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MolecularEntity DRAFT Profile

Version: 0.4-DRAFT (11 November 2019)

Bioschemas profile describing a MolecularEntity


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

Schema.org hierarchy

This Profile 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)





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 ofThing, 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
Schema:

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


ONE
View ≪inChI≫ example
inChIKey Text
Schema:

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


ONE
View ≪inChIKey≫ example
iupacName Text
Schema:

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


ONE
View ≪iupacName≫ example
molecularFormula Text
Schema:

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


ONE
View ≪molecularFormula≫ example
molecularWeight QuantitativeValue
Text
Schema:

This is the molecular weight of the entity being described, not of the parent. Units should be included in the form ‘ ', for example '12 amu' or as '.


ONE
View ≪molecularWeight≫ example
smiles Text
Schema:

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
associatedDisease MedicalCondition
PropertyValue
URL
Schema:

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.


MANY
bioChemInteraction BioChemEntity
Schema:

A BioChemEntity that is known to interact with this item.


MANY
View ≪bioChemInteraction≫ example
bioChemSimilarity BioChemEntity
Schema:

A similar BioChemEntity, e.g., obtained by fingerprint similarity algorithms.


MANY
View ≪bioChemSimilarity≫ example
biologicalRole DefinedTerm
Schema:

A role played by the BioChemEntity within a biological context.


MANY

Any suitable ontology such as ChEBI biological role

View ≪biologicalRole≫ example
chemicalRole DefinedTerm
Schema:

A role played by the BioChemEntity 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
hasBioChemEntityPart BioChemEntity
Schema:

Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property:isPartOfBioChemEntity.


hasMolecularFunction DefinedTerm
PropertyValue
URL
Schema:

Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.


hasRepresentation PropertyValue
Text
URL
Schema:

A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.


image ImageObject
URL
Schema:

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


MANY
View ≪image≫ example
isEncodedByBioChemEntity Gene
Schema:

Another BioChemEntity encoding by this one. Inverse property:encodesBioChemEntity.


isInvolvedInBiologicalProcess DefinedTerm
PropertyValue
URL
Schema:

Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.


isLocatedInSubcellularLocation DefinedTerm
PropertyValue
URL
Schema:

Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.


isPartOfBioChemEntity BioChemEntity
Schema:

Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property:hasBioChemEntityPart.


monoisotopicMolecularWeight QuantitativeValue
Text
Schema:

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 ‘ ', for example '770.230488 g/mol' or as '.


ONE
potentialUse DefinedTerm
Schema:

Intended use of the BioChemEntity 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
taxonomicRange DefinedTerm
Taxon
Text
URL
Schema:

The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.


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