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ProteinStructure DRAFT Specification v. 0.4

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

Other team members

Description

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


Schema.org hierarchy

This is a new Profile that fits into the schema.org hierarchy as follows:

Thing > BioChemEntity



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
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
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
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
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
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
Text
URL
Bioschemas: 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 ProteinStructure: Describe url of downloadable additionalProperty .
MANY
image ImageObject
URL
Schema: An image of the item. This can be a URL or a fully described ImageObject. MANY
isContainedIn BioChemEntity
URL
Bioschemas: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: containedIn.
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.
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.
MANY

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