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MolecularEntity Profile

Version: 0.5-RELEASE (07 April 2020)

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 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
name Text
 Schema:

The name of the item.


 ONE
url URL
 Schema:

URL of the item.


 MANY
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
inChIKey Text
 Schema:

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


 ONE
iupacName Text
 Schema:

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


 ONE
molecularFormula Text
 Schema:

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


 ONE
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
smiles Text
 Schema:

A specification in form of a line notation for describing the structure of chemical species using short ASCII strings. Double bond stereochemistry \ indicators may need to be escaped in the string in formats where the backslash is an escape character.


 MANY
Marginality: Optional.
alternateName Text
 Schema:

An alias for the item.


 MANY
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
bioChemSimilarity BioChemEntity
 Schema:

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


 MANY
biologicalRole DefinedTerm
 Schema:

A role played by the BioChemEntity within a biological context.


 MANY

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

A role played by the BioChemEntity 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
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
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
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
taxonomicRange DefinedTerm
Taxon
Text
URL
 Schema:

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