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BioChemEntity Specification v. 0.1

Bioschemas specification describing a physical entity.

Type

Thing > BioChemEntity
Bioschemas specifications and types list.

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. In order to specify the nature of this physical entity, additionalProperty must be used to specify the nature/type of this physical entity. For instance, http://semanticscience.org/resource/SIO_010043 can be used to refer to a protein. Bioschemas usage A BioChemEntity is a flexible and extensible wrapper for Life Sciences entities. Representations of physical entities in Life Sciences are usually recorded in datasets; the link to a dataset should be done via properties. A particular Life Sciences entity, refer to as a profile in Bioschemas, will customize BioChemEntity by modifying the marginality, cardinality and ontologies used. For instance, a protein profile would recommend pointing to an organism a part of the minimum information, but not necessarily to a sample or disease.


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.
Bioschemas:
contains BioChemEntity
URL
Schema: Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: isContainedIn.
Bioschemas:
hasRepresentation PropertyValue
Text
URL
Schema: A representation for this entity other than, for instance, an image (used image property for that) or the main web page/record (use mainEntityOfPage for that, and see background notes, http://schema.org/docs/datamodel.html#mainEntityBackground, for sameAs and url).
Bioschemas: 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
Schema: Indicates a BioChemEntity that this BioChemEntity is (in some sense) part of.
Bioschemas: Bioschemas usage. Additional to the use of name and description to describe this property in a human-readable way, additionalType should be used to specify the nature of the property/relation. For instance, if the property refers to a gene/protein disease association, you could use http://semanticscience.org/resource/SIO_000983 as additionalType for the additionalProperty.
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: Bioschemas usage. In Bioschemas location can be refer to a position in a 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.
preferredLabel Text
Schema: Indicates the preferred label to refer to a specific (sub)type of BioChemEntity
Bioschemas: Profile name
 
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: Bioschemas usage. 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 or so).
alternateName Text
Schema: An alias for the item.
Bioschemas:
description Text
Schema: A description of the item.
Bioschemas:
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.
Bioschemas:
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: Recommendation: identifiers.org whenever possible
image ImageObject

URL
Schema: An image of the item. This can be a URL or a fully described ImageObject.
Bioschemas:
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: Bioschemas usage. Link via Record or URL to the main Record representing this entity in a dataset
name Text
Schema: The name of the item.
Bioschemas:
potentialAction Action
Schema: Indicates a potential Action, which describes an idealized action in which this thing would play an 'object' role.
Bioschemas:
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:
url URL
Schema: URL of the item.
Bioschemas: Bioschemas usage. Link to any resource other than the Record and the official Webpage, for instance a Wikipedia page.

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