEntity by humans.
smiles Text A specification in form of a line notation for describing the structure of chemical species using short ASCII strings.
Properties from BioChemEntity
associatedDisease MedicalCondition  or
PropertyValue  or
URL 
Disease associated to this BioChemEntity. Such disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.
bioChemInteraction BioChemEntity A BioChemEntity that is known to interact with this item.
bioChemSimilarity BioChemEntity A similar BioChemEntity, e.g., obtained by fingerprint similarity algorithms.
biologicalRole DefinedTerm A role played by the BioChemEntity within a biological context.
hasBioChemEntityPart BioChemEntity Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part.
Inverse property: isPartOfBioChemEntity.
hasMolecularFunction DefinedTerm  or
PropertyValue  or
URL 
Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.
hasRepresentation PropertyValue  or
Text  or
URL 
A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.
isEncodedByBioChemEntity Gene Another BioChemEntity encoding by this one.
Inverse property: encodesBioChemEntity.
isInvolvedInBiologicalProcess DefinedTerm  or
PropertyValue  or
URL 
Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.
isLocatedInSubcellularLocation DefinedTerm  or
PropertyValue  or
URL 
Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.
isPartOfBioChemEntity BioChemEntity Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity.
Inverse property: hasBioChemEntityPart.
taxonomicRange DefinedTerm  or
Taxon  or
Text  or
URL 
The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.
Properties from Thing
additionalType URL An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.
alternateName Text An alias for the item.
description Text A description of the item.
disambiguatingDescription Text A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.
identifier PropertyValue  or
Text  or
URL 
The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.
image ImageObject  or
URL 
An image of the item. This can be a URL or a fully described ImageObject.
mainEntityOfPage CreativeWork  or
URL 
Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.
Inverse property: mainEntity.
name Text The name of the item.
potentialAction Action Indicates a potential Action, which describes an idealized action in which this thing would play an 'object' role.
sameAs URL URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.
subjectOf CreativeWork  or
Event 
A CreativeWork or Event about this Thing.
Inverse property: about.
url URL URL of the item.

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