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LabProtocol DRAFT Profile

Version: 0.5-DRAFT-2020_09_01 (01 September 2020)

Bioschemas profile describing a LabProtocol in Life Sciences. An experimental LabProtocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas.


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 Laboratory Protocols group.

Group Leader(s)
Other team members

Schema.org hierarchy

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

Thing > CreativeWork > LabProtocol

Description

This LabProtocol profile specification presents the markup for describing a LabProtocol type according to Bioschemas. An experimental LabProtocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas.

Summary of Changes

Changes since previous draft of the LabProtocols profile:
  • LabProtocol profile definition updated to the one on the type, see issue 331
  • Description property added, see issue 436
  • Title added as minimum, see issue 438.
  • Protocol advantage property description updated, see issue 440
  • Time properties updated (totalTime as it was plus performTime and prepTime as optional), see issue 441
  • ReagentUsed property description updated, now using CHEBI definition, also MolecularEntity and ChemicalSubstance to the range list added, see issue 442
  • LabProtocol now used as the parent type for this profile, see issue 443

Latest profiles

Latest release: none

Latest draft: 0.5-DRAFT-2020_09_01

Previous profiles

Previous version: 0.4-DRAFT-2020_07_23


Group Use Cases Cross Walk Task & Issues Examples Live Deploys
Laboratory Protocols

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


View all examples
Property Expected Type Description CD Controlled Vocabulary Example
Marginality: Minimum.
bioSampleUsed BioChemEntity
BioSample
DefinedTerm
Text
URL
Taxon
Schema:

BioSample 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

View ≪bioSampleUsed≫ example
headline Text
Schema:

Headline of the article.


Bioschemas:

Main title of the LabProtocol

ONE
View ≪headline≫ example
keywords Text
Schema:

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


ONE
View ≪keywords≫ example
labEquipmentUsed DefinedTerm
Text
URL
Schema:

A laboratory equipment used by a person to follow one or more steps described in this LabProtocol.


MANY

BAO, EFO, ERO, OBI

View ≪labEquipmentUsed≫ example
protocolPurpose CreativeWork
Text
Schema:

The purpose of the protocol enables readers to make a decision as to the suitability of the protocol to their experimental problem. (see more information here)


ONE
View ≪protocolPurpose≫ example
reagentUsed BioChemEntity
MolecularEntity
ChemicalSubstance
DefinedTerm
Text
URL
Schema:

Reagents used in the protocol. ChEBI and PubChem entities can be used whenever available. Commercial names are also acceptable. A reagent is defined as ‘A substance used in a chemical reaction to detect, measure, examine, or produce other substances’ in CHEBI:33893


MANY

ChEBI, PubChem

View ≪reagentUsed≫ example
Marginality: Recommended.
author Organization
Person
Schema:

The author of this content or rating. Please note that author is special in that HTML 5 provides a special mechanism for indicating authorship via the rel tag. That is equivalent to this and may be used interchangeably.


MANY
View ≪author≫ example
citation CreativeWork
Text
Schema:

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


MANY
View ≪citation≫ example
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
View ≪identifier≫ example
isPartOf CreativeWork
URL
Schema:

Indicates an item or CreativeWork that this item, or CreativeWork (in some sense), is part of. Inverse property: hasPart.


MANY
View ≪isPartOf≫ example
license CreativeWork
URL
Schema:

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


ONE
View ≪license≫ example
protocolAdvantage CreativeWork
Text
Schema:

Situations where the Protocol has been successfully employed including advantageous elements (e.g. better yield, shorter running time) (see more information here)


MANY
View ≪protocolAdvantage≫ example
protocolApplication CreativeWork
Text
Schema:

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. (see more information here)


MANY
View ≪protocolApplication≫ example
protocolLimitation CreativeWork
Text
Schema:

Situations where the Protocol would be unreliable or otherwise unsuccessful (see more information here)


MANY
View ≪protocolLimitation≫ example
protocolOutcome CreativeWork
Text
Schema:

Outcome or expected result by a protocol execution (see more information here)


MANY
View ≪protocolOutcome≫ example
softwareUsed SoftwareApplication
URL
Schema:

Software or tool used as part of the lab protocol to complete a part of it.


MANY
View ≪softwareUsed≫ example
step CreativeWork
HowToSection
HowToStep
Text
Schema:

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


MANY
View ≪step≫ example
totalTime Duration
Schema:

The total time required to perform instructions or a direction (including time to prepare the supplies), in ISO 8601 duration format.


ONE
View ≪totalTime≫ example
Marginality: Optional.
dateCreated Date
DateTime
Schema:

The date on which the CreativeWork was created or the item was added to a DataFeed.


ONE
View ≪dateCreated≫ example
dateModified Date
DateTime
Schema:

The date on which the CreativeWork was most recently modified or when the item’s entry was modified within a DataFeed.


Bioschemas:

Last modified date

ONE
View ≪dateModified≫ example
datePublished Date
Schema:

Date of first broadcast/publication.


Bioschemas:

Many is used to cover original printed and electronic publication dates.

MANY
View ≪datePublished≫ example
description Text
Schema:

A description of the item.


ONE
View ≪description≫ example
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 has removed Product from the Expected Types

MANY
View ≪isBasedOn≫ example
performTime Duration
Schema:

The length of time it takes to perform instructions or a direction (not including time to prepare the supplies), in ISO 8601 duration format.


ONE
View ≪performTime≫ example
prepTime Duration
Schema:

The length of time it takes to prepare the items to be used in instructions or a direction, in ISO 8601 duration format.


ONE
View ≪prepTime≫ example

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