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ProteinStructure DRAFT Profile

Version: 0.5-DRAFT-2018_08_15 (15 August 2018)

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


If you spot any errors or omissions with this type, please file an issue in our GitHub.


Key to specification table

CD = Cardinality

Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
@context URL Used to provide the context (namespaces) for the JSON-LD file.
Not needed in other serialisations.		 ONE
@type Text Schema.org/Bioschemas class for the resource declared using JSON-LD syntax. For other serialisations please use the appropriate mechanism.
While it is permissible to provide multiple types, it is preferred to use a single type.		 MANY Schema.org, Bioschemas
@id IRI Used to distinguish the resource being described in JSON-LD. For other serialisations use the appropriate approach. ONE
dct:conformsTo IRI Used to state the Bioschemas profile that the markup relates to. The versioned URL of the profile must be used.
Note that we use a CURIE in the table here but the full URL for Dublin Core terms must be used in the markup (http://purl.org/dc/terms/conformsTo), see example.		 ONE Bioschemas profile versioned URL
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
Marginality: Recommended.
alternateName Text
 Schema:

An alias for the item.


 MANY
boundMolecule Text
URL
 Bioschemas:

Bound molecules

 MANY
description Text
 Schema:

A description of the item.


 ONE
expressionSystem BioChemEntity
Taxon
 Bioschemas:

Organism where this protein extructure is expresed

 MANY
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
structureDeterminationMethod Text
URL
 Bioschemas:

Method used to determine the protein structure

 MANY
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
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.


 MANY
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 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
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.

 MANY