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ProteinStructure Profile

Version: 0.4 (25 February 2018)

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


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 structure.





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


Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
SIO:010081 BioChemEntity
URL
Bioschemas:

SIO:is transcribed from Used as a short and direct alternative to additionalProperty. Gene(s) from which this protein was transcribed from.

Bioschemas ProteinStructure: additionalType for this BioChemEntity container should be set to SIO:010035 (gene).

MANY
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
organism BioChemEntity
Bioschemas:

Indicates which organism this protein structure is in some sense part of. Bioschemas ProteinStructure: additionalType for this BioChemEntity container should be set to SIO:010000 (organism).

ONE
rdf:type URL
Bioschemas:

This is used by validation tools to indentify the profile used. You must use the value specified in the Controlled Vocabulary column.

ONE

SIO:011119 (biomolecular structure descriptor)

Marginality: Recommended.
SIO:000983 MedicalCondition
URL
Bioschemas:

SIO:gene-disease association Used as a short and direct alternative to additionalProperty. Disease associated with this protein, if any.

Bioschemas ProteinStructure: additionalType for this BioChemEntity container should be set to MedicalCode and SIO:010299 (disease).

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.


ONE
alternateName Text
Schema:

An alias for the item.


MANY
description Text
Schema:

A description of the item.


ONE
name Text
Schema:

The name of the item.


ONE
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:

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
contains BioChemEntity
URL
Bioschemas:

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

MANY
hasRepresentation PropertyValue orText orURL
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
image ImageObject
URL
Schema:

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


isContainedIn BioChemEntity orURL
Bioschemas:

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

MANY
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.


Bioschemas:

Link via DataRecord 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:

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

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