LabProtocol Cross Walk

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1	Crea	Bioschemas 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>
2	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., 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>
3								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,...>
4	schema.org			bioschemas				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,...>
5	Property	Expected Type	Description	BSC Description	Marginality	Cardinality	Controlled Vocabulary	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase	Name	Content Example	UseCase
6	Extends CreativeWork
7	additionalType	URL	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 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)		Optional	ONE	SP:ExperimentalProtocol
8	description	Text	A description of the item. Bioschemas usage. Use in LabProtocol to include the step by step process followed in this protocol.		Recommended	ONE
9	identifier	PropertyValue, Text, URL	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.		Recommended	ONE		identifier	DOI: https://doi.org/10.21769/BioProtoc.2159; doi: 10.3791/55164; doi:10.1101/pdb.prot4765	Match
10	citation	CreativeWork or URL	A citation or reference to a creative work, such as a publication, web page, scholarly article, etc.		Recommended	MANY		publication, 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
11	license	CreativeWork or URL	A license document that applies to this content, typically indicated by URL.		Recommended	ONE		license	Creative Commons Attribution licence (https://creativecommons.org/licenses/by/4.0/)	Match
12	isBasedOn	CreativeWork 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.		Optional	MANY		provenance	"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.abstract	Match
13	isPartOf	CreativeWork	Indicates a CreativeWork that this CreativeWork is (in some sense) part of.		Optional	MANY		source (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
14	hasPart	CreativeWork	Indicates 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.		Recommended	MANY
15	keywords	Text	Keywords or tags used to describe this content. Multiple entries in a keywords list are typically delimited by commas.		Minimum	MANY		keywords		Match
16	New properties
17	reagent	PhysicalEntity, Text or URL	Reagent 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)		Minimum	MANY		reagent	Reagents that are purchased ready-to-use, solutions (or mixtures) prepared in the lab, media, buffer, kits.	Match
18	purpose	Text	A goal towards an action is taken. Can be concrete or abstract.		Minimum	MANY		purpose	"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/10.1186/1746-4811-7-4	Match
19	instrument	Thing, Text or URL	The 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.		Minimum	MANY		device	1) 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
20	sample	PhysicalEntity, Text or URL	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.		Minimum	MANY		sample	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
21	software	SoftwareApplication	An application that can complete the request.		Recommended	MANY		software	MaxQuant quantitative proteomics software (http://www.biochem.mpg.de/5111795/maxquant); ImageJ (https://imagej.nih.gov/ij/); Mapdisto (http://mapdisto.free.fr/)	Match
22	duration	Duration	The time it takes to actually carry on the protocol, in ISO 8601 duration format.		Recommended	ONE		execution time	45 min; 3 hours; 5 days	Match
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