Sample Profile
Version: 0.2-RELEASE-2018_11_10 (10 November 2018)
Bioschemas profile for describing Samples in the life-science
If you spot any errors or omissions with this type, please file an issue in our GitHub.
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.
Latest profiles
Latest release: 0.2-RELEASE-2018_11_10
Previous profiles
Previous version: 0.2-DRAFT-2018_11_10
| Group | Use Cases | Cross Walk | Task & Issues | Examples | Live Deploys |
|---|---|---|---|---|---|
| Samples |
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You can read the draft 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 | 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.
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 | |