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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.


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.
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
description Text
 Schema:

A description of the item.


 ONE
taxonomicRange Taxon
Text
URL
 Schema:

The taxonomic grouping of the organism that expresses the Phenotype.

NCBITaxon
url URL
 Schema:

URL of the item.


Bioschemas:

Link to the official webpage associated to this entity.

 ONE
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
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,
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,
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
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
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
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