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Gene DRAFT Profile

Version: 1.1-DRAFT (24 June 2021)

Bioschemas profile describing a Gene 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.
description Text
 Schema:

A description of the item.


 ONE
encodesBioChemEntity BioChemEntity
 Schema:

Another BioChemEntity encoded by this one. Inverse property: isEncodedByBioChemEntity


Bioschemas:

For genes, this property is used to express in a generic way gene products encoded by this gene, for instance RNA or Protein.

 MANY
hasSequenceAnnotation SequenceAnnotation
URL
 Schema:

An annotation on the BioPolymerSequence associated with this BioChemEntity


Bioschemas:

For genes, it can be used to link to gene sequence annotations such as variants or so.

 MANY
isPartOfBioChemEntity BioChemEntity
 Schema:

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


Bioschemas:

For genes, it is recommended to at least specify the DNA/chromosome containing this gene

 MANY
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.


 MANY
alternativeOf Gene
 Schema:

Another gene which is a variation of this one.


Bioschemas:

Is variant of. Use this property to express when a gene is a variant of any other gene.

 MANY
associatedDisease MedicalCondition
PropertyValue
URL
 Schema:

Disease associated to this BioChemEntity


 MANY
expressedIn AnatomicalStructure
AnatomicalSystem
BioChemEntity
DefinedTerm
 Schema:

Tissue, organ, biological sample, etc in which activity of this gene has been observed experimentally. For example brain, digestive system.


 MANY
hasBioChemEntityPart BioChemEntity
 Schema:

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


 MANY
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.


 ONE
hasMolecularFunction DefinedTerm
PropertyValue
URL
 Bioschemas:

GO molecular function enabled by the gene/protein.

 MANY

Only the molecular function branch of Gene Ontology (GO)
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:

For genes it can be used to link to a page with the corresponding sequence. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty or a third-party ontology predicate.

 MANY
hasStatus Text
 Schema:

One of pseudogene, dead, killed, live, predicted, suppressed.


 ONE
image ImageObject
URL
 Schema:

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


 ONE
isInvolvedInBiologicalProcess DefinedTerm
PropertyValue
URL
 Bioschemas:

GO biological process this gene/protein is involved in.

 MANY

Only the biological process branch of Gene Ontology (GO)
isLocatedInSubcellularLocation DefinedTerm
PropertyValue
URL
 Bioschemas:

GO subcellular location this gene/protein is located in.

 MANY

Only the subcellular location branch of Gene Ontology (GO)
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.


 MANY

Taxonomies or any suitable controlled vocabulary