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LabProtocol Specification v. 0.2

Bioschemas specification describing LabProtocol in the life-science.


Contributors

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

Group Leader(s)
Other team members

Description

An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas.Experimental protocols are fundamental information structures that support the description of the processes by means of which results are generated in experimental research [1]. Experimental protocols describe how the data were produced, the steps undertaken and conditions under which these steps were carried out.
[1] Giraldo, O., García, A., López, F., & Corcho, O. (2017). Using semantics for representing experimental protocols. Journal of Biomedical Semantics, 8, 52. http://doi.org/10.1186/s13326-017-0160-y


Schema.org hierarchy

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

Thing > CreativeWork



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.
ChEBI:reagent BioChemEntity
Text
URL
Bioschemas:

Reagent used in the protocol. It can be a record in a Dataset describing the reagent or a BioChemEntity corresponding to the reagent or a URL pointing to the type of reagent used. ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable (URL if possible).

MANY

ChEBI PubChem

instrument Text
URL
Thing
Schema:

The object that helped the agent perform the action. e.g. John wrote a book with a pen.


Bioschemas:

For LabProtocols it would be a laboratory equipment use by a person to follow one or more steps described in this LabProtocol. Note: Bioschemas have added the following to the list of Expected Types: Text and URL.

MANY

BAO EFO ERO OBI

keywords Text
Schema:

Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.


ONE
purpose Text
Schema:

A goal towards an action is taken. Can be concrete or abstract.


Bioschemas:

Note: Bioschemas have changed the Expected Types by removing MedicalDevicePurpose and Thing, and adding Text.

ONE

SMART Protocols

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
sample BioChemEntity
Text
URL
Bioschemas:

Sample used in the protocol. It could be a record in a Dataset describing the sample or a physical object corresponding to the sample or a URL pointing to the type of sample used.

MANY

NCBI Taxonomy Uberon

Marginality: Recommended.
citation CreativeWork
Text
Schema:

A citation or reference to another creative work, such as another publication, web page, scholarly article, etc.


MANY
duration Duration
Schema:

The duration of the item (movie, audio recording, event, etc.) in ISO 8601 date format.


Bioschemas:

The time it takes to actually carry out the protocol, in ISO 8601 date format.

ONE
hasPart CreativeWork
Schema:

Indicates a CreativeWork that is (in some sense) a part of this CreativeWork. Inverse property: isPartOf.


Bioschemas:

A particular case in Bioschemas is LabProtocol where structural elements are used to described advantages (situations the Protocol has been successfully employed), limitations (situations the Protocol would be unreliable or otherwise unsuccessful), applications (Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. e.g. northern blot assays, sequencing, etc.), and outcomes (outcome or expected result by a protocol execution). For LabProtocol, in the applicationType, please use http://purl.org/net/SMARTprotocol#AdvantageOfTheProtocol for advantages, http://purl.org/net/SMARTprotocol#LimitationOfTheProtocol for limitations, http://purl.org/net/SMARTprotocol#ApplicationOfTheProtocol for applicability, and http://purl.org/net/SMARTprotocol#OutcomeOfTheProtocol for outcomes.

MANY

SMART Protocols

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.


ONE
isPartOf CreativeWork
Schema:

Indicates a CreativeWork that this CreativeWork is (in some sense) part of. Inverse property: hasPart.


MANY
license CreativeWork
URL
Schema:

A license document that applies to this content, typically indicated by URL.


ONE
software SoftwareApplication
Bioschemas:

An application that can complete the request.

MANY
step CreativeWork
HowToSection
HowToStep
Text
Schema:

A single step item (as HowToStep, text, document, video, etc.) or a HowToSection.


Bioschemas:

Use in LabProtocol to include the step by step process followed in this protocol.

MANY
Marginality: Optional.
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:

Optional for LabProtocol as it has its own type in schema.org. If used, the recommended URL is experimental protocol as defined by SMART Protocols (see Controlled Vocabulary).

ONE

SP:ExperimentalProtocol

isBasedOn CreativeWork
URL
Schema:

A resource that was used in the creation of this resource. This term can be repeated for multiple sources. For example, http://example.com/great-multiplication-intro.html. Supersedes isBasedOnUrl.


Bioschemas:

Note: Bioschemas have removed Product from the Expected Types.

MANY

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