GitHub Twitter

Phenotype DRAFT Profile

Version: 0.1-draft (15 November 2018)

Bioschemas profile describing a Phenotype in Life Sciences


Contributors

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

Group Leader(s)
Other team members

Schema.org hierarchy

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

Thing > Phenotype

Description

This Phenotype type specification presents the markup for describing a Phenotype.





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
image ImageObject
URL
Schema:

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


ONE
View ≪image≫ example
url URL
Schema:

URL of the item.


Bioschemas:

Link to the official webpage associated to this entity.

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

An alias for the item.


MANY
View ≪alternateName≫ example
anatomicalLocation DefinedTerm
Schema:

Any part of an organism, typically a component of an anatomical system. Organs, tissues, and cells are all anatomical locations.


MANY

Any term from a suitable ontology such as Foundational Model of Anatomy Ontology, EMAPA,

View ≪anatomicalLocation≫ example
isAssociatedWith BioChemEntity
Schema:

BioChemEntity that has some association with this Phenotype


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 Taxon
Text
URL
Schema:

The taxonomic grouping of the organism that expresses the Phenotype.


NCBITaxon

View ≪taxonomicRange≫ example
valueReference DefinedTerm
Schema:

A DefinedTerm in this code set.


MANY

Any term from a suitable ontology such as Human Phenotype Ontology, Mammalian Phenotype Ontology, Plant Phenotype Ontology

View ≪valueReference≫ example

Top ▲