GitHub Twitter

BioChemEntity DRAFT Specification v. 0.5

Bioschemas specification describing a biological, chemical or biochemical entity that exists in the physical world


Contributors

The following people have been involved in the creation of this specification document. They are all members of the Biological Entities group.

Group Leader(s)

Carlos Horro

Leyla Garcia

Philippe Rocca-Serra

Other team members

Description

A BioChemEntity is any object that exists in the physical world representing biological, chemical and biochemical entities, and cannot be better represented with any other existing type in schema.org (for instance there is a full extension for the Medical field).

Bioschemas usage
As BioChemEntity is a generic, flexible and extensible wrapper for entitties in Life Sciences. Specialized types (a.k.a. profiles in Bioschemas) should customize BioChemEntity by modifying the marginality, cardinality and specify what ontologies and terms should be used per property (if applicable). Profiles should be as specific as possible. For instance, a protein profile would recommend pointing to an organism as part of the minimum information, but not necessarily to a sample or disease. Representations of physical entities in Life Sciences are usually recorded in datasets; the link to a dataset should be done via properties, i.e., mainEntityOfPage. Whenever a suitable profile exists, the profile type should be used in addition to the BioChemEntity type. For instance, both BioChemEntity and Protein would be the types assigned to a protein. Other additional types are always possible via the additionalType property. For instance, http://purl.obolibrary.org/obo/PR_000000001 is the official type used for the Protein profile but http://semanticscience.org/resource/SIO_010043 or https://www.wikidata.org/wiki/Q8054 can be used as an additionaType if that results useful somehow to the data providers.


Schema.org hierarchy

This is a new Type 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
New properties for BioChemEntity (pending schema.org integration).
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.
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: Whenever possible, please use a property coined in a third-party well-known vocabulary. For instance, you can directly use http://purl.obolibrary.org/obo/RO_0002327 as a property to express how a protein or gene enables some GO molecular function. If you still want or need to use additionalProperty, please use (i) property name to specify the name of the property, (ii) additionalType (if possible) to better specify the nature of the property, and (iii) value to link to the object/range of this property.
hasCategoryCode CategoryCode 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.
contains BioChemEntity
URL
Bioschemas: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn. contains is equivalent to isPartOf but with BioChemEntuty as both the domain and range.
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 usage: This property could be used, for instance, to register a sequence protein as it is a representation of the protein. If you want to better define the nature of the representation, use a PropertyValue as described in additionalProperty.
isContainedIn BioChemEntity
URL
Bioschemas: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: containedIn. isContainedIn is equivalent to isPartOf but with BioChemEntity as domain and range.
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 the distinction. For instance, FALDO or PropertyValue (with properties value, minValue and maxValue) can be used for sequence coordinates.
Note: The list of Expected Types has been extended as schema.org/location only has Place, PostalAddress and Text.
Properties from Thing
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.
Bioschemas: Whenever a suitable profile exists, the profile type should be used in addition to the BioChemEntity type. Other additional types are always possible via the additionalType property. For instance, http://purl.obolibrary.org/obo/PR_000000001 is the type used for the Protein profile but http://semanticscience.org/resource/SIO_010043 or https://www.wikidata.org/wiki/Q8054 can be used as an additionalType if that is useful to the data providers.
alternateName Text Schema: An alias for the item.
description Text Schema: A descripton of the item.
disambiguatingDescription Text Schema: A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.
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.
Bioschemas: We recommend you use either an authoritative source or identifiers.org whenever possible.
image ImageObject
URL
Schema: An image of the item. This can be a URL or a fully described ImageObject.
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 DataRecord representing this entity in a dataset.
name Text Schema: The name of the item.
potentialAction Action Schema: Indicates a potential Action, which describes an idealized action in which this thing would play an 'object' role.
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.
subjectOf CreativeWork
Event
Schema: A CreativeWork or Event about this Thing. Inverse property: about.
url URL Schema: URL of the item.
Bioschemas: Link to the official webpage associated to this entity.

Top ▲