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.
Other team members
This profile specification presents the BioChemEntity usage when describing a Protein annotation.
Schema.org hierarchyThis 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|
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
Bioschemas: Should be set to any of the values listed in the Controlled Vocabulary.
|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||Missing!|
|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|
Schema: URL of the item.
Bioschemas: Link to the official webpage associated to this entity.
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.
|Bioschemas: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.||MANY|
|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.
|Schema: An image of the item. This can be a URL or a fully described ImageObject.||MANY|
|Bioschemas: Indicates a BioChemEntity that this BioChemEntity is (in some sense) a part of. Inverse property: contains.||MANY|
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.
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.
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.