Sample DRAFT Specification v. 0.1

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.

Schema.org hierarchy

This is a new Profile that fits into the schema.org hierarchy as follows:

Thing > BioChemEntity

Group	Use Cases	Cross Walk	Task & Issues	Examples	Live Deploys
Samples

You can read the release version of this specification here.

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
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	OBI:material sample
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
dataset	URL	Schema: A dataset contained in this catalog. Bioschemas: An access URL that provides a link to a dataset that contains data about this sample record. Note: Bioschemas has changed the Expected Type from Dataset to URL.	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

PropertyValue

Property	Expected Type	Description	CD
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
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