GitHub Twitter

ProteinAnnotation DRAFT Profile

Version: 0.5-DRAFT (13 November 2018)


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 Proteins group.

Group Leader(s)

Maria Martin

Leyla Garcia

Other team members

Schema.org hierarchy

This Profile fits into the schema.org hierarchy as follows:

Thing > BioChemEntity

Description

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

Summary of Changes

Changes since the previous release of the ProtainAnnotation Profile:

  • Examples added to many properties
  • additionalType demoted to Recommended level
  • rdf:type removed as part of the standard markup template
  • image promoted to Recommended level
  • hasCategoryCode added as an Optional level property

Latest profiles

Latest release: none

Latest draft: 0.6-DRAFT

Previous profiles

Previous version: 0.4-DRAFT-2018_02_25


Group Use Cases Cross Walk Task & Issues Examples Live Deploys
Proteins

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

View all examples
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
Marginality: Recommended.
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:

Should be used to specified the nature of the annotation, e.g., domain, active site, variant, GO annoation, etc. Please see the values listed in the Controlled Vocabulary for some examples

MANY

SIO:active_site SIO:binding_site SIO:molecular_site SIO:protein_domain SIO:protein_family

View ≪additionalType≫ example
alternateName Text
Schema:

An alias for the item.


MANY
View ≪alternateName≫ example
creationMethod PropertyValue
Bioschemas:

Method used to create this annotation.

ONE
View ≪creationMethod≫ example
description Text
Schema:

A description of the item.


ONE
View ≪description≫ example
image ImageObject
URL
Schema:

An image of the item. This can be a URL or a fully described ImageObject.


MANY
name Text
Schema:

The name of the item.


ONE
View ≪name≫ example
url URL
Schema:

URL of the item.


Bioschemas:

Link to the official webpage associated to this entity.

ONE
View ≪url≫ example
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:

As much a possible, do not use it! Alternatively, consider reusing properties/relations already coined in controlled vocabularies. We recommed to look at the OBO Relations Ontology (RO) or the Semanticscience Integrated Ontology (SIO) as starting points.

MANY
View ≪additionalProperty≫ example
contains BioChemEntity
URL
Bioschemas:

Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.

MANY
hasCategoryCode CategoryCode
Schema:

A Category code contained in this code set.


Bioschemas:

A controlled vocabulary term equivalent to this entity. For instance, an organism coined in NCBI taxonomy can be represented as a BioChemEntity. As it also exists as a term in an ontology, it would be nice to capture that information via categoryCode.

MANY

Any suitable controlled vocabulary

hasRepresentation PropertyValue
Text
URL
Schema:

A representation for this entity other than, for instance, an image (use image property for that) or the main web page/record (use mainEntityOfPage for that), and see background notes, for sameAs and url).


Bioschemas:

Representation of this entity. For instance, a chemical structure or sequence.

MANY
isContainedIn BioChemEntity
URL
Bioschemas:

Indicates a BioChemEntity that this BioChemEntity is (in some sense) a part of. Inverse property: contains.

MANY
View ≪isContainedIn≫ example
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:

The location can refer to a position in the chromosome or sequence or to a physical place where, for instance, a sample is stored. Using additionalType is advised to make this distinction. For instance, FALDO can be used for sequence co-ordinates. Note: The list of Expected Types has been extended as schema.org/location only has Place, PostalAddress and Text.

MANY
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.


MANY
View ≪mainEntityOfPage≫ example
mainEntityOfPage DataRecord
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 DataRecord or URL to the main Record representing this entity in a dataset. Note: Bioschemas has replaced CreativeWork with DataRecord in the Expected Types.

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:

Link to any resource other than the Record and the official webpage, for instance a Wikipedia page.

MANY

Top ▲