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ProteinAnnotation Specification v. 0.4

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


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


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

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

Thing > BioChemEntity

Key to specification table properties where the Expected Types have been changed, or new (i.e., Bioschemas created) properties/types are green. properties/types are red.

Pending 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
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. tools may have only weaker understanding of extra types, in particular those defined externally.
Bioschemas: Should be set to any of the values listed in the Controlled Vocabulary.
MANY SIO:active_site
identifier PropertyValue
Schema: The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. 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 Missing!
Marginality: Recommended
alternateName Text Schema: An alias for the item. MANY
creationMethod PropertyValue Bioschemas: Method used to create this annotation. ONE
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.
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 Note: Publishers should be aware that applications designed to use specific properties (e.g.,,, ...) 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.
contains BioChemEntity
Bioschemas: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn. MANY
hasRepresentation PropertyValue
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 Protein: Representation of this entity. For instance, a chemical structure or sequence.
image ImageObject
Schema: An image of the item. This can be a URL or a fully described ImageObject. MANY
isContainedIn BioChemEntity
Bioschemas: Indicates a BioChemEntity that this BioChemEntity is (in some sense) a part of. Inverse property: contains. MANY
location Place
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 only has Place, PostalAddress and Text.
mainEntityOfPage DataRecord
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.
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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