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Protein Profile

Version: 0.12-DRAFT (10 June 2021)

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.


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
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
description Text
 Schema:

A description of the item.


Bioschemas:

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

 ONE
hasSequenceAnnotation SequenceAnnotation
URL
 Schema:

An annotation on the BioPolymerSequence associated with this BioChemEntity


 MANY
isEncodedByBioChemEntity Gene
 Schema:

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


 MANY

Any suitable ontology
taxonomicRange DefinedTerm
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
url URL
 Schema:

URL of the item.


Bioschemas:

Link to the official webpage associated to this entity.

 ONE
Marginality: Optional.
alternateName Text
 Schema:

An alias for the item.


Bioschemas:

Use it for alternate names of this Protein

 MANY
bioChemInteraction BioChemEntity
 Schema:

A BioChemEntity that is known to interact with this item.


 MANY

Any suitable source of information
bioChemSimilarity BioChemEntity
 Schema:

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


 MANY
hasBioChemEntityPart BioChemEntity
 Schema:

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


 MANY

Any suitable ontology
hasBioPolymerSequence Text
 Schema:

A symbolic representation of a BioChemEnity. For example, a nucleotide sequence of a Gene or an amino acid sequence of a Protein.


 MANY
hasMolecularFunction DefinedTerm
PropertyValue
URL
 Schema:

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


Bioschemas:

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

 MANY

Any suitable ontology
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 link to a page containing the corresponding sequence protein. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty.

 MANY
image ImageObject
URL
 Schema:

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


 MANY
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 GO ontology).

 MANY

Any suitable ontology
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 GO ontology).

 MANY

Any suitable ontology
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
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 representing this entity in a dataset.

 ONE
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