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Protein DRAFT Profile

Version: 0.9-DRAFT (20 August 2019)

Bioschemas profile describing a Protein in Life Sciences.


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 Proteins group.

Group Leader(s)

Maria Martin

Leyla Garcia

Other team members

Schema.org hierarchy

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

Thing > BioChemEntity > Protein

Description

This Protein profile specification presents the most common properties used for a Protein plus examples on how to use them.





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
Marginality: Recommended.
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.


Bioschemas:

Disease associated to this protein, if any.

MANY

Any suitable disease ontology

View ≪associatedDisease≫ example
description Text
Schema:

A description of the item.


Bioschemas:

Protein function. We recommend to start the description with “Function: […]”.

ONE
View ≪description≫ example
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.


Bioschemas:

Bioschemas Protein: This property could be used, for instance, to register a sequence protein as it is a representation of the protein. If you want to better define the nature of the representation, use a PropertyValue where, for instance, the property name is Sequence, the value are protein sequences, and the referenceValue id the canonical sequence.

MANY
View ≪hasRepresentation≫ example
isEncodedByBioChemEntity DNA
Gene
RNA
Schema:

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


MANY
View ≪isEncodedByBioChemEntity≫ example
taxonomicRange CategoryCode
Taxon
Text
URL
Schema:

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


Bioschemas:

Bioschemas Protein: For proteins, it is recommended to use this property to specify the taxon/organism corresponding to a genome including a expressed gene that can be translated to this protein. For taxon/organism, it is a good practice to use hasCategoryCode to point to a controlled vacabulary such as NCBI taxon or UniProt Taxonomy.

MANY

Taxonomies or any suitable controlled vocabulary

View ≪taxonomicRange≫ example
url URL
Schema:

URL of the item.


Bioschemas:

Link to the official webpage associated to this entity.

ONE
View ≪url≫ example
Marginality: Optional.
alternateName Text
Schema:

An alias for the item.


Bioschemas:

Use it for alternate names of this Protein

MANY
View ≪alternateName≫ example
bioChemInteraction BioChemEntity
Schema:

A BioChemEntity that is known to interact with this item.


MANY
View ≪bioChemInteraction≫ example
bioChemSimilarity BioChemEntity
Schema:

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


MANY
View ≪bioChemSimilarity≫ example
hasBioChemEntityPart BioChemEntity
URL
Schema:

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


MANY
hasMolecularFunction DefinedTerm
PropertyValue
URL
Schema:

Molecular function performed by this BioChemEntity


Bioschemas:

Gene Ontology term corresponding to the Molecular Function branch of the GO ontology.

MANY

Gene Ontology

View ≪hasMolecularFunction≫ example
image ImageObject
URL
Schema:

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


MANY
View ≪image≫ example
isInvolvedInBiologicalProcess DefinedTerm
PropertyValue
URL
Schema:

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


Bioschemas:

Functional term corresponding to the biological process (typically the Biological Process branch of the Gene Ontology).

MANY

Gene Ontology

View ≪isInvolvedInBiologicalProcess≫ example
isLocatedInSubcellularLocation DefinedTerm
PropertyValue
URL
Schema:

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


Bioschemas:

Functional term corresponding to the subcellular location (typically the Subcellular Location branch of the Gene Ontology).

MANY

Gene Ontology

View ≪isLocatedInSubcellularLocation≫ example
isPartOfBioChemEntity BioChemEntity
Schema:

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


Bioschemas:

Bioschemas Protein: For proteins, it can be used to link to protein sequence annotations such as domains, sites, regions, etc.

MANY

Any suitable ontology

View ≪isPartOfBioChemEntity≫ example
mainEntityOfPage CreativeWork
URL
Schema:

Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details. Inverse property: mainEntity.


Bioschemas:

Link to the main DataRecord or WebPage representing this entity in a dataset.

ONE
View ≪mainEntityOfPage≫ 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.


Bioschemas:

Link to any resource other than the Record and the official webpage, for instance a Wikipedia page.

MANY
View ≪sameAs≫ example

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