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 |
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You can read the release version of this specification here.
Key to specification table
- Green properties/types are proposed by Bioschemas, or indicate proposed changes by Bioschemas to Schema.org
- Red properties/types exist in the core of Schema.org
- Blue properties/types exist in the pending area of Schema.org
- Black properties/types are reused from external vocabularies/ontologies
CD = Cardinality
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 |
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name |
Text |
Schema: The name of the item. |
ONE |
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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 |
|
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description |
Text |
Schema: A description of the item. |
ONE |
|
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taxonomicRange |
Taxon Text URL |
Schema: The taxonomic grouping of the organism that expresses the Phenotype. |
NCBITaxon |
|
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url |
URL |
Schema: URL of the item. Bioschemas: Link to the official webpage associated to this entity. |
ONE |
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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 |
|
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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 |
|
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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 |
|
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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 |
|
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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 |
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