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Gene DRAFT Profile

Version: 0.6-DRAFT-2020_04_02 (02 April 2020)

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.


Contributors

The following people have been involved in the creation of this specification document. They are all members of the Genes group.

Group Leader(s)
Other team members

Schema.org hierarchy

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

Thing > BioChemEntity > Gene

Description

This Gene profile specification presents the markup for describing a Gene.

Summary of Changes

Changes introduced on Gene profile 0.6-DRAFT-2020_04_02 in response to issue 353
  • encodes property updated to encodesBioChemEntity, still recommended
  • additionalProperty removed
  • associatedDisease range updated
  • examples using DefinedTerm now include link to external vocabularies via property inDefinedTermSet (hasMolecularFunction, isInvolvedInBiologicalProcess, taxonomicRange). Note: isTranscribedInto and isVariantOf do not exist on the Gene type so they were removed, isVariantOf was replaced on Gene type by alternativeOf)
  • hasCategoryCode property removed
Additional changes after looking at BioChemEntity and Gene types:
  • hasRepresentation moved to optional. There is another property
  • hasBioPolymerSequence for the sequence text. hasRepresentation can be used to link to a page containing the corresponding sequence so both are now optional and people can decide which one suits better to them
  • properties directly from Gene type not previously included on the Gene profile were added as optional (expressedIn and hasStatus)

Latest profiles

Latest release: 0.7-RELEASE

Previous profiles

Previous version: 0.5-DRAFT-2019_06_14


Group Use Cases Cross Walk Task & Issues Examples Live Deploys
Genes

You can read the release version of this specification here.




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.
description Text
Schema:

A description of the item.


ONE
View ≪description≫ example
encodesBioChemEntity BioChemEntity
Schema:

This property is used to link to gene products encoded (even indirectly) from this gene such as RNA or proteins.


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
View ≪encodesBioChemEntity≫ example
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
View ≪isPartOfBioChemEntity≫ 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.


MANY
View ≪alternateName≫ example
alternativeOf Gene
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


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


Bioschemas:

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

MANY
View ≪hasBioChemEntityPart≫ example
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)

View ≪hasMolecularFunction≫ 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:

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
View ≪hasRepresentation≫ example
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
View ≪image≫ example
isInvolvedInBiologicalProcess DefinedTerm
PropertyValue
URL
Bioschemas:

GO biological process this gene/protein is involved in.

MANY

Only the biological process branch of Gene Ontology (GO)

View ≪isInvolvedInBiologicalProcess≫ example
isLocatedInSubcellularLocation DefinedTerm
PropertyValue
URL
Bioschemas:

GO subcellular location this gene/protein is located in.

MANY

Only the subcellular location branch of Gene Ontology (GO)

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 via DataRecord to the main DataRecord representing this entity in a dataset. It is usually preferred to use mainEntity from a DataRecord to point to its corresponding entity.

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.


MANY
View ≪sameAs≫ example
taxonomicRange DefinedTerm
Taxon
Text
URL
Schema:

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


View ≪taxonomicRange≫ example

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