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Gene DRAFT Specification v. 0.2-draft

Bioschemas specification describing a Gene (BioChemEntity profile) in Life Sciences


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

Description

This Gene profile specification presents the BioChemEntity usage when describing a Gene.


Schema.org hierarchy

This is a new Profile that fits into the schema.org hierarchy as follows:

Thing > BioChemEntity



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.
SIO:is translated into BioChemEntity
Protein
Bioschemas:

SIO:010082 (is translated into). For genes, this property is used to link to gene products translated (even indirectly) from this gene such as proteins.

MANY

SIO

View ≪SIO:is translated into≫ example
description Text
Schema:

A description of the item.


ONE
View ≪description≫ example
hasRepresentation PropertyValue
Text
URL
Schema:

A representation for this entity other than, for instance, an image (used image property for that) or the main web page/record (use mainEntityOfPage for that, and see background notes, http://schema.org/docs/datamodel.html#mainEntityBackground, for sameAs and url).


Bioschemas:

For genes, this property could be used, for instance, to register a gene sequence as its representation. 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
image ImageObject
URL
Schema:

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


ONE
View ≪image≫ example
isContainedIn BioChemEntity
Schema:
Bioschemas:

Indicates a BioChemEntity that this BioChemEntity is (in some sense) part of.

Bioschemas Gene: For genes, it is recommended to at least specify the DNA/chromosome containing this gene and the taxon/organism associated to it. For taxon/organism, it is a good practice to use categoryCode to point to a controlled vocabulary such as NCBI taxon or UniProt Taxonomy.

MANY
View ≪isContainedIn≫ example
url URL
Schema:

URL of the item.


Bioschemas:

Link to the official webpage associated to this entity.

ONE
View ≪url≫ example
Marginality: Optional.
SIO:encodes BioChemEntity
Bioschemas:

SIO:010078 (encodes). For genes, this property is used to express in a generic way gene products encoded by this gene. Two more specific properties SIO:010082 and SIO:010080 should be used for translation and transcription respectevely.

MANY

SIO

SIO:is transcribed into BioChemEntity
Bioschemas:

SIO:010080 (is transcribed into). For genes, this property is used to link to gene products transcribed from this gene such as RNA.

MANY

SIO

SIO:is variant of BioChemEntity
Gene
Bioschemas:

SIO: 000272 (is variant of). Use this property to express when a gene is a variant of any other gene.

MANY

SIO

additionalProperty PropertyValue
Schema:

A property-value pair representing an additional characteristics of the entitity, e.g. a product feature or another characteristic for which there is no matching property in schema.org.

Note: Publishers should be aware that applications designed to use specific schema.org properties (e.g. http://schema.org/width, http://schema.org/color, http://schema.org/gtin13, …) will typically expect such data to be provided using those properties, rather than using the generic property/value mechanism.


Bioschemas:

Whenever possible, please use a property coined in a third-party well-know vocabulary. For instance, you can directly use http://purl.obolibrary.org/obo/RO_0002327 as a property to express how a protein or gene enables some GO molecular function. If you still want or need to use additionalProperty, please use (i) property name to specify the name of the property, (ii) additionalType (if possible) to better specify the nature of the property, and (iii) value to link to the object/range of this property.

MANY
additionalType URL
Schema:

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.


Bioschemas:

Any ontology term describing the gene concept. This is in addition to the official type used in Bioschemas.

Bioschemas Gene: Official proposed term for the profile describing a gene: SO:gene.

MANY
View ≪additionalType≫ example
alternateName Text
Schema:

An alias for the item.


MANY
View ≪alternateName≫ example
categoryCode CategoryCode
Schema:

A controlled vocabulary term equivalent to this entity. For instance, an organism coined in NCBI taxonomy can be represented as a BioChemEntity. As it also exists as a term in an ontology, it would be nice to capture that information via categoryCode.


MANY
contains BioChemEntity
Schema:

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


Bioschemas:

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

MANY
View ≪contains≫ example
location Place
PostalAddress
PropertyValue
Text
URL
Schema:

The location of for example where the event is happening, an organization is located, or where an action takes place.


Bioschemas:

For a particular gene, the molecular location is a precise description of its position in a chromosome. The molecular location is based on the sequence of DNA that make up the chromosome.

MANY
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

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