GitHub Twitter Bioschemas Bioschemas
Menu

Protein Specification v. 0.4-draft.1

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

Profile

Thing
Bioschemas specifications and types list.

Description:

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


Property Expected Type Description CD Controlled Vocabulary
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.
Bioschemas:
ONE
name Text
Schema: The name of the item.
Bioschemas:
ONE
Marginality: Recommended.
bioschemas:associatedDisease MedicalCondition
URL
Schema: Disease associated to this protein, if any
Bioschemas: Proposed official property: SO:associated_with, see http://purl.obolibrary.org/obo/so#associated_with
MANY SIO SIO OMIM any other well-known ontology describing diseases
bioschemas:transcribedFrom BioChemEntity
bioschemas:Gene
URL
Schema: Gene(s) from which this protein was transcribed from. In addtion to the schema:BioChemEntity type, this property also expects a bioschemas:Gene profile
Bioschemas: Proposed official property: SIO:010081, see http://semanticscience.org/resource/SIO_010081.rdf
MANY SIO SIO
description Text
Schema: A description of the item.
Bioschemas: Protein function. We recommend to start the description with "Function: [...]"
ONE
image ImageObject
URL
Schema: An image of the item. This can be a URL or a fully described ImageObject.
Bioschemas:
MANY
isContainedIn BioChemEntity
URL
Schema: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.
Bioschemas: For proteins, it is recommended to at least specify the taxon/organism associated to it
MANY NCBI Taxon UniProt taxonomy
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: 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. If appropriate terms/properties exist in controlled vocabularies, those should be used directly.
MANY
additionalType URL
Schema: 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.
Bioschemas: Any ontology term describing the protein concept. This is in addition to the official type to describe a protein Official proposed term: http://purl.obolibrary.org/obo/PR_000000001
MANY SIO PR SO others
alternateName Text
Schema: An alias for the item.
Bioschemas:
MANY
contains BioChemEntity
URL
Schema: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.
Bioschemas:
MANY
hasRepresentation PropertyValue
Text
URL
Schema: 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: 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 Yes as it better suits to describe the nature of the representation
location Place
PostalAddress
PropertyValue
Text
URL
Schema: The location of for example where the event is happening, an organization is located, or where an action takes place.
Bioschemas: 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 Yes as it better suits to describe the location.
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.
Bioschemas: Link via Record or URL to the main Record representing this entity in a dataset
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.
Bioschemas:
MANY

Top ▲