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Sample Profile

Version: 0.2 (10 November 2018)

Bioschemas profile for describing Samples in the life-science


Contributors

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

Group Leader(s)
Other team members

Schema.org hierarchy

This Profile fits into the schema.org hierarchy as follows:

Thing > Sample

Description

To deliver on the identified use cases for samples, we have identified a minimal set of properties to encapsulate identification, linking, and metadata descriptions. Some of these properties are existing standard schema.org properties, others require Bioschemas extensions. Table 1 outlines the minimal set of properties for the ‘Sample’ concept and Table 2 shows our recommendations for use of the ‘PropertyValue’ concept to markup additional characteristics of a sample described within a sample page. We also propose a new concept, ‘Biomedical Code’, which is a generalisation of the existing ‘Medical Code’ concept defined in the health-lifesci.schema.org extension.





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 Example
Marginality: Minimum.
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:

Unique sample IDs. Where possible this should be an identifiers.org compliant prefixed id e.g. a BioSamples ID biosample:SAME12345.

MANY
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
Marginality: Recommended.
url URL
Schema:

URL of the item.


Bioschemas:

An access URL for this sample, e.g., in BioSamples or in a Biobank or elsewhere.

ONE
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 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:

A property-value pair representing an additional characteristics of the entity, e.g. “Organism: Homo sapiens” or “tissue type: leaf”. For details of how to use PropertyValue see below.

MANY
description Text
Schema:

A description of the item.


Bioschemas:

A description of the sample in free text. This should not contain information that could be better expressed as key/value pairs. These should be expressed using additionalProperty.

ONE
name Text
Schema:

The name of the item.


Bioschemas:

A human readable name for the sample. This should not be an additional identifier. Additional identifiers should be added to the identifier field.

MANY
subjectOf CreativeWork
Event
Schema:

A CreativeWork or Event about this Thing.. Inverse property: about.


Bioschemas:

Provides a link to a dataset that contains data about this sample record.

MANY



PropertyValue

Property Expected Type Description CD Controlled Vocabulary
Marginality: Minimum
name Text Schema: The name of the item.
Bioschemas: The name of the additional property. Otherwise known as a key or attribute.
ONE
value Boolean
Number
Text
Schema: The value of the quantitative value or property value node.
  • For QuantitativeValue and MonetaryAmount, the recommended type for values is 'Number'.
  • For PropertyValue, it can be 'Text;', 'Number', 'Boolean', or 'StructuredValue'.

  • Bioschemas: Attribute value.
    Note: Bioschemas have removed StructuredValue from the Expected Types.
ONE
Marginality: Recommended
valueReference CategoryCode Schema: A pointer to a secondary value that provides additional information on the original value, e.g. a reference temperature.
Bioschemas: Catagory code to enhance the value this could be a link to an ontology term in the Ontology Lookup Service.
Note: Bioschemas has added CategoryCode to the ExpectedTypes (of valueReference) and removed Enumeration, PropertyValue, QualitativeValue QuantitativeValue, and StructuredValue.
MANY
Marginality: Optional
unitCode Text
URL
Schema: The unit of measurement given using the UN/CEFACT Common Code (3 characters) or a URL. Other codes than the UN/CEFACT Common Code may be used with a prefix followed by a colon. ONE
unitText Text Schema: A string or text indicating the unit of measurement. Useful if you cannot provide a standard unit code for unitCode. ONE



CategoryCode

Property Expected Type Description CD Controlled Vocabulary
Marginality: Minimum
name Text Schema: The name of the item.
Bioschemas: A human readable label.
MANY
codeValue Text Schema: A short textual code that uniquely identifies the value. MANY
url URL Schema: URL of the item.
Bioschemas: The URI for the vocabulary code.
MANY

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