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MolecularEntity DRAFT Profile

Version: 0.2-DRAFT-2018_11_14 (14 November 2018)

Bioschemas profile describing a MolecularEntity


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


Key to specification table

CD = Cardinality

Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
@context URL Used to provide the context (namespaces) for the JSON-LD file.
Not needed in other serialisations.		 ONE
@type Text Schema.org/Bioschemas class for the resource declared using JSON-LD syntax. For other serialisations please use the appropriate mechanism.
While it is permissible to provide multiple types, it is preferred to use a single type.		 MANY Schema.org, Bioschemas
@id IRI Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach. ONE
dct:conformsTo IRI Used to state the Bioschemas profile that the markup relates to. The versioned URL of the profile must be used.
Note that we use a CURIE in the table here but the full URL for Dublin Core terms must be used in the markup (http://purl.org/dc/terms/conformsTo), see example.		 ONE Bioschemas profile versioned URL
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
name Text
 Schema:

The name of the item.


 ONE
url URL
 Schema:

URL of the item.


 MANY
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
inChIKey Text
 Bioschemas:

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

 ONE
iupacName Text
 Bioschemas:

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

 ONE
molecularFormula Text
 Bioschemas:

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

 ONE
molecularWeight Number
 Bioschemas:

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

 ONE
smiles Text
 Bioschemas:

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

 MANY
Marginality: Optional.
alternateName Text
 Schema:

An alias for the item.


 MANY
biochemicalInteraction BioChemEntity
 Bioschemas:

A BioChemEntity that is known to interact with the item.

 MANY
biochemicalSimilarity BioChemEntity
 Bioschemas:

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

 MANY
biologicalRole DefinedTerm
 Bioschemas:

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

 MANY

Any suitable ontology such as ChEBI biological role
chemicalRole DefinedTerm
 Bioschemas:

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

 MANY

Any suitable ontology such as ChEBI Chemical Role
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
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
potentialUse DefinedTerm
 Bioschemas:

Intended use of the molecular entity by humans.

 MANY

Any suitable ontology such as ChEBI Application
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