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MolecularEntity DRAFT Profile

Version: 0.2-draft (15 November 2018)

Bioschemas profile describing a MolecularEntity


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

Schema.org hierarchy

This Profile fits into the schema.org hierarchy as follows:

Thing > BioChemEntity > MolecularEntity

Description

This specification describes a MolecularEntity which is any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.





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


View all examples
Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
identifier PropertyValue
Text
URL
Schema:

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.


ONE
View ≪identifier≫ example
name Text
Schema:

The name of the item.


ONE
View ≪name≫ example
url URL
Schema:

URL of the item.


MANY
View ≪url≫ example
Marginality: Recommended.
inChI Text
Bioschemas:

Non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.

ONE
View ≪inChI≫ example
inChIKey Text
Bioschemas:

InChIKey is a hashed version of the full InChI (using the SHA-256 algorithm)

ONE
View ≪inChIKey≫ example
iupacName Text
Bioschemas:

Systematic method of naming organic chemical compounds as recommended by the International Union of Pure and Applied Chemistry (IUPAC).

ONE
View ≪iupacName≫ example
molecularFormula Text
Bioschemas:

The empirical formula is the simplest whole number ratio of all the atoms in a molecule.

ONE
View ≪molecularFormula≫ example
molecularWeight Number
Bioschemas:

This is the molecular weight of the entity being described, not of the parent.

ONE
View ≪molecularWeight≫ example
smiles Text
Bioschemas:

A specification in form of a line notation for describing the structure of chemical species using short ASCII strings

MANY
View ≪smiles≫ example
Marginality: Optional.
alternateName Text
Schema:

An alias for the item.


MANY
View ≪alternateName≫ example
biochemicalInteraction BioChemEntity
Bioschemas:

A BioChemEntity that is known to interact with the item.

MANY
View ≪biochemicalInteraction≫ example
biochemicalSimilarity BioChemEntity
Bioschemas:

A similar molecular entity, e.g., obtained by fingerprint similarity algorithms.

MANY
View ≪biochemicalSimilarity≫ example
biologicalRole DefinedTerm
Bioschemas:

A role played by the molecular entity within a biological context.

MANY

Any suitable ontology such as ChEBI biological role

View ≪biologicalRole≫ example
chemicalRole DefinedTerm
Bioschemas:

A role played by the molecular entity within a chemical context.

MANY

Any suitable ontology such as ChEBI Chemical Role

View ≪chemicalRole≫ example
description Text
Schema:

A description of the item.


ONE
disambiguatingDescription Text
Schema:

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.


ONE
image ImageObject
URL
Schema:

An image of the item. This can be a URL or a fully described ImageObject.


MANY
View ≪image≫ example
monoisotopicMolecularWeight Number
Bioschemas:

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.

ONE
View ≪monoisotopicMolecularWeight≫ example
potentialUse DefinedTerm
Bioschemas:

Intended use of the molecular entity by humans.

MANY

Any suitable ontology such as ChEBI Application

View ≪potentialUse≫ example
sameAs URL
Schema:

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.


MANY
View ≪sameAs≫ example

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