LabProtocol Mapping
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SubtitleBioschemas specification describing LabProtocol in the life-science.Lab protocols<USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME><USE CASE NAME>
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DescriptionAn 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., Garcia, A., Corcho, O.: SMART Protocols: SeMAntic RepresenTation for Experimental Protocols, Riva del Garda, Trentino, Italy (2014). 4th Workshop on Linked Science 2014- Making Sense Out of Data (LISC2014)
<USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL><USE CASE URL>
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Olga Giraldo<CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...><CONTRIBUTOR1, CONTRIBUTOR2,...>
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schema.orgbioschemas
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PropertyExpected TypeDescriptionBSC DescriptionMarginalityCardinality
Controlled Vocabulary
NameContent ExampleUseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
Content Example
UseCaseName
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UseCaseName
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UseCaseName
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UseCaseName
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UseCaseName
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UseCaseName
Content Example
UseCaseName
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UseCaseName
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UseCaseName
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UseCaseName
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UseCaseName
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UseCaseName
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UseCaseName
Content Example
UseCase
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Extends CreativeWork
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additionalTypeURLAn 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 usage.

Optional for LabProtocol as it has its own type in schema.org. If used, the recommended URL is SmartProtocols (http://purl.org/net/SMARTprotocol#ExperimentalProtocol)
OptionalONESP:ExperimentalProtocol
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descriptionTextA description of the item.

Bioschemas usage.
Use in LabProtocol to include the step by step process followed in this protocol.
RecommendedONE
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identifierPropertyValue, Text, URLThe 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.RecommendedONEidentifierDOI: https://doi.org/10.21769/BioProtoc.2159; doi: 10.3791/55164; doi:10.1101/pdb.prot4765Match
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citationCreativeWork or URLA citation or reference to a creative work, such as a publication, web page, scholarly article, etc.RecommendedMANYpublication, citation, reference"This protocol is related to the following articles:
Effective detection of variation in single-cell transcriptomes using MATQ-seq
Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng, and Chenghang Zong
Nature Methods doi:10.1038/nmeth.4145
". EXAMPLE SOURCE: http://cshprotocols.cshlp.org/cgi/collection/dna_isolation_in_plants
Match
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licenseCreativeWork or URLA license document that applies to this content, typically indicated by URL.RecommendedONElicenseCreative Commons Attribution licence (https://creativecommons.org/licenses/by/4.0/)Match
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isBasedOnCreativeWork or
URL
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.OptionalMANYprovenance"This protocol was adapted from “How to Study Gene Expression,” Chapter 7, in Arabidopsis:A Laboratory Manual (eds. Weigel and Glazebrook). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2002." EXAMPLE SOURCE: http://cshprotocols.cshlp.org/content/2007/2/pdb.prot4690.abstractMatch
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isPartOfCreativeWork
Indicates a CreativeWork that this CreativeWork is (in some sense) part of.
OptionalMANYsource (repository, journal, others)Bio-protocol (http://www.bio-protocol.org/e2159); JOVE (https://www.jove.com/video/55164/characterization-calcification-events-using-live-optical-electron)Match
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hasPartCreativeWorkIndicates a CreativeWork that is (in some sense) a part of this CreativeWork.
Inverse property: isPartOf.

Bioschemas usage.

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.
RecommendedMANY
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keywordsText
Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.
MinimumMANYkeywordsMatch
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New properties
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reagentPhysicalEntity, Text or URLReagent used in the protocol. It can be a record in a Dataset describing the reagent or a PhysicalEntity 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)MinimumMANYreagentReagents that are purchased ready-to-use, solutions (or mixtures) prepared in the lab, media, buffer, kits.Match
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purposeTextA goal towards an action is taken. Can be concrete or abstract.MinimumMANYpurpose"Development of a method to isolate small RNAs from different plant species (…) that no need of first total RNA extraction and is not based on the commercially available TRIzol" EXAMPLE SOURCE: https://plantmethods.biomedcentral.com/articles/10.1186/1746-4811-7-4Match
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instrumentThing, Text or URLThe object that helped the agent perform the action. e.g. John wrote a book with a pen.

For LabProtocols it would be a laboratory equipment use by a person to follow one or more steps described in this LabProtocol.
MinimumMANYdevice1) An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. 2) A voltmeter is a measurement device which is intended to perform some measure function. 3) next-generation sequencer is a device used to detect variants by targeted gene sequencing in, for example, cancer and genetic disorders; type a bacteria or virus; or characterize novel microbes.Match
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samplePhysicalEntity, Text or URLSample 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.MinimumMANYsample
The sample tested in a protocol may be an organism or a part of it. Some examples include: whole organisms such as Oriza sativa (rice), mangifera indica (mango), Mus musculus (mouse); anatomical parts like leaf, cells, tissues, membranes, organs, skeletal system, muscular system, nervous system, reproductive system, cardiovascular system; biomolecules like nucleic acids and proteins; body fluids (Blood serum, saliva, semen, amniotic fluid, cerebrospinal fluid, gastric acid, etc)
Match
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softwareSoftwareApplicationAn application that can complete the request.RecommendedMANYsoftwareMaxQuant quantitative proteomics software (http://www.biochem.mpg.de/5111795/maxquant); ImageJ (https://imagej.nih.gov/ij/); Mapdisto (http://mapdisto.free.fr/)Match
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durationDurationThe time it takes to actually carry on the protocol, in ISO 8601 duration format.RecommendedONEexecution time45 min; 3 hours; 5 daysMatch
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