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BioChemEntity Specification v. 0.5

Bioschemas specification describing a physical entity


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 and cannot be better represented with any other existing type in schema.org. This includes theoretical objects that may potentially be invented/created, but do not currently exist. For example, synthetic possible chemicals.
BioChemEntity is a flexible and extensible wrapper for Life Sciences entities.


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.
contains BioChemEntity
URL
Bioschemas: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.
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).
isContainedIn BioChemEntity
URL
Bioschemas: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: containedIn.
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 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: As BioChemEntity is a generic wrapper for entitties in Life Sciences, customized types (a.k.a. profiles in Bioschemas) should specify what ontologies and terms should be used. SIO (http://bioportal.bioontology.org/ontologies/SIO) covers a wide range of concepts in Life Sciences and accept suggestions about additions (see https://github.com/micheldumontier/semanticscience/issues), other ontologies are possible as well. Customized types should be as specific as possible. For instance, http://semanticscience.org/resource/SIO_010043 would work for a protein while http://semanticscience.org/resource/SIO_000985 for a gene coding a protein (which is more specific than gene as described by http://semanticscience.org/resource/SIO_010035). If no better optoin, a generic term could be used as well (like http://semanticscience.org/resource/SIO_000004).
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.
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 Record or URL to the main Record representing this entity in a dataset.
Note: Please use a DataRecord where possible.
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 any resource other than the Record and the official Webpage, for instance a Wikipedia page.

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