Phenotype DRAFT Profile

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: alternateName
{
    "@type": "Phenotype",
    "alternateName": "abnormal finger morphology"
}


//Property: anatomicalLocation
{
  "@type": "Phenotype",
  "anatomicalLocation": {
                "@type": "DefinedTerm",
                "name": "limb digit",
                "inDefinedTermSet": "http://purl.obolibrary.org/obo/emapa.owl",
                "termCode": "EMAPA_32725"
        }
}


//Property: associatedDisease
{
  "@type": "Phenotype",
        "associatedDisease": "https://omim.org/entry/605909?search=parkinson&highlight=parkinson"
}


//Property: bioChemAssociation
{
  "@type": "Phenotype",
        "isAssociatedWith": {
                "@type": "Gene",
                "name": "Ascc2"
        }
}


//Property: description
{
    "@type": "Phenotype",
    "description": "any structural anomaly of the fingers or toes"
}


//Property: identifier
//Using a text
{
    "@type": "Phenotype",
    "identifier": "MP:0002110"
}
//Using a URL directly (looks like a text)
{
    "@type": "Phenotype",
    "identifier": "http://purl.obolibrary.org/obo/MP_0002110"
}
//Using a URL modeled as schema:URL (equivalent to the previous one but more verbose)
{
    "@type": "Phenotype",
    "identifier": {
      "@type": "URL",
      "url": "http://purl.obolibrary.org/obo/MP_0002110"
    }
}


//Property: image
//Using a URL directly (looks like a text)
{
  "@type": "Phenotype",
  "image": "http://www.ebi.ac.uk/mi/impc/phenotype-archive/media/images/900/M00571072_00021593_download_tn_large.jpg"
}



//Property: mainEntityOfPage
//Preferred way from DataRecord
{

  "@type": "DataRecord",
  "@id": "http://www.mousephenotype.org/data/phenotypes/MP:0002110"
  "mainEntity": {
    "@type": "Phenotype",
    "name": "Name and any other property for this Phenotype entity"
  }
}

//Also possible from Phenotype
{
  "@type": "Phenotype",
  "mainEntityOfPage": { "@id": "http://www.mousephenotype.org/data/phenotypes/MP:0002110" }
}


//Property: name
{
  "@type": "Phenotype",
  "name": "abnormal digit morphology"
}


//Property: sameAs
{
  "@type": "Phenotype",
  "sameAs": "http://www.informatics.jax.org/vocab/mp_ontology/MP:0002110"
}


//Property: taxonomicRange
{
  "@type": "Phenotype",
   "taxonomicRange": {
                "@type": "Taxon",
                "name": "Mus musculus",
                "url": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090"
      }
}


//Property: url
{
  "@type": "Phenotype",
  "url": "http://www.mousephenotype.org/data/phenotypes/MP:0002110"
}


//Property: valueReference
{
  "@type": "Phenotype",
   "valueReference": {
                "@type": "DefinedTerm",
                "inDefinedTermSet": "http://purl.obolibrary.org/obo/mp.owl",
                "termCode": "MP:0002110"
        }
}

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 Property ≪identifier≫ example `//Using a text { "@type": "Phenotype", "identifier": "MP:0002110" } //Using a URL directly (looks like a text) { "@type": "Phenotype", "identifier": "http://purl.obolibrary.org/obo/MP_0002110" } //Using a URL modeled as schema:URL (equivalent to the previous one but more verbose) { "@type": "Phenotype", "identifier": { "@type": "URL", "url": "http://purl.obolibrary.org/obo/MP_0002110" } }`
name	Text	Schema: The name of the item.	ONE		View ≪name≫ example Property ≪name≫ example `{ "@type": "Phenotype", "name": "abnormal digit morphology" }`
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 Property ≪bioChemAssociation≫ example `{ "@type": "Phenotype", "isAssociatedWith": { "@type": "Gene", "name": "Ascc2" } }`
description	Text	Schema: A description of the item.	ONE		View ≪description≫ example Property ≪description≫ example `{ "@type": "Phenotype", "description": "any structural anomaly of the fingers or toes" }`
taxonomicRange	Taxon Text URL	Schema: The taxonomic grouping of the organism that expresses the Phenotype.		NCBITaxon	View ≪taxonomicRange≫ example Property ≪taxonomicRange≫ example `{ "@type": "Phenotype", "taxonomicRange": { "@type": "Taxon", "name": "Mus musculus", "url": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090" } }`
url	URL	Schema: URL of the item. Bioschemas: Link to the official webpage associated to this entity.	ONE		View ≪url≫ example Property ≪url≫ example `{ "@type": "Phenotype", "url": "http://www.mousephenotype.org/data/phenotypes/MP:0002110" }`
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 Property ≪alternateName≫ example `{ "@type": "Phenotype", "alternateName": "abnormal finger morphology" }`
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 Property ≪anatomicalLocation≫ example `{ "@type": "Phenotype", "anatomicalLocation": { "@type": "DefinedTerm", "name": "limb digit", "inDefinedTermSet": "http://purl.obolibrary.org/obo/emapa.owl", "termCode": "EMAPA_32725" } }`
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 Property ≪associatedDisease≫ example `{ "@type": "Phenotype", "associatedDisease": "https://omim.org/entry/605909?search=parkinson&highlight=parkinson" }`
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 Property ≪image≫ example `//Using a URL directly (looks like a text) { "@type": "Phenotype", "image": "http://www.ebi.ac.uk/mi/impc/phenotype-archive/media/images/900/M00571072_00021593_download_tn_large.jpg" }`
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 Property ≪mainEntityOfPage≫ example `//Preferred way from DataRecord { "@type": "DataRecord", "@id": "http://www.mousephenotype.org/data/phenotypes/MP:0002110" "mainEntity": { "@type": "Phenotype", "name": "Name and any other property for this Phenotype entity" } } //Also possible from Phenotype { "@type": "Phenotype", "mainEntityOfPage": { "@id": "http://www.mousephenotype.org/data/phenotypes/MP:0002110" } }`
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 Property ≪sameAs≫ example `{ "@type": "Phenotype", "sameAs": "http://www.informatics.jax.org/vocab/mp_ontology/MP:0002110" }`
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 Property ≪valueReference≫ example `{ "@type": "Phenotype", "valueReference": { "@type": "DefinedTerm", "inDefinedTermSet": "http://purl.obolibrary.org/obo/mp.owl", "termCode": "MP:0002110" } }`