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MolecularEntity DRAFT Type

Version: 0.2-RC (2019-06-14)


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

http://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.




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


Property Expected Type Description
Properties from MolecularEntity (pending schema.org integration).
chemicalRole DefinedTerm A role played by the molecular entity within a chemical contex.
inChI Text Non-proprietary identifier for chemical substances 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 organic 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 Mass This is the molecular weight of the entity being described, not of the parent. Units should be included in the form '<Number> <Mass unit of measure>', for example '0.01 mg'.
monoisotopicMolecularWeight Mass 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> <Mass unit of measure>', for example '0.01 mg'.
potentialUse DefinedTerm Intended use of the molecular entity 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 (pending schema.org integration).
associatedDisease MedicalCondition or
PropertyValue or
URL
Disease associated to this BioChemEntity. Such a 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 know to interact with this item.
bioChemSimilarity BioChemEntity A similar molecular entity, e.g., obtained by fingerprint similarity algorithm.
biogicalRole DefinedTerm A role played by the molecular entity 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
PropertyValueor
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 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 descripton 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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