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Phenotype DRAFT Profile

Version: 0.2-DRAFT (05 June 2020)

Bioschemas profile describing a Phenotype 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 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.

Changes from Previous Version

  • isAssociatedWith BioChemEntity switch to recommended and renamed as bioChemAssociation with an improved description
  • taxonomicRange switch to recommended
  • image switch to optional and many
  • additionalType dropped
  • additionalProperty description changed
  • new property: associatedDisease
  • new properties for GO associations: hasMolecularFunction, isInvolvedInBiologicalProcess and isLocatedInSubcellularLocation

Latest profiles

Latest release: none

Latest draft: 0.2-DRAFT

Previous profiles

Previous version: 0.1-DRAFT-2018_11_15


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

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.
bioChemAssociation BioChemEntity
Schema:

BioChemEntity, e.g., gene, associated to this Phenotype and relevant for its characterization, particularly useful for the molecular basis of this Phenotype.


MANY
View ≪bioChemAssociation≫ example
description Text
Schema:

A description of the item.


ONE
View ≪description≫ example
taxonomicRange Taxon
Text
URL
Schema:

The taxonomic grouping of the organism that expresses the Phenotype.


NCBITaxon

View ≪taxonomicRange≫ 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:

Before using this property, make sure none of the existing ones covers your case. Whenever possible, please use a property coined in a third-party well-know vocabulary. Please always use (i) property name to specify the name of the property, (ii) additionalType (if possible) to better specify the nature of the property (e.g., link to the third-party well-known vocabulary term), 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
associatedDisease MedicalCondition
PropertyValue
URL
Schema:

Disease associated to this BioChemEntity. Such a disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.


MANY

Any term from a suitable ontology such as OMIM, DO,

View ≪associatedDisease≫ example
hasMolecularFunction DefinedTerm
PropertyValue
URL
Schema:

Molecular function performed by this Phenotype.


MANY

GO molecular function branch

image ImageObject
URL
Schema:

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


MANY
View ≪image≫ example
isInvolvedInBiologicalProcess DefinedTerm
PropertyValue
URL
Schema:

Biological process this Phenotype is involved in.


MANY

GO biological process branch

isLocatedInSubcellularLocation DefinedTerm
PropertyValue
URL
Schema:

Subcellular location where this Phenotype is located.


MANY

GO subcellular location branch

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
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

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