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Protein Specification v. 0.0.4

Bioschemas specification describing a Protein (PhysicalEntity profile) in Life Sciences

Profile

Thing
Bioschemas specifications and types list.

Description:

This Protein profile specification presents the PhysicalEntity usage when describing a Protein.


Property Expected Type Description CD Controlled Vocabulary
Cardinality: Minimum.
additionalType URL
An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.
MANY SIO
identifier PropertyValue
Text
URL
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
additionalProperty.transcribed_from PropertyValue
“additionalProperty” : {  “additionalType”: “http://semanticscience.org/resource/SIO_010081”  “name”: “transcribed from”,  “value”: {    “@type”: “StructuredValue”    additionalType: “http://semanticscience.org/resource/SIO_010035”,    “name”: “”  } }
ONE SIO SIO
isContainedIn.organism PhysicalEntity
"isContainedIn": {    "@type": "PhysicalEntity",      "additionalType": "http://semanticscience.org/resource/SIO_010000",    "identifier": "",    "name": "Homo sapiens",    "url": ""  }
ONE
Cardinality: Recommended.
alternateName Text
An alias for the item.
MANY
description Text
A description of the item.
ONE
name Text
The name of the item.
ONE
url URL
URL of the item.
ONE
additionalProperty.disease_ association PropertyValue
“additionalProperty” : {  “additionalType”: “http://semanticscience.org/resource/SIO_000983”  “name”: “disease association”,  “value”: {    “@type”: [“StructuredValue”, “MedicalCondition”],    “additionalType”: “http://semanticscience.org/resource/SIO_010299”,    “name”: “”,    “identifier”: “”,    "code": {        "@type": "MedicalCode",        "code": "",        "codingSystem": ""      }  } }
MANY SIO SIO
Cardinality: Optional.
image ImageObject
URL
An image of the item. This can be a URL or a fully described ImageObject.
MANY
mainEntityOfPage CreativeWork
URL
Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.
ONE
sameAs URL
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
additionalProperty PropertyValue
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 usage. Additional to the use of name and description to describe this property in a human-readable way, additionalType should be used to specify the nature of the property/relation. For instance, if the property refers to a gene/protein disease association, you could use http://semanticscience.org/resource/SIO_000983 as additionalType for the additionalProperty.
MANY
isContainedIn PhysicalEntity
URL
Indicates a PhysicalEntity that this PhysicalEntity is (in some sense) part of.
MANY
contains PhysicalEntity
URL
Indicates a PhysicalEntity that is (in some sense) a part of this PhysicalEntity. Inverse property: isPartOf.
MANY
location Place, PostalAddress, PropertyValue, Text
URL
The location of for example where the event is happening, an organization is located, or where an action takes place. Bioschemas usage. In Bioschemas location can be refer to a position in a chromosome or sequence or to a physical place where, for instance, a sample is stored. Using additionalType is advised to make the distinction. For instance, FALDO can be used for sequence coordinates.
MANY
hasRepresentation PropertyValue, Text
URL
A representation for this entity other than, for instance, an image (used image property for that) or the main web page/record (use mainEntityOfPage for that, and see background notes, http://schema.org/docs/datamodel.html#mainEntityBackground, for sameAs and url). Bioschemas usage. This property could be used, for instance, to register a sequence protein as it is a representation of the protein. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty.
MANY

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